Claims
- 1. An isolated polynucleotide of a Streptococcus pneumoniae genomic sequence, wherein the polynucleotide comprises a nucleotide sequence having at least about 95% identity to a nucleotide sequence chosen from one of SEQ ID NO: 1 through SEQ ID NO: 215 or SEQ ID NO:431 through SEQ ID NO:591, a degenerate variant thereof, or a fragment thereof.
- 2. The polynucleotide of claim 1, wherein the polynucleotide is a complement to a nucleotide sequence chosen from one of SEQ ID NO: 1 through SEQ ID NO: 215 or SEQ ID NO:431 through SEQ ID NO:591, a degenerate variant thereof, or a fragment thereof.
- 3. The polynucleotide of claim 2, wherein the polynucleotide is selected from the group consisting of DNA, chromosomal DNA, cDNA and RNA.
- 4. The polynucleotide of claim 3, wherein the polynucleotide further comprises heterologous nucleotides.
- 5. An isolated polynucleotide which hybridizes to a nucleotide sequence chosen from one of SEQ ID NO: 1 through SEQ ID NO: 215 or SEQ. ID NO:431 through SEQ ID NO:591, a complement thereof, a degenerate variant thereof, or a fragment thereof, under high stringency hybridization conditions.
- 6. The polynucleotide of claim 5, wherein the polynucleotide hybridizes under intermediate stringency hybridization conditions.
- 7. An isolated polynucleotide of a Streptococcus pneumoniae genomic sequence, wherein the polynucleotide comprises a nucleotide sequence chosen from one of SEQ ID NO: 1 through SEQ ID NO: 215 or SEQ ID NO:431 through SEQ ID NO:591, a fragment thereof, or a degenerate variant thereof, and encodes a polypeptide, a biological equivalent thereof, or a fragment thereof, selected from the group consisting of:
(a) a Streptococcus pneumoniae polypeptide having 0, 1 or 2 transmembrane domains; (b) a Streptococcus pneumoniae polypeptide having 3 or more transmembrane domains; (c) a Streptococcus pneumoniae polypeptide having an outer membrane domain or a periplasmic domain; (d) a Streptococcus pneumoniae polypeptide having an inner membrane domain; (e) a Streptococcus pneumoniae polypeptide identified by Blastp analysis; (f) a Streptococcus pneumoniae polypeptide identified by Pfam analysis; (g) a Streptococcus pneumoniae lipoprotein; (h) a Streptococcus pneumoniae polypeptide having a LPXTG motif, wherein the polypeptide is covalently attached to the peptidoglycan layer; (i) a Streptococcus pneumoniae polypeptide having a peptidoglycan binding motif, wherein the polypeptide is associated with the peptidoglycan layer; (j) a Streptococcus pneumoniae polypeptide having a signal sequence and a C-terminal Tyrosine or a C-terminal Phenylalanine amino acid; (k) a Streptococcus pneumoniae polypeptide having a tripeptide RGD amino acid sequence; (I) a Streptococcus pneumoniae polypeptide identified by proteomics as surface exposed; and (m) a Streptococcus pneumoniae polypeptide identified by proteomics as membrane associated.
- 8. The polynucleotide of claim 7, wherein the polynucleotide is a complement to a nucleotide sequence chosen from one of SEQ ID NO: 1 through SEQ ID NO: 215 or SEQ ID NO:431 through SEQ ID NO:591, a degenerate variant thereof, or a fragment thereof.
- 9. The polynucleotide of claim 8, wherein the polynucleotide is selected from the group consisting of DNA, chromosomal DNA, cDNA and RNA.
- 10. The polynucleotide of claim 9, wherein the polynucleotide further comprises heterologous nucleotides.
- 11. The polynucleotide of claim 10, wherein the polynucleotide encodes a fusion polypeptide.
- 12. The polynucleotide of claim 7, wherein the polynucleotide encoding a polypeptide having 0, 1 or 2 transmembrane domains comprises a nucleotide sequence chosen from one of SEQ ID NO: 1, SEQ ID NO: 3, SEQ ID NO: 4, SEQ ID NO: 7, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 11, SEQ ID NO: 13, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 22, SEQ ID NO: 23, SEQ ID NO: 24, SEQ ID NO: 25, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 32, SEQ ID NO: 34, SEQ ID NO: 36, SEQ ID NO: 39, SEQ ID NO: 41, SEQ ID NO: 42, SEQ ID NO: 45, SEQ ID NO: 47, SEQ ID NO: 49, SEQ ID NO: 50, SEQ ID NO: 51, SEQ ID NO: 53, SEQ ID NO: 55, SEQ ID NO: 57, SEQ ID NO: 58, SEQ ID NO: 60, SEQ ID NO: 61, SEQ ID NO: 62, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 66, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 72, SEQ ID NO: 73, SEQ ID NO: 74, SEQ ID NO: 78, SEQ ID NO: 79, SEQ ID NO: 81, SEQ ID NO: 83, SEQ ID NO: 85, SEQ ID NO: 86, SEQ ID NO: 89, SEQ ID NO: 91, SEQ ID NO: 92, SEQ ID NO: 95, SEQ ID NO: 96, SEQ ID NO: 97, SEQ ID NO: 100, SEQ ID NO: 104, SEQ ID NO: 105, SEQ ID NO: 106, SEQ ID NO: 109, SEQ ID NO: 110, SEQ ID NO: 111, SEQ ID NO: 113, SEQ ID NO: 116, SEQ ID NO: 121, SEQ ID NO: 122, SEQ ID NO: 123, SEQ ID NO: 125, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 128, SEQ ID NO: 131, SEQ ID NO: 132, SEQ ID NO: 134, SEQ ID NO: 136, SEQ ID NO: 137, SEQ ID NO: 138, SEQ ID NO: 141, SEQ ID NO: 142, SEQ ID NO: 143, SEQ ID NO: 144, SEQ ID NO: 147, SEQ ID NO: 148, SEQ ID NO: 149, SEQ ID NO: 150, SEQ ID NO: 155, SEQ ID NO: 156, SEQ ID NO: 158, SEQ ID NO: 161, SEQ ID NO: 162, SEQ ID NO: 165, SEQ ID NO: 170, SEQ ID NO: 171, SEQ ID NO: 172, SEQ ID NO: 174, SEQ ID NO: 176, SEQ ID NO: 179, SEQ ID NO: 183, SEQ ID NO: 185, SEQ ID NO: 187, SEQ ID NO: 192, SEQ ID NO: 195, SEQ ID NO: 196, SEQ ID NO: 197, SEQ ID NO: 199, SEQ ID NO: 200, SEQ ID NO: 201, SEQ ID NO: 202, SEQ ID NO: 204, SEQ ID NO: 205, SEQ ID NO: 207, SEQ ID NO: 209 and SEQ ID NO: 210.
- 13. The polynucleotide of claim 7, wherein the polynucleotide encoding a polypeptide having 3 or more transmembrane domains comprises a nucleotide sequence chosen from one of SEQ ID NO: 2, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 30, SEQ ID NO: 31, SEQ ID NO: 33, SEQ ID NO: 35, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 40, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 46, SEQ ID NO: 48, SEQ ID NO: 52, SEQ ID NO: 54, SEQ ID NO: 56, SEQ ID NO: 59, SEQ ID NO: 65, SEQ ID NO: 71, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO: 80, SEQ ID NO: 82, SEQ ID NO: 84, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 90, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 98, SEQ ID NO: 99, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 112, SEQ ID NO: 114, SEQ ID NO: 115, SEQ ID NO: 117, SEQ ID NO: 118, SEQ ID NO: 119, SEQ ID NO: 120, SEQ ID NO: 124, SEQ ID NO: 129, SEQ ID NO: 130, SEQ ID NO: 133, SEQ ID NO: 135, SEQ ID NO: 139, SEQ ID NO: 140, SEQ ID NO: 145, SEQ ID NO: 146, SEQ ID NO: 151, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 154, SEQ ID NO: 157, SEQ ID NO: 159, SEQ ID NO: 160, SEQ ID NO: 163, SEQ ID NO: 164, SEQ ID NO: 166, SEQ ID NO: 167, SEQ ID NO: 168, SEQ ID NO: 169, SEQ ID NO: 173, SEQ ID NO: 175, SEQ ID NO: 177, SEQ ID NO: 178, SEQ ID NO: 180, SEQ ID NO: 181, SEQ ID NO: 182, SEQ ID NO: 184, SEQ ID NO: 186, SEQ ID NO: 188, SEQ ID NO: 189, SEQ ID NO: 190, SEQ ID NO: 191, SEQ ID NO: 193, SEQ ID NO: 194, SEQ ID NO: 198, SEQ ID NO: 203, SEQ ID NO: 206, SEQ ID NO: 208, SEQ ID NO: 211, SEQ ID NO: 212, SEQ ID NO: 213, SEQ ID NO: 214 and SEQ ID NO: 215.
- 14. The polynucleotide of claim 7, wherein the polynucleotide encoding a polypeptide having an outer membrane domain or a periplasmic domain comprises a nucleotide sequence chosen from one of SEQ ID NO: 3, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 23, SEQ ID NO: 39, SEQ ID NO: 50, SEQ ID NO: 62, SEQ ID NO: 67, SEQ ID NO: 78, SEQ ID NO: 85, SEQ ID NO: 125, SEQ ID NO: 134, SEQ ID NO: 147, SEQ ID NO: 165, SEQ ID NO: 172 and SEQ ID NO: 179.
- 15. The polynucleotide of claim 7, wherein the polynucleotide encoding a polypeptide having an inner membrane domain comprises a nucleotide sequence chosen from one of SEQ ID NO: 2, SEQ ID NO: 5, SEQ ID NO: 6, SEQ ID NO: 7, SEQ ID NO: 10, SEQ ID NO: 11, SEQ ID NO: 12, SEQ ID NO: 13, SEQ ID NO: 14, SEQ ID NO: 15, SEQ ID NO: 16, SEQ ID NO: 17, SEQ ID NO: 19, SEQ ID NO: 20, SEQ ID NO: 21, SEQ ID NO: 22, SEQ ID NO: 26, SEQ ID NO: 27, SEQ ID NO: 28, SEQ ID NO: 29, SEQ ID NO: 30, SEQ ID NO: 31, SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, SEQ ID NO: 35, SEQ ID NO: 36, SEQ ID NO: 37, SEQ ID NO: 38, SEQ ID NO: 40, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 46, SEQ ID NO: 47, SEQ ID NO: 48, SEQ ID NO: 51, SEQ ID NO: 52, SEQ ID NO: 53, SEQ ID NO: 54, SEQ ID NO: 56, SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO: 61, SEQ ID NO: 65, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 71, SEQ ID NO: 73, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 81, SEQ ID NO: 82, SEQ ID NO: 83, SEQ ID NO: 84, SEQ ID NO: 86 SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 90, SEQ ID NO: 91, SEQ ID NO: 93, SEQ ID NO: 94, SEQ ID NO: 95, SEQ ID NO: 96, SEQ ID NO: 97, SEQ ID NO: 98, SEQ ID NO: 99, SEQ ID NO: 100, SEQ ID NO: 101, SEQ ID NO: 102, SEQ ID NO: 103, SEQ ID NO: 105, SEQ ID NO: 106, SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 112, SEQ ID NO: 113, SEQ ID NO: 114, SEQ ID NO: 115, SEQ ID NO: 117, SEQ ID NO: 118, SEQ ID NO: 119, SEQ ID NO: 120, SEQ ID NO: 121, SEQ ID NO: 122, SEQ ID NO: 123, SEQ ID NO: 124, SEQ ID NO: 126, SEQ ID NO: 127, SEQ ID NO: 128, SEQ ID NO: 129, SEQ ID NO: 130, SEQ ID NO: 131, SEQ ID NO: 132, SEQ ID NO: 133, SEQ ID NO: 135, SEQ ID NO: 136, SEQ ID NO: 139, SEQ ID NO: 140, SEQ ID NO: 141, SEQ ID NO: 142, SEQ ID NO: 144, SEQ ID NO: 145, SEQ ID NO: 146, SEQ ID NO: 148, SEQ ID NO: 150, SEQ ID NO: 151, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 154, SEQ ID NO: 156, SEQ ID NO: 157, SEQ ID NO: 158, SEQ ID NO: 159, SEQ ID NO: 160, SEQ ID NO: 162, SEQ ID NO: 163, SEQ ID NO: 164, SEQ ID NO: 166, SEQ ID NO: 167, SEQ ID NO: 168, SEQ ID NO: 169, SEQ ID NO: 170, SEQ ID NO: 173, SEQ ID NO: 175, SEQ ID NO: 176, SEQ ID NO: 177, SEQ ID NO: 178, SEQ ID NO: 180, SEQ ID NO: 181, SEQ ID NO: 182, SEQ ID NO: 184, SEQ ID NO: 186, SEQ ID NO: 187, SEQ ID NO: 188, SEQ ID NO: 189, SEQ ID NO: 190, SEQ ID NO: 191, SEQ ID NO: 192, SEQ ID NO: 193, SEQ ID NO: 194, SEQ ID NO: 195, SEQ ID NO: 198, SEQ ID NO: 200, SEQ ID NO: 203, SEQ ID NO: 206, SEQ ID NO: 208, SEQ ID NO: 209, SEQ ID NO: 211, SEQ ID NO: 212, SEQ ID NO: 213, SEQ ID NO: 214 and SEQ ID NO: 215.
- 16. The polynucleotide of claim 7, wherein the polynucleotide encoding a polypeptide identified by Blastp analysis comprises a nucleotide sequence chosen from one of SEQ ID NO: 1, SEQ ID NO: 2, SEQ ID NO: 7, SEQ ID NO: 10, SEQ ID NO: 12, SEQ ID NO: 16, SEQ ID NO: 20, SEQ ID NO: 24, SEQ ID NO: 27, SEQ ID NO: 30, SEQ ID NO: 31, SEQ ID NO: 32, SEQ ID NO: 33, SEQ ID NO: 34, SEQ ID NO: 35, SEQ ID NO: 38, SEQ ID NO: 40, SEQ ID NO: 42, SEQ ID NO: 43, SEQ ID NO: 44, SEQ ID NO: 48, SEQ ID NO: 51, SEQ ID NO: 53, SEQ ID NO: 59, SEQ ID NO: 60, SEQ ID NO: 61, SEQ ID NO: 65, SEQ ID NO: 67, SEQ ID NO: 68, SEQ ID NO: 69, SEQ ID NO: 70, SEQ ID NO: 71, SEQ ID NO: 75, SEQ ID NO: 76, SEQ ID NO: 77, SEQ ID NO: 78, SEQ ID NO: 79, SEQ ID NO: 80, SEQ ID NO: 87, SEQ ID NO: 88, SEQ ID NO: 90, SEQ ID NO: 94, SEQ ID NO: 95, SEQ ID NO: 96, SEQ ID NO: 98, SEQ ID NO: 100, SEQ ID NO: 103, SEQ ID NO: 105, SEQ ID NO: 107, SEQ ID NO: 108, SEQ ID NO: 109, SEQ ID NO: 112, SEQ ID NO: 113, SEQ ID NO: 115, SEQ ID NO: 117, SEQ ID NO: 118, SEQ ID NO: 122, SEQ ID NO: 123, SEQ ID NO: 124, SEQ ID NO: 127, SEQ ID NO: 129, SEQ ID NO: 131, SEQ ID NO: 132, SEQ ID NO: 133, SEQ ID NO: 134, SEQ ID NO: 135, SEQ ID NO: 136, SEQ ID NO: 138, SEQ ID NO: 139, SEQ ID NO: 141, SEQ ID NO: 144, SEQ ID NO: 146, SEQ ID NO: 147, SEQ ID NO: 151, SEQ ID NO: 152, SEQ ID NO: 154, SEQ ID NO: 155, SEQ ID NO: 157, SEQ ID NO: 158, SEQ ID NO: 159, SEQ ID NO: 160, SEQ ID NO: 161, SEQ ID NO: 162, SEQ ID NO: 163, SEQ ID NO: 165, SEQ ID NO: 166, SEQ ID NO: 167, SEQ ID NO: 169, SEQ ID NO: 172, SEQ ID NO: 173, SEQ ID NO: 176, SEQ ID NO: 177, SEQ ID NO: 178, SEQ ID NO: 180, SEQ ID NO: 181, SEQ ID NO: 182, SEQ ID NO: 184, SEQ ID NO: 185, SEQ ID NO: 186, SEQ ID NO: 188, SEQ ID NO: 189, SEQ ID NO: 191, SEQ ID NO: 193, SEQ ID NO: 196, SEQ ID NO: 197, SEQ ID NO: 198, SEQ ID NO: 199, SEQ ID NO: 200, SEQ ID NO: 201, SEQ ID NO: 202, SEQ ID NO: 204, SEQ ID NO: 205, SEQ ID NO: 206, SEQ ID NO: 207, SEQ ID NO: 208, SEQ ID NO: 210, SEQ ID NO: 212, SEQ ID NO: 213 and SEQ ID NO: 214.
- 17. The polynucleotide of claim 7, wherein the polynucleotide encoding a polypeptide identified by Pfam analysis comprises a nucleotide sequence chosen from one of SEQ ID NO: 4, SEQ ID NO: 18, SEQ ID NO: 19, SEQ ID NO: 41, SEQ ID NO: 45, SEQ ID NO: 55, SEQ ID NO: 57, SEQ ID NO: 58, SEQ ID NO: 63, SEQ ID NO: 64, SEQ ID NO: 66, SEQ ID NO: 72, SEQ ID NO: 74, SEQ ID NO: 89, SEQ ID NO: 92, SEQ ID NO: 104, SEQ ID NO: 111, SEQ ID NO: 116, SEQ ID NO: 119, SEQ ID NO: 128, SEQ ID NO: 137, SEQ ID NO: 142, SEQ ID NO: 143, SEQ ID NO: 149, SEQ ID NO: 151, SEQ ID NO: 152, SEQ ID NO: 153, SEQ ID NO: 157, SEQ ID NO: 159, SEQ ID NO: 160, SEQ ID NO: 162, SEQ ID NO: 163, SEQ ID NO: 164, SEQ ID NO: 165, SEQ ID NO: 166, SEQ ID NO: 169, SEQ ID NO: 171, SEQ ID NO: 174, SEQ ID NO: 176, SEQ ID NO: 180, SEQ ID NO: 182, SEQ ID NO: 183, SEQ ID NO: 184, SEQ ID NO: 186, SEQ ID NO: 188, SEQ ID NO 189, SEQ ID NO: 195, SEQ ID NO: 198, SEQ ID NO 199, SEQ ID NO: 205, SEQ ID NO: 212 and SEQ ID NO: 213.
- 18. The polynucleotide of claim 7, wherein the polynucleotide encoding a lipoprotein comprises a nucleotide sequence chosen from one of SEQ ID NO: 3, SEQ ID NO: 8, SEQ ID NO: 9, SEQ ID NO: 13, SEQ ID NO: 21, SEQ ID NO: 26, SEQ ID NO: 34, SEQ ID NO: 62, SEQ ID NO: 67, SEQ ID NO: 85, SEQ ID NO: 134, SEQ ID NO: 147, SEQ ID NO: 150, SEQ ID NO: 168, SEQ ID NO: 170 and SEQ ID NO: 173.
- 19. The polynucleotide of claim 7, wherein the polynucleotide encoding a polypeptide having a LPXTG motif and covalently attached to the peptidoglycan layer comprises a nucleotide sequence chosen from one of SEQ ID NO: 13, SEQ ID NO: 21, SEQ ID NO: 34 and SEQ ID NO: 170.
- 20. The polynucleotide of claim 7, wherein the polynucleotide encoding a polypeptide having a peptidoglycan binding motif and associated with the peptidoglycan layer comprises a nucleotide sequence chosen from one of SEQ ID NO: 25, SEQ ID NO: 49 and SEQ ID NO: 110.
- 21. The polynucleotide of claim 7, wherein the polynucleotide encoding a polypeptide having a signal sequence and a C-terminal Tyrosine or a C-terminal Phenylalanine amino acid comprises a nucleotide sequence chosen from one of SEQ ID NO:11, SEQ ID NO:39, SEQ ID NO:73, SEQ ID NO:97, SEQ ID NO:106, SEQ ID NO: 125 and SEQ ID NO:187.
- 22. The polynucleotide of claim 7, wherein the polynucleotide encoding a polypeptide having a tripeptide RGD amino acid sequence comprises a nucleotide sequence chosen from one of SEQ ID NO:1, SEQ ID NO:21, SEQ ID NO:66 and SEQ ID NO:67.
- 23. The polynucleotide of claim 7, wherein the polynucleotide encoding a polypeptide identified by proteomics as surface exposed comprises a nucleotide sequence chosen from one of SEQ ID NO:14, SEQ ID NO:16, SEQ ID NO:17, SEQ ID NO:46, SEQ ID NO:64, SEQ ID NO:66, SEQ ID NO:67, SEQ ID NO:69, SEQ ID NO:71, SEQ ID NO:74, SEQ ID NO:91, SEQ ID NO:103, SEQ ID NO:116, SEQ ID NO:128, SEQ ID NO:131, SEQ ID NO:136, SEQ ID NO:151, SEQ ID NO:156, SEQ ID NO:159, SEQ ID NO:162, SEQ ID NO:164, SEQ ID NO:172, SEQ ID NO:176, SEQ ID NO:178, SEQ ID NO:179, SEQ ID NO:180, SEQ ID NO:182 and SEQ ID NO:205.
- 24. The polynucleotide of claim 7, wherein the polynucleotide encoding a polypeptide identified by proteomics as membrane associated comprises a nucleotide sequence chosen from of one of SEQ ID NO:431 through SEQ ID NO: 591.
- 25. An isolated polypeptide encoded by a polynucleotide of a Streptococcus pneumoniae genomic sequence, wherein the polynucleotide comprises a nucleotide sequence having at least about 95% identity to a nucleotide sequence chosen from one of SEQ ID NO: 1 through SEQ ID NO: 215 or SEQ ID NO: 431 through SEQ ID NO: 591, a degenerate variant thereof, or a fragment thereof.
- 26. The polypeptide of claim 25, wherein the polypeptide is a fusion polypeptide.
- 27. The polypeptide of claim 25, which immunoreacts with seropositive serum of an individual infected with Streptococcus pneumoniae.
- 28. The polypeptide of claim 25, further defined as:
(a) a Streptococcus pneumoniae polypeptide having 0, 1 or 2 transmembrane domains; (b) a Streptococcus pneumoniae polypeptide having 3 or more transmembrane domains; (c) a Streptococcus pneumoniae polypeptide having an outer membrane domain or a periplasmic domain; (d) a Streptococcus pneumoniae polypeptide having an inner membrane domain; (e) a Streptococcus pneumoniae polypeptide identified by Blastp analysis; (f) a Streptococcus pneumoniae polypeptide identified by Pfam analysis; (g) a Streptococcus pneumoniae lipoprotein; (h) a Streptococcus pneumoniae polypeptide having a LPXTG motif, wherein the polypeptide is covalently attached to the peptidoglycan layer; (i) a Streptococcus pneumoniae polypeptide having a peptidoglycan binding motif, wherein the polypeptide is associated with the peptidoglycan layer; (j) a Streptococcus pneumoniae polypeptide having a signal sequence and a C-terminal Tyrosine or a C-terminal Phenylalanine amino acid; (k) a Streptococcus pneumoniae polypeptide having a tripeptide RGD amino acid sequence; (l) a Streptococcus pneumoniae polypeptide identified by proteomics as surface exposed; and (m) a Streptococcus pneumoniae polypeptide identified by proteomics as membrane associated.
- 29. The polypeptide of claim 28, wherein the polypeptide having 0, 1 or 2 transmembrane domains comprises an amino acid sequence chosen from one of SEQ ID NO: 216, SEQ ID NO: 218, SEQ ID NO: 219, SEQ ID NO: 222, SEQ ID NO: 223, SEQ ID NO: 224, SEQ ID NO: 226, SEQ ID NO: 228, SEQ ID NO: 231, SEQ ID NO: 232, SEQ ID NO: 233, SEQ ID NO: 234, SEQ ID NO: 237, SEQ ID NO: 238, SEQ ID NO: 239, SEQ ID NO: 240, SEQ ID NO: 243, SEQ ID NO: 244, SEQ ID NO: 247, SEQ ID NO: 249, SEQ ID NO: 251, SEQ ID NO: 254, SEQ ID NO: 256, SEQ ID NO: 257, SEQ ID NO: 260, SEQ ID NO: 262, SEQ ID NO: 264, SEQ ID NO: 265, SEQ ID NO: 266, SEQ ID NO: 268, SEQ ID NO: 270, SEQ ID NO: 272, SEQ ID NO: 273, SEQ ID NO: 275, SEQ ID NO: 276, SEQ ID NO: 277, SEQ ID NO: 278, SEQ ID NO: 279, SEQ ID NO: 281, SEQ ID NO: 282, SEQ ID NO: 283, SEQ ID NO: 284, SEQ ID NO: 285, SEQ ID NO: 286, SEQ ID NO: 287, SEQ ID NO: 289, SEQ ID NO: 293, SEQ ID NO: 294, SEQ ID NO: 296, SEQ ID NO: 298, SEQ ID NO: 300, SEQ ID NO: 301, SEQ ID NO: 304, SEQ ID NO: 306, SEQ ID NO: 307, SEQ ID NO: 310, SEQ ID NO: 311, SEQ ID NO: 312, SEQ ID NO: 315, SEQ ID NO: 319, SEQ ID NO: 320, SEQ ID NO: 321, SEQ ID NO: 324, SEQ ID NO: 325, SEQ ID NO: 326, SEQ ID NO: 328, SEQ ID NO: 331, SEQ ID NO: 336, SEQ ID NO: 337, SEQ ID NO: 338, SEQ ID NO: 340, SEQ ID NO: 341, SEQ ID NO: 342, SEQ ID NO: 343, SEQ ID NO: 346, SEQ ID NO: 347, SEQ ID NO: 349, SEQ ID NO: 351, SEQ ID NO: 352, SEQ ID NO: 353, SEQ ID NO: 356, SEQ ID NO: 357, SEQ ID NO: 358, SEQ ID NO: 359, SEQ ID NO: 362, SEQ ID NO: 363, SEQ ID NO: 364, SEQ ID NO: 365, SEQ ID NO: 370, SEQ ID NO: 371, SEQ ID NO: 373, SEQ ID NO: 376, SEQ ID NO: 377, SEQ ID NO: 380, SEQ ID NO: 385, SEQ ID NO: 386, SEQ ID NO: 387, SEQ ID NO: 389, SEQ ID NO: 391, SEQ ID NO: 394, SEQ ID NO: 398, SEQ ID NO: 400, SEQ ID NO: 402, SEQ ID NO: 407, SEQ ID NO: 410, SEQ ID NO: 411, SEQ ID NO: 412, SEQ ID NO: 414, SEQ ID NO: 415, SEQ ID NO: 416, SEQ ID NO: 417, SEQ ID NO: 419, SEQ ID NO: 420, SEQ ID NO: 422, SEQ ID NO: 424, SEQ ID NO: 425, a fragment thereof or a degenerate variant thereof.
- 30. The polypeptide of claim 28, wherein the polypeptide having 3 or more transmembrane domains comprises an amino acid sequence chosen from one of SEQ ID NO: 217, SEQ ID NO: 220, SEQ ID NO: 221, SEQ ID NO: 225, SEQ ID NO: 227, SEQ ID NO: 229, SEQ ID NO: 230, SEQ ID NO: 235, SEQ ID NO: 236, SEQ ID NO: 241, SEQ ID NO: 242, SEQ ID NO: 245, SEQ ID NO: 246, SEQ ID NO: 248, SEQ ID NO: 250, SEQ ID NO: 252, SEQ ID NO: 253, SEQ ID NO: 255, SEQ ID NO: 258, SEQ ID NO: 259, SEQ ID NO: 261, SEQ ID NO: 263, SEQ ID NO: 267, SEQ ID NO: 269, SEQ ID NO: 271, SEQ ID NO: 274, SEQ ID NO: 280, SEQ ID NO: 286, SEQ ID NO: 290, SEQ ID NO: 291, SEQ ID NO: 292, SEQ ID NO: 295, SEQ ID NO: 297, SEQ ID NO: 299, SEQ ID NO: 302, SEQ ID NO: 303, SEQ ID NO: 305, SEQ ID NO: 308, SEQ ID NO: 309, SEQ ID NO: 313, SEQ ID NO: 314, SEQ ID NO: 316, SEQ ID NO: 317, SEQ ID NO: 318, SEQ ID NO: 322, SEQ ID NO: 323, SEQ ID NO: 327, SEQ ID NO: 329, SEQ ID NO: 330, SEQ ID NO: 332, SEQ ID NO: 333, SEQ ID NO: 334, SEQ ID NO: 335, SEQ ID NO: 339, SEQ ID NO: 344, SEQ ID NO: 345, SEQ ID NO: 348, SEQ ID NO: 350, SEQ ID NO: 354, SEQ ID NO: 355, SEQ ID NO: 360, SEQ ID NO: 361, SEQ ID NO: 366, SEQ ID NO: 367, SEQ ID NO: 368, SEQ ID NO: 369, SEQ ID NO: 372, SEQ ID NO: 374, SEQ ID NO: 375, SEQ ID NO: 378, SEQ ID NO: 379, SEQ ID NO: 381, SEQ ID NO: 382, SEQ ID NO: 383, SEQ ID NO: 384, SEQ ID NO: 388, SEQ ID NO: 390, SEQ ID NO: 392, SEQ ID NO: 393, SEQ ID NO: 395, SEQ ID NO: 396, SEQ ID NO: 397, SEQ ID NO: 399, SEQ ID NO: 401, SEQ ID NO: 403, SEQ ID NO: 404, SEQ ID NO: 405, SEQ ID NO: 406, SEQ ID NO: 408, SEQ ID NO: 409, SEQ ID NO: 413, SEQ ID NO: 418, SEQ ID NO: 421, SEQ ID NO: 423, SEQ ID NO: 426, SEQ ID NO: 427, SEQ ID NO: 428, SEQ ID NO: 429, SEQ ID NO: 430, a fragment thereof or a degenerate variant thereof.
- 31. The polypeptide of claim 28, wherein the polypeptide having an outer membrane or a periplasmic domain comprises an amino acid sequence chosen from one of SEQ ID NO: 218, SEQ ID NO: 223, SEQ ID NO: 224, SEQ ID NO: 238, SEQ ID NO: 254, SEQ ID NO: 265, SEQ ID NO: 277, SEQ ID NO: 282, SEQ ID NO: 293, SEQ ID NO: 300, SEQ ID NO: 340, SEQ ID NO: 349, SEQ ID NO: 362, SEQ ID NO: 380, SEQ ID NO: 387, SEQ ID NO: 394, a fragment thereof or a degenerate variant thereof.
- 32. The polypeptide of claim 28, wherein the polypeptide having an inner membrane domain comprises an amino acid sequence chosen from one of SEQ ID NO: 217, SEQ ID NO: 220, SEQ ID NO: 221, SEQ ID NO: 222, SEQ ID NO: 225, SEQ ID NO: 226, SEQ ID NO: 227, SEQ ID NO: 228, SEQ ID NO: 229, SEQ ID NO: 230, SEQ ID NO: 231, SEQ ID NO: 232, SEQ ID NO: 234, SEQ ID NO: 235, SEQ ID NO: 236, SEQ ID NO: 237, SEQ ID NO: 241, SEQ ID NO: 242, SEQ ID NO: 243, SEQ ID NO: 244, SEQ ID NO: 245, SEQ ID NO: 246, SEQ ID NO: 247, SEQ ID NO: 248, SEQ ID NO: 249, SEQ ID NO: 250, SEQ ID NO: 251, SEQ ID NO: 252, SEQ ID NO: 253, SEQ ID NO: 255, SEQ ID NO: 258, SEQ ID NO: 259, SEQ ID NO: 261, SEQ ID NO: 262, SEQ ID NO: 263, SEQ ID NO: 266, SEQ ID NO: 267, SEQ ID NO: 268, SEQ ID NO: 269, SEQ ID NO: 271, SEQ ID NO: 274, SEQ ID NO: 275, SEQ ID NO: 276, SEQ ID NO: 280, SEQ ID NO: 283, SEQ ID NO: 284, SEQ ID NO: 285, SEQ ID NO: 286, SEQ ID NO: 288, SEQ ID NO: 290, SEQ ID NO: 291, SEQ ID NO: 292, SEQ ID NO: 294, SEQ ID NO: 295, SEQ ID NO: 296, SEQ ID NO: 297, SEQ ID NO: 298, SEQ ID NO: 299, SEQ ID NO: 301 SEQ ID NO: 302, SEQ ID NO: 303, SEQ ID NO: 305, SEQ ID NO: 306, SEQ ID NO: 308, SEQ ID NO: 309, SEQ ID NO: 310, SEQ ID NO: 311, SEQ ID NO: 312, SEQ ID NO: 313, SEQ ID NO: 314, SEQ ID NO: 315, SEQ ID NO: 316, SEQ ID NO: 317, SEQ ID NO: 318, SEQ ID NO: 320, SEQ ID NO: 321, SEQ ID NO: 322, SEQ ID NO: 323, SEQ ID NO: 324, SEQ ID NO: 327, SEQ ID NO: 328, SEQ ID NO: 329, SEQ ID NO: 330, SEQ ID NO: 332, SEQ ID NO: 333, SEQ ID NO: 334, SEQ ID NO: 335, SEQ ID NO: 336, SEQ ID NO: 337, SEQ ID NO: 338, SEQ ID NO: 339, SEQ ID NO: 341, SEQ ID NO: 342, SEQ ID NO: 343, SEQ ID NO: 344, SEQ ID NO: 345, SEQ ID NO: 346, SEQ ID NO: 347, SEQ ID NO: 348, SEQ ID NO: 350, SEQ ID NO: 351, SEQ ID NO: 354, SEQ ID NO: 355, SEQ ID NO: 356, SEQ ID NO: 357, SEQ ID NO: 359, SEQ ID NO: 360, SEQ ID NO: 361, SEQ ID NO: 362, SEQ ID NO: 365, SEQ ID NO: 366, SEQ ID NO: 367, SEQ ID NO: 368, SEQ ID NO: 369, SEQ ID NO: 371, SEQ ID NO: 372, SEQ ID NO: 373, SEQ ID NO: 374, SEQ ID NO: 375, SEQ ID NO: 377, SEQ ID NO: 378, SEQ ID NO: 379, SEQ ID NO: 381, SEQ ID NO: 382, SEQ ID NO: 383, SEQ ID NO: 384, SEQ ID NO: 385, SEQ ID NO: 388, SEQ ID NO: 390, SEQ ID NO: 391, SEQ ID NO: 392, SEQ ID NO: 393, SEQ ID NO: 395, SEQ ID NO: 396, SEQ ID NO: 397, SEQ ID NO: 399, SEQ ID NO: 401, SEQ ID NO: 402, SEQ ID NO: 403, SEQ ID NO: 404, SEQ ID NO: 405, SEQ ID NO: 406, SEQ ID NO: 407, SEQ ID NO: 408, SEQ ID NO: 409, SEQ ID NO: 410, SEQ ID NO: 413, SEQ ID NO: 415, SEQ ID NO: 418, SEQ ID NO: 421, SEQ ID NO: 423, SEQ ID NO: 424, SEQ ID NO: 426, SEQ ID NO: 427, SEQ ID NO: 428, SEQ ID NO: 429, SEQ ID NO: 430, a fragment thereof or a degenerate variant thereof.
- 33. The polypeptide of claim 28, wherein the polypeptide identified by Blastp analysis comprises an amino acid sequence chosen from one of SEQ ID NO: 216, SEQ ID NO: 217, SEQ ID NO: 222, SEQ ID NO: 225, SEQ ID NO: 227, SEQ ID NO: 231, SEQ ID NO: 235, SEQ ID NO: 239, SEQ ID NO: 242, SEQ ID NO: 245, SEQ ID NO: 246, SEQ ID NO: 247, SEQ ID NO: 248, SEQ ID NO: 249, SEQ ID NO: 250, SEQ ID NO: 253, SEQ ID NO: 255, SEQ ID NO: 257, SEQ ID NO: 258, SEQ ID NO: 259, SEQ ID NO: 263, SEQ ID NO: 266, SEQ ID NO: 268, SEQ ID NO: 269, SEQ ID NO: 275, SEQ ID NO: 276, SEQ ID NO: 280, SEQ ID NO: 282, SEQ ID NO: 283, SEQ ID NO: 284, SEQ ID NO: 285, SEQ ID NO: 286, SEQ ID NO: 290, SEQ ID NO: 291, SEQ ID NO: 292, SEQ ID NO: 293, SEQ ID NO: 294, SEQ ID NO: 295, SEQ ID NO: 302, SEQ ID NO: 303, SEQ ID NO: 305, SEQ ID NO: 309, SEQ ID NO: 310, SEQ ID NO: 311, SEQ ID NO: 313, SEQ ID NO: 315, SEQ ID NO: 318, SEQ ID NO: 320, SEQ ID NO: 322, SEQ ID NO: 323, SEQ ID NO: 324, SEQ ID NO: 327, SEQ ID NO: 328, SEQ ID NO: 330, SEQ ID NO: 332, SEQ ID NO: 333, SEQ ID NO: 337, SEQ ID NO: 338, SEQ ID NO: 339, SEQ ID NO: 342, SEQ ID NO: 344, SEQ ID NO: 346, SEQ ID NO: 347, SEQ ID NO: 348, SEQ ID NO: 349, SEQ ID NO: 350, SEQ ID NO: 351, SEQ ID NO: 353, SEQ ID NO: 354, SEQ ID NO: 356, SEQ ID NO: 359, SEQ ID NO: 361, SEQ ID NO: 362, SEQ ID NO: 366, SEQ ID NO: 367, SEQ ID NO: 369, SEQ ID NO: 370, SEQ ID NO: 372, SEQ ID NO: 373, SEQ ID NO: 374, SEQ ID NO: 375, SEQ ID NO: 376, SEQ ID NO: 377, SEQ ID NO: 378, SEQ ID NO: 380, SEQ ID NO: 381, SEQ ID NO: 382, SEQ ID NO: 384, SEQ ID NO: 387, SEQ ID NO: 388, SEQ ID NO: 391, SEQ ID NO: 392, SEQ ID NO: 393, SEQ ID NO: 395, SEQ ID NO: 396, SEQ ID NO: 397, SEQ ID NO: 399, SEQ ID NO: 400, SEQ ID NO: 401, SEQ ID NO: 403, SEQ ID NO: 404, SEQ ID NO: 406, SEQ ID NO: 408, SEQ ID NO: 411, SEQ ID NO: 412, SEQ ID NO: 413, SEQ ID NO: 414, SEQ ID NO: 415, SEQ ID NO: 416, SEQ ID NO: 417, SEQ ID NO: 419, SEQ ID NO: 420, SEQ ID NO: 421, SEQ ID NO: 422, SEQ ID NO: 423, SEQ ID NO: 425, SEQ ID NO: 427, SEQ ID NO: 428, SEQ ID NO: 429, a fragment thereof or a degenerate variant thereof.
- 34. The polypeptide of claim 28, wherein the polypeptide identified by Pfam analysis comprises an amino acid sequence chosen from one of SEQ ID NO: 219, SEQ ID NO: 233, SEQ ID NO: 234, SEQ ID NO: 255, SEQ ID NO: 260, SEQ ID NO: 270, SEQ ID NO: 272, SEQ ID NO: 273, SEQ ID NO: 278, SEQ ID NO: 279, SEQ ID NO: 281, SEQ ID NO: 287, SEQ ID NO: 289, SEQ ID NO: 304, SEQ ID NO: 307, SEQ ID NO: 319, SEQ ID NO: 326, SEQ ID NO: 331, SEQ ID NO: 334, SEQ ID NO: 343, SEQ ID NO: 352, SEQ ID NO: 357, SEQ ID NO: 358, SEQ ID NO: 364, SEQ ID NO: 366, SEQ ID NO: 367, SEQ ID NO: 368, SEQ ID NO: 372, SEQ ID NO: 374, SEQ ID NO: 375, SEQ ID NO: 377, SEQ ID NO: 378, SEQ ID NO: 379, SEQ ID NO: 380, SEQ ID NO: 381, SEQ ID NO: 384, SEQ ID NO: 386, SEQ ID NO: 389, SEQ ID NO: 391, SEQ ID NO: 395, SEQ ID NO: 397, SEQ ID NO: 398, SEQ ID NO: 399, SEQ ID NO: 401, SEQ ID NO: 403, SEQ ID NO 404, SEQ ID NO: 410, SEQ ID NO: 413, SEQ ID NO 414, SEQ ID NO: 420, SEQ ID NO: 427, SEQ ID NO: 428, a fragment thereof or a degenerate variant thereof.
- 35. The polypeptide of claim 28, wherein the polypeptide is a lipoprotein and comprises an amino acid sequence chosen from one of SEQ ID NO: 218, SEQ ID NO: 223, SEQ ID NO: 224, SEQ ID NO: 228, SEQ ID NO: 236, SEQ ID NO: 241, SEQ ID NO: 249, SEQ ID NO: 277, SEQ ID NO: 282, SEQ ID NO: 300, SEQ ID NO: 349, SEQ ID NO: 362, SEQ ID NO: 365, SEQ ID NO: 383, SEQ ID NO: 385, SEQ ID NO: 388, a fragment thereof or a degenerate variant thereof.
- 36. The polypeptide of claim 28, wherein the polypeptide having a LPXTG motif and covalently attached to the peptidoglycan layer comprises an amino acid sequence chosen from one of SEQ ID NO: 228, SEQ ID NO: 236, SEQ ID NO: 249, SEQ, SEQ ID NO: 385, a fragment thereof or a degenerate variant thereof.
- 37. The polypeptide of claim 28, wherein the polypeptide having a peptidoglycan binding motif and associated with the peptidoglycan layer comprises an amino acid sequence selected from one of SEQ ID NO: 240, SEQ ID NO: 264, SEQ ID NO: 325, a fragment thereof or a degenerate variant thereof.
- 38. The polypeptide of claim 28, wherein the polypeptide having a signal sequence and a C-terminal Tyrosine or Phenylalanine amino acid comprises an amino acid sequence chosen from one of SEQ ID NO:226, SEQ ID NO:254, SEQ ID NO:289, SEQ ID NO:312, SEQ ID NO:321, SEQ ID NO: 340, SEQ ID NO:402, a fragment thereof or a degenerate variant thereof.
- 39. The polypeptide of claim 28, wherein the polypeptide having a tripeptide RGD sequence that potentially is involved in cell attachment comprises an amino acid sequence chosen from one of SEQ ID NO:216, SEQ ID NO:236, SEQ ID NO:281, SEQ ID NO:282, a fragment thereof or a degenerate variant thereof.
- 40. The polypeptide of claim 28, wherein the polypeptide identified by proteomics as surface exposed comprises an amino acid sequence chosen from one of SEQ ID NO: 229, SEQ ID NO: 231, SEQ ID NO: 232, SEQ ID NO: 261, SEQ ID NO: 279, SEQ ID NO: 281, SEQ ID NO: 282, SEQ ID NO: 284, SEQ ID NO: 286, SEQ ID NO: 289, SEQ ID NO: 306, SEQ ID NO: 318, SEQ ID NO: 331, SEQ ID NO: 343, SEQ ID NO: 346, SEQ ID NO: 351, SEQ ID NO: 366, SEQ ID NO: 371, SEQ ID NO: 374, SEQ ID NO: 377, SEQ ID NO: 379, SEQ ID NO: 387, SEQ ID NO: 391, SEQ ID NO: 393, SEQ ID NO: 394, 395, SEQ ID NO: 397, SEQ ID NO: 420, a fragment thereof or a degenerate variant thereof.
- 41. The polypeptide of claim 28, wherein the polypeptide identified by proteomics as surface exposed comprises an amino acid sequence chosen from one of SEQ ID NO:592 through SEQ ID NO: 752, a fragment thereof or a degenerate variant thereof.
- 42. An isolated polypeptide comprising an amino acid sequence having at least about 95% identity to an amino acid sequence chosen from one of SEQ ID NO: 216 through SEQ ID NO: 430 or SEQ ID NO: 592 through SEQ ID NO:752.
- 43. The polypeptide of claim 42, wherein the polypeptide is a fusion polypeptide
- 44. The polypeptide of claim 42, which immunoreacts with seropositive serum of an individual infected with Streptococcus pneumoniae.
- 45. The polypeptide of claim 42, further defined as:
(a) a Streptococcus pneumoniae polypeptide having 0, 1 or 2 transmembrane domains; (b) a Streptococcus pneumoniae polypeptide having 3 or more transmembrane domains; (c) a Streptococcus pneumoniae polypeptide having an outer membrane domain or a periplasmic domain; (d) a Streptococcus pneumoniae polypeptide having an inner membrane domain; (e) a Streptococcus pneumoniae polypeptide identified by Blastp analysis; (f) a Streptococcus pneumoniae polypeptide identified by Pfam analysis; (g) a Streptococcus pneumoniae lipoprotein; (h) a Streptococcus pneumoniae polypeptide having a LPXTG motif, wherein the polypeptide is covalently attached to the peptidoglycan layer; (i) a Streptococcus pneumoniae polypeptide having a peptidoglycan binding motif, wherein the polypeptide is associated with the peptidoglycan layer; (j) a Streptococcus pneumoniae polypeptide having a signal sequence and a C-terminal Tyrosine or a C-terminal Phenylalanine amino acid; (k) a Streptococcus pneumoniae polypeptide having a tripeptide RGD amino add sequence; (l) a Streptococcus pneumoniae polypeptide identified by proteomics as surface exposed; and (m) a Streptococcus pneumoniae polypeptide identified by proteomics as membrane associated.
- 46. The polypeptide of claim 45, wherein the polypeptide having a 0, 1 or 2 transmembrane domains comprises an amino acid sequence chosen from one of SEQ ID NO: 216, SEQ ID NO: 218, SEQ ID NO: 219, SEQ ID NO: 222, SEQ ID NO: 223, SEQ ID NO: 224, SEQ ID NO: 226, SEQ ID NO: 228, SEQ ID NO: 231, SEQ ID NO: 232, SEQ ID NO: 233, SEQ ID NO: 234, SEQ ID NO: 237, SEQ ID NO: 238, SEQ ID NO: 239, SEQ ID NO: 240, SEQ ID NO: 243, SEQ ID NO: 244, SEQ ID NO: 247, SEQ ID NO: 249, SEQ ID NO: 251, SEQ ID NO: 254, SEQ ID NO: 256, SEQ ID NO: 257, SEQ ID NO: 260, SEQ ID NO: 262, SEQ ID NO: 264, SEQ ID NO: 265, SEQ ID NO: 266, SEQ ID NO: 268, SEQ ID NO: 270, SEQ ID NO: 272, SEQ ID NO: 273, SEQ ID NO: 275, SEQ ID NO: 276, SEQ ID NO: 277, SEQ ID NO: 278, SEQ ID NO: 279, SEQ ID NO: 281, SEQ ID NO: 282, SEQ ID NO: 283, SEQ ID NO: 284, SEQ ID NO: 285, SEQ ID NO: 286, SEQ ID NO: 287, SEQ ID NO: 289, SEQ ID NO: 293, SEQ ID NO: 294, SEQ ID NO: 296, SEQ ID NO: 298, SEQ ID NO: 300, SEQ ID NO: 301, SEQ ID NO: 304, SEQ ID NO: 306, SEQ ID NO: 307, SEQ ID NO: 310, SEQ ID NO: 311, SEQ ID NO: 312, SEQ ID NO: 315, SEQ ID NO: 319, SEQ ID NO: 320, SEQ ID NO: 321, SEQ ID NO: 324, SEQ ID NO: 325, SEQ ID NO: 326, SEQ ID NO: 328, SEQ ID NO: 331, SEQ ID NO: 336, SEQ ID NO: 337, SEQ ID NO: 338, SEQ ID NO: 340, SEQ ID NO: 341, SEQ ID NO: 342, SEQ ID NO: 343, SEQ ID NO: 346, SEQ ID NO: 347, SEQ ID NO: 349, SEQ ID NO: 351, SEQ ID NO: 352, SEQ ID NO: 353, SEQ ID NO: 356, SEQ ID NO: 357, SEQ ID NO: 358, SEQ ID NO: 359, SEQ ID NO: 362, SEQ ID NO: 363, SEQ ID NO: 364, SEQ ID NO: 365, SEQ ID NO: 370, SEQ ID NO: 371, SEQ ID NO: 373, SEQ ID NO: 376, SEQ ID NO: 377, SEQ ID NO: 380, SEQ ID NO: 385, SEQ ID NO: 386, SEQ ID NO: 387, SEQ ID NO: 389, SEQ ID NO: 391, SEQ ID NO: 394, SEQ ID NO: 398, SEQ ID NO: 400, SEQ ID NO: 402, SEQ ID NO: 407, SEQ ID NO: 410, SEQ ID NO: 411, SEQ ID NO: 412, SEQ ID NO: 414, SEQ ID NO: 415, SEQ ID NO: 416, SEQ ID NO: 417, SEQ ID NO: 419, SEQ ID NO: 420, SEQ ID NO: 422, SEQ ID NO: 424, SEQ ID NO: 425], a biological equivalent thereof, or a fragment thereof.
- 47. The polypeptide of claim 45, wherein the polypeptide having 3 or more transmembrane domains comprises an amino acid sequence chosen from one of SEQ ID NO: 217, SEQ ID NO: 220, SEQ ID NO: 221, SEQ ID NO: 225, SEQ ID NO: 227, SEQ ID NO: 229, SEQ ID NO: 230, SEQ ID NO: 235, SEQ ID NO: 236, SEQ ID NO: 241, SEQ ID NO: 242, SEQ ID NO: 245, SEQ ID NO: 246, SEQ ID NO: 248, SEQ ID NO: 250, SEQ ID NO: 252, SEQ ID NO: 253, SEQ ID NO: 255, SEQ ID NO: 258, SEQ ID NO: 259, SEQ ID NO: 261, SEQ ID NO: 263, SEQ ID NO: 267, SEQ ID NO: 269, SEQ ID NO: 271, SEQ ID NO: 274, SEQ ID NO: 280, SEQ ID NO: 286, SEQ ID NO: 290, SEQ ID NO: 291, SEQ ID NO: 292, SEQ ID NO: 295, SEQ ID NO: 297, SEQ ID NO: 299, SEQ ID NO: 302, SEQ ID NO: 303, SEQ ID NO: 305, SEQ ID NO: 308, SEQ ID NO: 309, SEQ ID NO: 313, SEQ ID NO: 314, SEQ ID NO: 316, SEQ ID NO: 317, SEQ ID NO: 318, SEQ ID NO: 322, SEQ ID NO: 323, SEQ ID NO: 327, SEQ ID NO: 329, SEQ ID NO: 330, SEQ ID NO: 332, SEQ ID NO: 333, SEQ ID NO: 334, SEQ ID NO: 335, SEQ ID NO: 339, SEQ ID NO: 344, SEQ ID NO: 345, SEQ ID NO: 348, SEQ ID NO: 350, SEQ ID NO: 354, SEQ ID NO: 355, SEQ ID NO: 360, SEQ ID NO: 361, SEQ ID NO: 366, SEQ ID NO: 367, SEQ ID NO: 368, SEQ ID NO: 369, SEQ ID NO: 372, SEQ ID NO: 374, SEQ ID NO: 375, SEQ ID NO: 378, SEQ ID NO: 379, SEQ ID NO: 381, SEQ ID NO: 382, SEQ ID NO: 383, SEQ ID NO: 384, SEQ ID NO: 388, SEQ ID NO: 390, SEQ ID NO: 392, SEQ ID NO: 393, SEQ ID NO: 395, SEQ ID NO: 396, SEQ ID NO: 397, SEQ ID NO: 399, SEQ ID NO: 401, SEQ ID NO: 403, SEQ ID NO: 404, SEQ ID NO: 405, SEQ ID NO: 406, SEQ ID NO: 408, SEQ ID NO: 409, SEQ ID NO: 413, SEQ ID NO: 418, SEQ ID NO: 421, SEQ ID NO: 423, SEQ ID NO: 426, SEQ ID NO: 427, SEQ ID NO: 428, SEQ ID NO: 429, SEQ ID NO: 430, a biological equivalent thereof, or a fragment thereof.
- 48. The polypeptide of claim 45, wherein the polypeptide having an outer membrane domain or a periplasmic domain comprises an amino acid sequence chosen from one of SEQ ID NO: 218, SEQ ID NO: 223, SEQ ID NO: 224, SEQ ID NO: 238, SEQ ID NO: 254, SEQ ID NO: 265, SEQ ID NO: 277, SEQ ID NO: 282, SEQ ID NO: 293, SEQ ID NO: 300, SEQ ID NO: 340, SEQ ID NO: 349, SEQ ID NO: 362, SEQ ID NO: 380, SEQ ID NO: 387, SEQ ID NO: 394, a biological equivalent thereof, or a fragment thereof.
- 49. The polypeptide of claim 45, wherein the polypeptide having an inner membrane domain comprises an amino acid sequence chosen from one of SEQ ID NO: 217, SEQ ID NO: 220, SEQ ID NO: 221, SEQ ID NO: 222, SEQ ID NO: 225, SEQ ID NO: 226, SEQ ID NO: 227, SEQ ID NO: 228, SEQ ID NO: 229, SEQ ID NO: 230, SEQ ID NO: 231, SEQ ID NO: 232, SEQ ID NO: 234, SEQ ID NO: 235, SEQ ID NO: 236, SEQ ID NO: 237, SEQ ID NO: 241, SEQ ID NO: 242, SEQ ID NO: 243, SEQ ID NO: 244, SEQ ID NO: 245, SEQ ID NO: 246, SEQ ID NO: 247, SEQ ID NO: 248, SEQ ID NO: 249, SEQ ID NO: 250, SEQ ID NO: 251, SEQ ID NO: 252, SEQ ID NO: 253, SEQ ID NO: 255, SEQ ID NO: 258, SEQ ID NO: 259, SEQ ID NO: 261, SEQ ID NO: 262, SEQ ID NO: 263, SEQ ID NO: 266, SEQ ID NO: 267, SEQ ID NO: 268, SEQ ID NO: 269, SEQ ID NO: 271, SEQ ID NO: 274, SEQ ID NO: 275, SEQ ID NO: 276, SEQ ID NO: 280, SEQ ID NO: 283, SEQ ID NO: 284, SEQ ID NO: 285, SEQ ID NO: 286, SEQ ID NO: 288, SEQ ID NO: 290, SEQ ID NO: 291, SEQ ID NO: 292, SEQ ID NO: 294, SEQ ID NO: 295, SEQ ID NO: 296, SEQ ID NO: 297, SEQ ID NO: 298, SEQ ID NO: 299, SEQ ID NO: 301 SEQ ID NO: 302, SEQ ID NO: 303, SEQ ID NO: 305, SEQ ID NO: 306, SEQ ID NO: 308, SEQ ID NO: 309, SEQ ID NO: 310, SEQ ID NO: 311, SEQ ID NO: 312, SEQ ID NO: 313, SEQ ID NO: 314, SEQ ID NO: 315, SEQ ID NO: 316, SEQ ID NO: 317, SEQ ID NO: 318, SEQ ID NO: 320, SEQ ID NO: 321, SEQ ID NO: 322, SEQ ID NO: 323, SEQ ID NO: 324, SEQ ID NO: 327, SEQ ID NO: 328, SEQ ID NO: 329, SEQ ID NO: 330, SEQ ID NO: 332, SEQ ID NO: 333, SEQ ID NO: 334, SEQ ID NO: 335, SEQ ID NO: 336, SEQ ID NO: 337, SEQ ID NO: 338, SEQ ID NO: 339, SEQ ID NO: 341, SEQ ID NO: 342, SEQ ID NO: 343, SEQ ID NO: 344, SEQ ID NO: 345, SEQ ID NO: 346, SEQ ID NO: 347, SEQ ID NO: 348, SEQ ID NO: 350, SEQ ID NO: 351, SEQ ID NO: 354, SEQ ID NO: 355, SEQ ID NO: 356, SEQ ID NO: 357, SEQ ID NO: 359, SEQ ID NO: 360, SEQ ID NO: 361, SEQ ID NO: 362, SEQ ID NO: 365, SEQ ID NO: 366, SEQ ID NO: 367, SEQ ID NO: 368, SEQ ID NO: 369, SEQ ID NO: 371, SEQ ID NO: 372, SEQ ID NO: 373, SEQ ID NO: 374, SEQ ID NO: 375, SEQ ID NO: 377, SEQ ID NO: 378, SEQ ID NO: 379, SEQ ID NO: 381, SEQ ID NO: 382, SEQ ID NO: 383, SEQ ID NO: 384, SEQ ID NO: 385, SEQ ID NO: 388, SEQ ID NO: 390, SEQ ID NO: 391, SEQ ID NO: 392, SEQ ID NO: 393, SEQ ID NO: 395, SEQ ID NO: 396, SEQ ID NO: 397, SEQ ID NO: 399, SEQ ID NO: 401, SEQ ID NO: 402, SEQ ID NO: 403, SEQ ID NO: 404, SEQ ID NO: 405, SEQ ID NO: 406, SEQ ID NO: 407, SEQ ID NO: 408, SEQ ID NO: 409, SEQ ID NO: 410, SEQ ID NO: 413, SEQ ID NO: 415, SEQ ID NO: 418, SEQ ID NO: 421, SEQ ID NO: 423, SEQ ID NO: 424, SEQ ID NO: 426, SEQ ID NO: 427, SEQ ID NO: 428, SEQ ID NO: 429, SEQ ID NO: 430, a biological equivalent thereof, or a fragment thereof.
- 50. The polypeptide of claim 45, wherein the polypeptide identified by Blastp analysis comprises an amino acid sequence chosen from one of SEQ ID NO: 216, SEQ ID NO: 217, SEQ ID NO: 222, SEQ ID NO: 225, SEQ ID NO: 227, SEQ ID NO: 231, SEQ ID NO: 235, SEQ ID NO: 239, SEQ ID NO: 242, SEQ ID NO: 245, SEQ ID NO: 246, SEQ ID NO: 247, SEQ ID NO: 248, SEQ ID NO: 249, SEQ ID NO: 250, SEQ ID NO: 253, SEQ ID NO: 255, SEQ ID NO: 257, SEQ ID NO: 258, SEQ ID NO: 259, SEQ ID NO: 263, SEQ ID NO: 266, SEQ ID NO: 268, SEQ ID NO: 269, SEQ ID NO: 275, SEQ ID NO: 276, SEQ ID NO: 280, SEQ ID NO: 282, SEQ ID NO: 283, SEQ ID NO: 284, SEQ ID NO: 285, SEQ ID NO: 286, SEQ ID NO: 290, SEQ ID NO: 291, SEQ ID NO: 292, SEQ ID NO: 293, SEQ ID NO: 294, SEQ ID NO: 295, SEQ ID NO: 302, SEQ ID NO: 303, SEQ ID NO: 305, SEQ ID NO: 309, SEQ ID NO: 310, SEQ ID NO: 311, SEQ ID NO: 313, SEQ ID NO: 315, SEQ ID NO: 318, SEQ ID NO: 320, SEQ ID NO: 322, SEQ ID NO: 323, SEQ ID NO: 324, SEQ ID NO: 327, SEQ ID NO: 328, SEQ ID NO: 330, SEQ ID NO: 332, SEQ ID NO: 333, SEQ ID NO: 337, SEQ ID NO: 338, SEQ ID NO: 339, SEQ ID NO: 342, SEQ ID NO: 344, SEQ ID NO: 346, SEQ ID NO: 347, SEQ ID NO: 348, SEQ ID NO: 349, SEQ ID NO: 350, SEQ ID NO: 351, SEQ ID NO: 353, SEQ ID NO: 354, SEQ ID NO: 356, SEQ ID NO: 359, SEQ ID NO: 361, SEQ ID NO: 362, SEQ ID NO: 366, SEQ ID NO: 367, SEQ ID NO: 369, SEQ ID NO: 370, SEQ ID NO: 372, SEQ ID NO: 373, SEQ ID NO: 374, SEQ ID NO: 375, SEQ ID NO: 376, SEQ ID NO: 377, SEQ ID NO: 378, SEQ ID NO: 380, SEQ ID NO: 381, SEQ ID NO: 382, SEQ ID NO: 384, SEQ ID NO: 387, SEQ ID NO: 388, SEQ ID NO: 391, SEQ ID NO: 392, SEQ ID NO: 393, SEQ ID NO: 395, SEQ ID NO: 396, SEQ ID NO: 397, SEQ ID NO: 399, SEQ ID NO: 400, SEQ ID NO: 401, SEQ ID NO: 403, SEQ ID NO: 404, SEQ ID NO: 406, SEQ ID NO: 408, SEQ ID NO: 411, SEQ ID NO: 412, SEQ ID NO: 413, SEQ ID NO: 414, SEQ ID NO: 415, SEQ ID NO: 416, SEQ ID NO: 417, SEQ ID NO: 419, SEQ ID NO: 420, SEQ ID NO: 421, SEQ ID NO: 422, SEQ ID NO: 423, SEQ ID NO: 425, SEQ ID NO: 427, SEQ ID NO: 428, SEQ ID NO: 429, a biological equivalent thereof, or a fragment thereof.
- 51. The polypeptide of claim 45, wherein the polypeptide identified by Pfam analysis comprises an amino acid sequence chosen from one of SEQ ID NO: 219, SEQ ID NO: 233, SEQ ID NO: 234, SEQ ID NO: 255, SEQ ID NO: 260, SEQ ID NO: 270, SEQ ID NO: 272, SEQ ID NO: 273, SEQ ID NO: 278, SEQ ID NO: 279, SEQ ID NO: 281, SEQ ID NO: 287, SEQ ID NO: 289, SEQ ID NO: 304, SEQ ID NO: 307, SEQ ID NO: 319, SEQ ID NO: 326, SEQ ID NO: 331, SEQ ID NO: 334, SEQ ID NO: 343, SEQ ID NO: 352, SEQ ID NO: 357, SEQ ID NO: 358, SEQ ID NO: 364, SEQ ID NO: 366, SEQ ID NO: 367, SEQ ID NO: 368, SEQ ID NO: 372, SEQ ID NO: 374, SEQ ID NO: 375, SEQ ID NO: 377, SEQ ID NO: 378, SEQ ID NO: 379, SEQ ID NO: 380, SEQ ID NO: 381, SEQ ID NO: 384, SEQ ID NO: 386, SEQ ID NO: 389, SEQ ID NO: 391, SEQ ID NO: 395, SEQ ID NO: 397, SEQ ID NO: 398, SEQ ID NO: 399, SEQ ID NO: 401, SEQ ID NO: 403, SEQ ID NO 404, SEQ ID NO: 410, SEQ ID NO: 413, SEQ ID NO 414, SEQ ID NO: 420, SEQ ID NO: 427, SEQ ID NO: 428, a biological equivalent thereof, or a fragment thereof.
- 52. The polypeptide of claim 45, wherein the polypeptide is a lipoprotein, the polypeptide comprises an amino acid sequence chosen from one of SEQ ID NO: 218, SEQ ID NO: 223, SEQ ID NO: 224, SEQ ID NO: 228, SEQ ID NO: 236, SEQ ID NO: 241, SEQ ID NO: 249, SEQ ID NO: 277, SEQ ID NO: 282, SEQ ID NO: 300, SEQ ID NO: 349, SEQ ID NO: 362, SEQ ID NO: 365, SEQ ID NO: 383, SEQ ID NO: 385, SEQ ID NO: 388, a biological equivalent thereof, or a fragment thereof.
- 53. The polypeptide of claim 45, wherein the polypeptide having a LPXTG motif and covalently associated with the peptidoglycan layer comprises an amino acid sequence chosen from one of SEQ ID NO: 228, SEQ ID NO: 236, SEQ ID NO: 249, SEQ, SEQ ID NO: 385, a biological equivalent thereof, or a fragment thereof.
- 54. The polypeptide of claim 45, wherein the polypeptide having a peptidoglycan binding motif and associated with the peptidoglycan layer comprises an amino acid sequence chosen from one of SEQ ID NO: 240, SEQ ID NO: 264, SEQ ID NO: 325, a biological equivalent thereof, or a fragment thereof.
- 55. The polypeptide of claim 45, wherein the polypeptide having a signal sequence and a C-terminal Tyrosine or Phenylalanine amino acid comprises an amino acid sequence chosen from one of SEQ ID NO:226, SEQ ID NO:254, SEQ ID NO:289, SEQ ID NO:312, SEQ ID NO:321, SEQ IN NO: 340, SEQ ID NO:402, a biological equivalent thereof, or a fragment thereof.
- 56. The polypeptide of claim 45, wherein the polypeptide having a tripeptide RGD sequence that potentially is involved in cell attachment comprises an amino acid sequence chosen from one of SEQ ID NO:216, SEQ ID NO:236, SEQ ID NO:281, SEQ ID NO:282, a biological equivalent thereof, or a fragment thereof.
- 57. The polypeptide of claim 45, wherein the polypeptide identified by proteomics as surface exposed comprises an amino acid sequence chosen from one of SEQ ID NO: 229, SEQ ID NO: 231, SEQ ID NO: 232, SEQ ID NO: 261, SEQ ID NO: 279, SEQ ID NO: 281, SEQ ID NO: 282, SEQ ID NO: 284, SEQ ID NO: 286, SEQ ID NO: 289, SEQ ID NO: 306, SEQ ID NO: 318, SEQ ID NO: 331, SEQ ID NO: 343, SEQ ID NO: 346, SEQ ID NO: 351, SEQ ID NO: 366, SEQ ID NO: 371, SEQ ID NO: 374, SEQ ID NO: 377, SEQ ID NO: 379, SEQ ID NO: 387, SEQ ID NO: 391, SEQ ID NO: 393, SEQ ID NO: 394, 395, SEQ ID NO: 397, SEQ ID NO: 420, a biological equivalent thereof, or a fragment thereof.
- 58. The polypeptide of claim 45, wherein the polypeptide identified by proteomics as surface exposed comprises an amino acid sequence chosen from of one of SEQ ID NO:592 through SEQ ID NO:752, a biological equivalent thereof, or a fragment thereof.
- 59. A recombinant expression vector comprising a nucleotide sequence having at least about 95% identity to a nucleotide sequence chosen from one of SEQ ID NO: 1 through SEQ ID NO: 215 or SEQ ID NO: 431 through SEQ ID NO: 591, a degenerate variant thereof, or a fragment thereof.
- 60. The vector of claim 59, wherein the polynucleotide is selected from the group consisting of DNA, chromosomal DNA, cDNA, RNA and antisense RNA.
- 61. The vector of claim 60, wherein the polynucleotide comprises heterologous nucleotide sequences.
- 62. The vector of claim 61, wherein the polynucleotide is operatively linked to one or more gene expression regulatory elements.
- 63. The vector of claim 62, wherein the polynucleotide encodes a polypeptide comprising an amino acid sequence having at least about 95% identity to an amino acid sequence chosen from one of SEQ ID NO: 216 through SEQ ID NO: 430 or SEQ ID NO: 592 through SEQ ID NO: 752, a biological equivalent thereof, or a fragment thereof.
- 64. The vector of claim 59, wherein the vector is a plasmid.
- 65. A genetically engineered host cell, transfected, transformed or infected with the vector of claim 59.
- 66. The host cell of claim 65, wherein the host cell is a bacterial cell.
- 67. The host cell of claim 66, wherein the polynucleotide is expressed to produce the encoded polypeptide, a biological equivalent thereof, or a fragment thereof.
- 68. An antibody specific for a Streptococcus pneumoniae polynucleotide chosen from one of SEQ ID NO: 1 through SEQ ID NO: 215 or SEQ ID NO: 431 through SEQ ID NO: 591, a fragment thereof, a degenerate variant thereof, or a Streptococcus pneumoniae polypeptide chosen from one of SEQ ID NO: 216 through SEQ ID NO: 430 or SEQ ID NO: 592 through SEQ ID NO: 752, a biological equivalent thereof, or a fragment thereof.
- 69. The antibody of claim 68, wherein the antibody is selected from the group consisting of monoclonal, polyclonal, chimeric, humanized and single chain.
- 70. The antibody of claim 69, wherein the antibody is monoclonal.
- 71. The antibody of claim 70, wherein the antibody is humanized.
- 72. An immunogenic composition comprising a polypeptide having an amino acid sequence chosen from one or more of SEQ ID NO: 216 through SEQ ID NO: 430 or SEQ ID NO: 592 through SEQ ID NO: 752, a biological equivalent thereof, or a fragment thereof.
- 73. The immunogenic composition of claim 72, further comprising a pharmaceutically acceptable carrier.
- 74. The immunogenic composition of claim 72, further comprising one or more adjuvants.
- 75. The immunogenic composition of claim 72, wherein the polypeptide is further defined as:
(a) a Streptococcus pneumoniae polypeptide having 0, 1 or 2 transmembrane domains; (b) a Streptococcus pneumoniae polypeptide having 3 or more transmembrane domains; (c) a Streptococcus pneumoniae polypeptide having an outer membrane domain or a periplasmic domain; (d) a Streptococcus pneumoniae polypeptide having an inner membrane domain; (e) a Streptococcus pneumoniae polypeptide identified by Blastp analysis; (f) a Streptococcus pneumoniae polypeptide identified by Pfam analysis; (g) a Streptococcus pneumoniae lipoprotein; (h) a Streptococcus pneumoniae polypeptide having a LPXTG motif, wherein the polypeptide is covalently attached to the peptidoglycan layer; (i) a Streptococcus pneumoniae polypeptide having a peptidoglycan binding motif, wherein the polypeptide is associated with the peptidoglycan layer; (j) a Streptococcus pneumoniae polypeptide having a signal sequence and a C-terminal Tyrosine or a C-terminal Phenylalanine amino acid; (k) a Streptococcus pneumoniae polypeptide having a tripeptide RGD amino acid sequence; (l) a Streptococcus pneumoniae polypeptide identified by proteomics as surface exposed; and (m) a Streptococcus pneumoniae polypeptide identified by proteomics as membrane associated.
- 76. The immunogenic composition of claim 75, wherein the polypeptide further comprises heterologous amino acids.
- 77. The immunogenic composition of claim 75, wherein the polypeptide is a fusion polypeptide.
- 78. The immunogenic composition of claim 75, wherein the polypeptide is encoded by a polynucleotide comprising a nucleotide sequence having at least about 95% identity to a nucleotide sequence chosen from one of SEQ ID NO: 1 through SEQ ID NO: 215 or SEQ ID NO: 431 through SEQ ID NO: 591, a degenerate variant thereof, or a fragment thereof.
- 79. The immunogenic composition of claim 78, wherein the polynucleotide further comprises heterologous nucleotides.
- 80. An immunogenic composition comprising a polynucleotide having a nucleotide sequence chosen from one of SEQ ID NO: 1 through SEQ ID NO: 215 or SEQ ID NO: 431 through SEQ ID NO: 591, a degenerate variant thereof, or a fragment thereof and is comprised in an expression vector.
- 81. The immunogenic composition of claim 80, wherein the vector is plasmid DNA.
- 82. The immunogenic composition of claim 81, wherein the polynucleotide comprises heterologous nucleotides.
- 83. The immunogenic composition of claim 82, wherein the polynucleotide is operatively linked to one or more gene expression regulatory elements.
- 84. The immunogenic composition of claim 83, wherein the polynucleotide directs the expression of a neutralizing epitope of Streptococcus pneumoniae.
- 85. The immunogenic composition of claim 84, further comprising one or more adjuvants.
- 86. A pharmaceutical composition comprising a polypeptide and a pharmaceutically acceptable carrier, wherein the polypeptide comprises an amino acid chosen from one of SEQ ID NO: 216 through SEQ ID NO: 430 or SEQ ID NO: 592 through SEQ ID NO: 752, a biological equivalent thereof, or a fragment thereof.
- 87. The pharmaceutical composition of claim 86, wherein the polypeptide is further defined as:
(a) a Streptococcus pneumoniae polypeptide having 0, 1 or 2 transmembrane domains; (b) a Streptococcus pneumoniae polypeptide having 3 or more transmembrane domains; (c) a Streptococcus pneumoniae polypeptide having an outer membrane domain or a periplasmic domain; (d) a Streptococcus pneumoniae polypeptide having an inner membrane domain; (e) a Streptococcus pneumoniae polypeptide identified by Blastp analysis; (f) a Streptococcus pneumoniae polypeptide identified by Pfam analysis; (g) a Streptococcus pneumoniae lipoprotein; (h) a Streptococcus pneumoniae polypeptide having a LPXTG motif, wherein the polypeptide is covalently attached to the peptidoglycan layer; (i) a Streptococcus pneumoniae polypeptide having a peptidoglycan binding motif, wherein the polypeptide is associated with the peptidoglycan layer; (j) a Streptococcus pneumoniae polypeptide having a signal sequence and a C-terminal Tyrosine or a C-terminal Phenylalanine amino acid; (k) a Streptococcus pneumoniae polypeptide having a tripeptide RGD amino acid sequence; (l) a Streptococcus pneumoniae polypeptide identified by proteomics as surface exposed; and (m) a Streptococcus pneumoniae polypeptide identified by proteomics as membrane associated.
- 88. The pharmaceutical composition of claim 87, wherein the polypeptide further comprises heterologous amino acids.
- 89. The pharmaceutical composition of claim 87, wherein the polypeptide is a fusion polypeptide.
- 90. A DNA chip comprising an array of polynucleotides, wherein at least one of the polynucleotides comprise a nucleotide sequence chosen from one of SEQ ID NO: 1 through SEQ ID NO: 215 or SEQ ID NO: 431 through SEQ ID NO: 591, a complement thereof, a degenerate variant thereof, or a fragment thereof.
- 91. A protein chip comprising an array of polypeptides, wherein at least one of the polypeptides comprises an amino acid sequence chosen from one of SEQ ID NO: 216 through SEQ ID NO: 430 or SEQ ID NO: 592 through SEQ ID NO: 752, a biological equivalent thereof, or a fragment thereof.
- 92. A method of immunizing against Streptococcus pneumoniae comprising administering to a host an immunizing amount of an immunogenic composition comprising a polypeptide and a pharmaceutically acceptable carrier, wherein the polypeptide comprises an amino acid sequence chosen from one or more of SEQ ID NO: 216 through SEQ ID NO: 430 or SEQ ID NO: 592 through SEQ ID NO: 752, a biological equivalent thereof, or a fragment thereof.
- 93. The method of claim 92, wherein the polypeptide is a fusion polypeptide.
- 94. The method of claim 92, further comprising an adjuvant.
- 95. A method for the detection and/or identification of Streptococcus pneumoniae in a biological sample comprising:
(a) contacting the sample with an oligonucleotide probe of a polynucleotide comprising the nucleotide sequence chosen from one of SEQ ID NO: 1 through SEQ ID NO: 215 or SEQ ID NO: 431 through SEQ ID NO: 591, a degenerate variant thereof, or a fragment thereof, under conditions permitting hybridization; and (b) detecting the presence of hybridization complexes in the sample, wherein hybridization complexes indicate the presence of Streptococcus pneumoniae in the sample.
- 96. A method for the detection and/or identification of Streptococcus pneumoniae in a biological sample comprising:
(a) contacting the sample with an oligonucleotide primer of a polynucleotide comprising the nucleotide sequence chosen from one of SEQ ID NO: 1 through SEQ ID NO: 215 or SEQ ID NO: 431 through SEQ ID NO: 591, a degenerate variant thereof, or a fragment thereof, in the presence of nucleotides and a polymerase enzyme under conditions permitting primer extension; and (b) detecting the presence of primer extension products in the sample, wherein extension products indicate the presence of Streptococcus pneumoniae in the sample.
- 97. A method for the detection and/or identification of Streptococcus pneumoniae in a biological sample comprising:
(a) contacting the sample with an antibody specific for a polypeptide comprising an amino acid sequence chosen from one of SEQ ID NO: 216 through SEQ ID NO: 430 or SEQ ID NO: 592 through SEQ ID NO: 752, a biological equivalent thereof, or a fragment thereof, under conditions permitting immune complex formation; and (b) detecting the presence of immune complexes in the sample, wherein immune complexes indicate the presence of Streptococcus pneumoniae in the sample.
- 98. A method for the detection and/or identification of antibodies to Streptococcus pneumoniae in a biological sample comprising:
(a) contacting the sample with a polypeptide comprising an amino acid sequence chosen from one of SEQ ID NO: 216 through SEQ ID NO: 430 or SEQ ID NO: 592 through SEQ ID NO: 752, a biological equivalent thereof, or a fragment thereof, under conditions permitting immune complex formation; and (b) detecting the presence of immune complexes in the sample, wherein immune complexes indicate the presence of Streptococcus pneumoniae in the sample.
- 99. A kit comprising a container containing an isolated polynucleotide comprising an nucleotide sequence chosen from one of SEQ ID NO: 1 through SEQ ID NO: 215 or SEQ ID NO: 431 through SEQ ID NO: 591, a degenerate variant thereof, or a fragment thereof.
- 100. The kit of claim 99, wherein the polynucleotide is a primer or a probe.
- 101. The kit of claim 100, wherein the polynucleotide is a primer and the kit further comprises a container containing a polymerase.
- 102. The kit of claim 99, wherein the kit further comprises a container containing dNTP.
- 103. A kit comprising a container containing an antibody that immunospecifically binds to a polypeptide comprising the amino acid sequence chosen from one of SEQ ID NO: 216 through SEQ ID NO: 430 or SEQ ID NO: 592 through SEQ ID NO: 752, a biological equivalent thereof, or a fragment thereof.
- 104. A kit comprising a container containing an antibody that immunospecifically binds to a fusion polypeptide comprising at least the amino acid sequence chosen from one of SEQ ID NO: 216 through SEQ ID NO: 430 or SEQ ID NO: 592 through SEQ ID NO: 752, a biological equivalent thereof, or a fragment thereof.
- 105. A method for producing a polypeptide which comprises culturing the genetically engineered host cell of claim 66 under conditions suitable to produce the polypeptide and recovering the polypeptide from the culture.
Parent Case Info
[0001] This application claims priority from copending provisional application serial No. 60/283,948, filed on Apr. 16, 2001, the entire disclosure of which is hereby incorporated by reference and provisional application serial number 60/284,443, filed Apr. 18, 2001, the entire disclosure of which is hereby incorporated by reference.
PCT Information
Filing Document |
Filing Date |
Country |
Kind |
PCT/US02/11524 |
4/12/2002 |
WO |
|