TABLE 2.
Position, predicted molecular sizes, RBSs, and database sequence homologies for the BK5-T ORFs
| BK5-T ORF | Previous namea | Molecular size (kDa) | Predicted start position | Predicted stop positionb | Putative RBSc | ORF homologyd | Organism matched | % Identity (over no. of amino acids) | Accession no. |
|---|---|---|---|---|---|---|---|---|---|
| 1 | 18.2 | 77 | 550 | acuaaaaGAAAGGAGaaaaaaug | ORF21 | S. thermophilus φ7201 | 46 (151) | AAF43514 | |
| ORF2 | S. thermophilus DT1 | 43 (151) | AAD21878 | ||||||
| ORF152 | S. thermophilus φSfi21 | 44 (151) | AAD41028 | ||||||
| ORF161 | S. thermophilus φSfi19 | 43 (151) | AAD44055 | ||||||
| ORF149 | L. gasseri φadh | 38 (144) | |||||||
| ORF4 | L. lactis subsp. cremories | 35 (139) | CAA11696 | ||||||
| ORF4 | L. casei A2 | 24 (146) | CAA66177 | ||||||
| 2 | 75.6 | 537 | 2,510 | ggcauucuuugauGGAGGugaug | ORF623 | S. thermophilus φSfi19 | 64 (623) | AAD44056 | |
| ORF623 | S. thermophilus φSfi21 | 63 (623) | AAD41029 | ||||||
| ORF624 | L. gasseri φadh | 59 (625) | CAB52518 | ||||||
| ORF22 | S. thermophilus φ7201 | 57 (624) | AAF43515 | ||||||
| ORF3 | S. thermophilus DT1 | 64 (365) | AAD21880 | ||||||
| ORF4 | S. thermophilus DT1 | 62 (231) | AAD21879 | ||||||
| 3 | 12.8 | 1,385 | 1,065 | ucugGAuAGGAaGUugaaauuug | |||||
| 4 | 7.7 | 2,479 | 2,688 | ccuugaugacgaaauagaugaug | ORF5 (head-tail joining) | S. thermophilus DT1 | 45 (55) | AD21881 | |
| ORF23 | S. thermophilus φ7201 | 42 (55) | AAF43516 | ||||||
| ORF59c | S. thermophilus φSfi21 | 44 (55) | AAD41030 | ||||||
| ORF59 | S. thermophilus φSfi19 | 43 (53) | AAD44057 | ||||||
| 5 | 43.5 | 2,685 | 3,863 | auagaaaaGAAgGGAGGugauug | ORF387 | S. thermophilus φSfi19 | 56 (389) | AAD44058 | |
| ORF384 | S. thermophilus φSfi21 | 56 (388) | AAD41031 | ||||||
| ORF6 | S. thermophilus DT1 | 57 (381) | AAD21882 | ||||||
| ORF24 | S. thermophilus φ7201 | 57 (383) | AAF43517 | ||||||
| ORF397 | L. gasseri φadh | 51 (356) | CAB52519 | ||||||
| ORFH | L. casei A2 | 24 (291) | CAB63683 | ||||||
| ORF4 (portal) | S. aureus φPVL | 24 (306) | BAA31877 | ||||||
| GP34 | S. actinophage φC31 | 21 (331) | CAA07104 | ||||||
| ORF1305 | P. aeruginosa D3 | 22 (368) | AAD38955 | ||||||
| 6 | 2.6 | 3,906 | 4,619 | uauucuuaGAAAGGAGGuaaaug | ORF7 | S. thermophilus DT1 | 53 (238) | AAD21883 | |
| ORF25 | S. thermophilus φ7201 | 54 (237) | AAF43518 | ||||||
| ORF221 | S. thermophilus φSfi21 | 52 (237) | AAD41032 | ||||||
| ORF242 | L. gasseri φadh | 41 (239) | CAB52520 | ||||||
| ORF891 | P. aeruginosa D3 | 38 (167) | AAD38956 | ||||||
| ClpP | Listeria monocytogenes | 29 (139) | AAF04744 | ||||||
| ClpP | Streptomyces coelicolor | 25 (146) | AAC70947 | ||||||
| 7 | 44.7 | 4,631 | 5,845 | gaaaaauAAAGGAGacucaaaug | ORF397—major structural | S. thermophilus φSfi19 | 60 (395) | AAD44059 | |
| ORF397—major structural | S. thermophilus φSfi21 | 59 (399) | AAD41033 | ||||||
| MPL—major structural | S. thermophilus φ7201 | 59 (395) | AAD43519 | ||||||
| ORF8—major structural | S. thermophilus DT1 | 65 (289) | AAD21884 | ||||||
| ORF395—major structural | L. gasseri φadh | 47 (409) | CAB52521 | ||||||
| ORF27 | B. subtilis φ105 | 34 (396) | AB016282 | ||||||
| Major structural protein | L. casei A2 | 22 (357) | CAB63685 | ||||||
| ORF1188—major structural | P. aeruginosa D3 | 20 (400) | AAD38957 | ||||||
| ORF7—major structural | S. aureus φPVL | 25 (359) | BAA31880 | ||||||
| 8 | 12.1 | 5,853 | 6,176 | ugcagGAAAGuAGGuaauuuaug | ORF27 | S. thermophilus φ7201 | 32 (103) | AAF43520 | |
| ORF106 | S. thermophilus φSfi21 | 29 (103) | AAC39275 | ||||||
| ORF104 | S. thermophilus φSfi19 | 29 (103) | AAC39289 | ||||||
| ORF9 | S. thermophilus DT1 | 27 (103) | AAD21885 | ||||||
| ORFK | Leuconostoc oenos L10 | 28 (86) | AAA66331 | ||||||
| ORF126b | L. gasseri φadh | 29 (105) | CAB52522 | ||||||
| 9 | 1.3 | 6,151 | 6,504 | uucguGgAAGGAGGcgcaagaug | ORF28 | S. thermophilus φ7201 | 31 (113) | AAF43521 | |
| ORF10 | S. thermophilus DT1 | 30 (113) | AAD21886 | ||||||
| ORF116 | S. thermophilus φSfi19 | 30 (113) | AAC39290 | ||||||
| ORF116 | S. thermophilus φSfi21 | 27 (113) | AAC39276 | ||||||
| ORF126c | L. gasseri φadh | 22 (120) | CAB52523 | ||||||
| 10 | 19.1 | 6,506 | 7,012 | gaagaaGAAgGGAGcuuaauaug | ORFA | L. oenos L10 | 39 (147) | AAA66332 | |
| ORF141b | S. thermophilus φSfi21 | 26 (163) | AAC39277 | ||||||
| ORF29 | S. thermophilus φ7201 | 29 (165) | AAC43522 | ||||||
| ORF11 | S. thermophilus DT1 | 30 (165) | AAC21887 | ||||||
| ORF140 | S. thermophilus φSfi19 | 30 (162) | AAC44060 | ||||||
| ORF159b | L. gasseri φadh | 28 (178) | CAB52524 | ||||||
| 11 | 14.7 | 7,009 | 7,404 | gaaaAAAGaAGGaauaacuuaug | ORFI | L. oenos L10 | 37 (110) | AAA66333 | |
| ORF123 | S. thermophilus φSfi19 | 32 (107) | T09268 | ||||||
| ORF30 | S. thermophilus φ7201 | 33 (107) | AAF43523 | ||||||
| ORF12 | S. thermophilus DT1 | 33 (107) | AAD21888 | ||||||
| ORF123 | S. thermophilus φSfi21 | 32 (107) | AAC39278 | ||||||
| 12 | 20.6 | 7,435 | 8,028 | auuuaaGAAAGGAauuuaaaaug | ORF203—major structural | S. thermophilus φSfi19 | 46 (198) | AAC39293 | |
| ORF13—major structural | S. thermophilus DT1 | 46 (195) | AAD21889 | ||||||
| ORF202—major structural | S. thermophilus φSfi21 | 45 (199) | AAC39279 | ||||||
| MPS—major structural | S. thermophilus φ7201 | 45 (198) | AAB71820 | ||||||
| ORF E | L. oenos L10 | 43 (193) | AAA66334 | ||||||
| ORF237—major tail | L. gasseri φadh | 28 (134) | CAB52526 | ||||||
| 13 | 15.9 | 8,173 | 8,592 | uaaaauagAGGAGauauacaaug | ORF14 | S. thermophilus DT1 | 31 (121) | AAD21890 | |
| ORF117 | S. thermophilus φSfi19 | 28 (121) | AAC39294 | ||||||
| ORF117 | S. thermophilus φSfi21 | 29 (121) | AAC39280 | ||||||
| ORF32 | S. thermophilus φ7201 | 26 (121) | AAF43524 | ||||||
| 14 | 18.2 | 8,821 | 9,312 | uuaaaaaucAGGAGaaauucaug | |||||
| 15 | 183.5 | 9,394 | 14,535 | aaaauuAGAAAGGAGuaaaaaug | ORF48 (minor capsid) | Lactobacillus plantarum φgle | 30 (1,369) | CAA66745 | |
| ORF465 | L. casei A2 | 30 (450) | CAB63691 | ||||||
| ORF16 | S. thermophilus DT1 | 37 (320) | AAD21892 | ||||||
| ORF360 | Lactobacillus delbrueckii LL-H | 35 (306) | AAC00548 | ||||||
| ORF15 | S. thermophilus DT1 | 22 (1,291) | AAD21891 | ||||||
| ORF33 | S. thermophilus φ7201 | 24 (552) | AAF43525 | ||||||
| ORF1560 (minor tail) | S. thermophilus φSfi21 | 23 (1,753) | AAC39281 | ||||||
| ORF1626 (minor tail) | S. thermophilus φSfi19 | 23 (1,789) | AAC39295 | ||||||
| 16 | ′410 | 60 | 14,532 | 16,178 | agauuAGGAGGuauuaugauuug | ORF34 | S. thermophilus φ7201 | 25 (564) | AAF43526 |
| ORF17 | S. thermophilus DT1 | 26 (564) | AAD21893 | ||||||
| ORF515 | S. thermophilus φSfi19 | 27 (567) | AAC39296 | ||||||
| ORF515 | S. thermophilus φSfi21 | 27 (567) | AAC39282 | ||||||
| ORF I—structural tail | L. casei A2 | 26 (236) | CAB63694 | ||||||
| 17 | 64#1 | 7.7 | 15,646 | 15,840 | aggaggacaagaauuaaauaaug | ||||
| 18 | 1904 | 205.8 | 16,178 | 21,892 | uggaaAGAAAGGuaucuauaaug | ORF35 | S. thermophilus φ7201 | 36 (515) | AAF43527 |
| ORF18 | S. thermophilus DT1 | 32 (738) | AAF21894 | ||||||
| ORF45 | S. thermophilus O1205 | 38 (509) | AAC79560 | ||||||
| ORF38 | S. thermophilus φ7201 | 39 (560) | AAF43530 | ||||||
| ORF1276 | S. thermophilus φSfi21 | 33 (1,058) | AAC39283 | ||||||
| ORF1291 | S. thermophilus φSfi19 | 34 (1,058) | AAC39297 | ||||||
| 19 | 66 | 7.6 | 18,981 | 19,181 | aaaagacGGAaauaacgguaaug | ||||
| 20 | 71#1 | 8.3 | 19,434 | 19,649 | uguagccuauaugGGUaccaaug | ||||
| 21 | 71#2 | 8.3 | 19,902 | 20,117 | uguagccuauaugGGUaccaaug | ||||
| 22 | 71#3 | 8.3 | 20,370 | 20,585 | uguagccuauaugGGUaccaaug | ||||
| 23 | 69#1 | 8.1 | 20,838 | 21,044 | uguagccuauaugGGUaccaaug | ||||
| 24 | 78 | 8.7 | 21,907 | 22,143 | aacuagaaacAAGGAGaaaaaug | ||||
| 25 | 75 | 8.9 | 22,156 | 22,383 | aaaaauAGAAAGcAGGgguuaug | ||||
| 26 | 95 | 10.5 | 22,396 | 22,683 | gauucugAAGGAGaaagaacaug | ORF24 | S. aureus φPVL | 37 (70) | BAA31897 |
| BH0967 (holin) | Bacillus halodurans | 36 (72) | BAB04686 | ||||||
| GP26 | B. subtilis SPP1 | 39 (82) | CAA66519 | ||||||
| XPAF2—holin | B. subtilis | 40 (81) | P36549 | ||||||
| XPAG2—holin | B. licheniformis | 35 (81) | BAA08562 | ||||||
| 27 | 259 | 27.9 | 22,683 | 23,462 | uucacagAAGGAGGcgaauaaug | Lysin | L. lactis φ31 | 9 (173) | AC04153 |
| N-acetylmuramoyl-l- alanine amidase | Pneumococcus sp. Dp-1 | 43 (148) | CAB07986 | ||||||
| ORF288 | S. thermophilus φSfi21 | 30 (128) | AAC39288 | ||||||
| ORF288 | S. thermophilus φSfi19 | 30 (128) | AAD44061 | ||||||
| ORF288 | S. thermophilus φSfi11 | 30 (128) | AAC34421 | ||||||
| 28 | 74 | 8.1 | 22,996 | 22,772 | ugugaguguaaGAGcagugaaug | ||||
| 29 | 86 | 9.5 | 23,512 | 23,252 | aguaaucuaaaaauaguuucaug | ||||
| 30 | 536 | 61.9 | 23,679 | 25,289 | cugauucGGAGugugugagaaug | ||||
| 31 | 101 | 11.3 | 25,210 | 24,905 | uuauuccuuuaccuucucccaug | ||||
| 32 | 374 | 43.3 | 27,035 | 25,911 | aaauGGAGuaaaaaucaaauaug | —Integrase | L. lactis Tuc2009 | 99 (374) | AAA32608 |
| —Integrase | L. lactis φLC3 | 99 (374) | AAA32254 | ||||||
| ORF1—Integrase | L. lactis rlt | 98 (374) | AAB18676 | ||||||
| BH3551 | B. halodurans | 36 (376) | BAB07270 | ||||||
| ORF359 | S. thermophilus TPJ34 | 33 (376) | AAC03454 | ||||||
| ORF1 | S. thermophilus O1205 | 33 (373) | AAC79517 | ||||||
| ORF8 (Integrase) | L. plantarum φgle | 31 (381) | CAA66758 | ||||||
| —Integrase | L. lactis TPW22 | 30 (379) | AAF12706 | ||||||
| ORFB—integrase | L. casei A2 | 26 (391) | CAA73344 | ||||||
| —Integrase | S. aureus φ13 | 30 (372) | CAA57755 | ||||||
| ORF2—integrase | S. aureus φ42 | 30 (372) | AAA91615 | ||||||
| 33 | 258 | 28.7 | 27,949 | 27,173 | agcuagauaGGAGuauuuauaug | Exp3 | L. lactis MG1363 | 43 (128) | AAC14595 |
| 34 | 64#2 | 7.6 | 27,496 | 27,690 | uuuccauccauuauuuagcaaug | ||||
| 35 | 297 | 33.3 | 28,898 | 28,005 | aauauuaaggGGAGaugggaaug | cI repressor | L. lactis Tuc2009 | 73 (285) | AAA21825 |
| Rro—cI repressor | L. lactis rlt | 74 (280) | AAB18678 | ||||||
| Repressor | L. lactis φLC3 | 99 (74) | AAB53017 | ||||||
| 36 | 63 | 7.5 | 29,155 | 29,346 | gaaggcaaauGGAGGuucuaaug | ORF9 | L. lactis TPW22 | 93 (55) | AAF12713 |
| ORF61b | L. lactis u136.1 | 56 (61) | AAF74094 | ||||||
| ORF61a | L. lactis ul36.2 | 56 (61) | AAF74109 | ||||||
| ORF57 | L. lactis φ31.1 | 52 (54) | AAF43117 | ||||||
| ORF9 | L. lactis TP901-1 | 52 (54) | CAA74618 | ||||||
| ORF8 | L. lactis rlt | 52 (54) | AAB18683 | ||||||
| 37 | 79 | 9 | 29,574 | 29,813 | aagcaaAGAAAGGAGccaguaug | ORF29 | S. thermophilus DT1 | 37 (46) | AAD21905 |
| ORF67 (Cro) | S. thermophilus TPJ34 | 32 (47) | AAC03458 | ||||||
| 38 | 266 | 30.6 | 29,826 | 30,626 | cuaguuAGAAAGGcgaaaacaug | ORF5 | L. lactis rlt | 97 (266) | AAB18680 |
| ORFA | L. casei A2 | 50 (147) | CAA73339 | ||||||
| ORF291 | L. delbrueckii LL-H | 39 (280) | AAB06224 | ||||||
| ORF169a | L. delbrueckii mv4 | 44 (154) | AAG31333 | ||||||
| 39 | 111 | 12.9 | 30,639 | 30,974 | cuagcuAGAAAGGgaagcacaug | ORF6 | L. lactis rlt | 97 (109) | AAB18681 |
| ORF13 | L. plantarum φgle | 26 (107) | CAA66763 | ||||||
| ORF96 | L. casei A2 | 27 (96) | CAB63664 | ||||||
| 40 | 42 | 4.8 | 30,971 | 31,099 | uuuucAGGAGGgaguggucuaug | L. lactis phage ul36.2 | 95 (42) | AF212847 | |
| L. lactis strain SMQ-86 | 95 (42) | AF212844 | |||||||
| 41 | 113 | 13.7 | 31,112 | 31,453 | uccgcuAGAAAGGAGagauuuug | L. lactis ul36.2 | 91 (68) | AF212847 | |
| L. lactis phage ul36.1 | 91 (68) | AF212846 | |||||||
| L. lactis phage ul36 | 91 (68) | AF212845 | |||||||
| L. lactis strain SMQ-86 | 91 (68) | AF212844 | |||||||
| 42 | 72 | 8.5 | 31,333 | 31,551 | acgcuagaaaaGAGaaauuuaug | ||||
| 43 | 88 | 10.3 | 32,039 | 31,773 | augGAAAGGAGGaaugaagcaug | ||||
| 44 | 80 | 9.6 | 32,146 | 32,385 | acauAGAAAGGAaauuaaaaaug | ||||
| 45 | 169 | 20 | 32,457 | 32,966 | auaacaaaucGGAGGAaauaaug | ORF169 | L. lactis φ31 | 98 (169) | AAC48870 |
| ORF163 | L. casei A2 | 31 (160) | CAB63666 | ||||||
| ORF157 | S. thermophilus φSfi18 | 35 (165) | AAF63083 | ||||||
| ORF157 | S. thermophilus φSfi11 | 35 (165) | AAF63054 | ||||||
| ORF157 | S. thermophilus φSfi19 | 35 (165) | AAF63083 | ||||||
| ORF157 | S. thermophilus φSfi21 | 35 (165) | AAC72433 | ||||||
| ORF8 | S. thermophilus O1205 | 33 (165) | AAC79524 | ||||||
| 46 | 234 | 26.5 | 32,966 | 33,670 | gaaaguuuGAGGuuuagauaaug | ORF9 | S. thermophilus O1205 | 61 (230) | AAC79525 |
| ORF233 | S. thermophilus φSfi21 | 61 (230) | AAC72434 | ||||||
| ORF233 | S. thermophilus φSfi19 | 60 (230) | AAC97920 | ||||||
| ORF233 | S. thermophilus φSfi11 | 60 (230) | AAC63055 | ||||||
| ORF32 | S. thermophilus DT1 | 59 (230) | AAD21908 | ||||||
| ORF240 | L. casei A2 | 56 (232) | CAB63668 | ||||||
| 47 | 69 | 7.5 | 33,231 | 33,021 | ccaaguuaucguaaucaccuaug | ||||
| 48 | 70′ | 19.4 | 33,670 | 34,191 | aaauuugAAGGAGaaaaauaaug | SSB protein | B. subtilis | 28 (103) | P37455 |
| ORFE13 | L. lactis bIL170 | 31 (77) | AAC27225 | ||||||
| ORF34 | L. lactis sk1 | 30 (76) | AAB70074 | ||||||
| 49 | 31 | 34,325 | 35,134 | uauagaAGAAAGGAGaaaguuug | ORF269 | L. lactis φ31.1 | 82 (269) | AAF43120 | |
| 50 | 8.4 | 35,115 | 35,336 | agaaguGGAGGcuuuaauaaaug | ORF73 | L. lactis φ31.1 | 97 (73) | AAF43121 | |
| ORF73 | L. lactis ul36.1 | 97 (73) | AAF74098 | ||||||
| 51 | 16.2 | 35,314 | 35,715 | agcaaccgaauuaaugauauaug | ORF14 | L. lactis r1t | 96 (130) | AAB18689 | |
| ORF129 | L. lactis ul36 | 97 (129) | AAF74082 | ||||||
| ORF19 | L. lactis Tuc2009 | 96 (129) | AAD37104 | ||||||
| 52 | 9.4 | 35,719 | 35,958 | aaauuacaGAGGuauaaaccaug | ORF20 | L. lactis Tuc2009 | 99 (79) | AAD37105 | |
| ORF16 | L. lactis r1t | 92 (79) | AAB18691 | ||||||
| ORF79a | L. lactis ul36 | 91 (79) | AAF74083 | ||||||
| ORF79b | L. lactis ul36.1 | 43 (46) | AAF74100 | ||||||
| ORF79 | L. lactis φ31.1 | 43 (46) | AAF43123 | ||||||
| 53 | 13 | 36,069 | 36,416 | cuaaaauauGAGGuaguaauaug | ORF139b (dUPTase) | L. lactis φ31.1 | 82 (92) | AAF43128 | |
| ORF139a (dUPTase) | L. lactis ul36 | 82 (92) | AAF74088 | ||||||
| ORF139b (dUPTase) | L. lactis ul36.1 | 82 (92) | AAF74104 | ||||||
| ORF3 (dUPTase) | L. lactis S114 | 80 (92) | CAA72644 | ||||||
| ORF20 (dUPTase) | L. lactis r1t | 80 (92) | AAB18695 | ||||||
| 54 | 11.1 | 36,413 | 36,712 | ggcucaacuggGGAGGugugaug | ORF120 | L. lactis φ31.1 | 39 (103) | AAF43131 | |
| ORF120a | L. lactis ul36 | 39 (103) | AAF7409 | ||||||
| 55 | 12.9 | 37,084 | 36,746 | aaaGAGGAAuggauauuuacaug | |||||
| 56 | 12.7 | 37,207 | 37,530 | ucaaugAAaGAGGUucaggaaug | ORF29 | L. lactis sk1 | 94 (107) | AAB70069 | |
| ORFE22 | L. lactis bIL170 | 93 (107) | AAF009630 | ||||||
| 57 | 9.3 | 37,604 | 37,834 | gacugguggGGAGGgauugaaug | |||||
| 58 | 6.7 | 37,831 | 38,004 | uuugauAAGGAGGacaaccaaug | ORF66 | L. lactis φ31.1 | 55 (60) | AAF43134 | |
| 59 | 6.9 | 38,001 | 38,180 | aacguguucggGGAGGaaugaug | |||||
| 60 | 5.5 | 38,444 | 38,587 | uaaacucaacuGGAGGaaaaaug | |||||
| 61 | 15.5 | 38,664 | 39,065 | uacucGGAGGgacuuuuuaauug | 16.9-kDa protein | L. lactis S114 | 35 (81) | CAA72647 | |
| 62 | 4.8 | 39,288 | 39,416 | caaguaguGAGugaaaguccuug | |||||
| 63 | 20.6 | 39,434 | 39,949 | ugauGAAAGGAGaugcuaucuug | ORF170 | L. gasseri φadh | 46 (162) | CAB52516 | |
| ORF170 | S. thermophilus φSfi19 | 44 (154) | AAD44054 | ||||||
| ORF20 | S. thermophilus φ7201 | 44 (154) | AAF43513 | ||||||
| ORF175 | S. thermophilus φSfi21 | 41 (155) | AAD41027 | ||||||
| ORF46 | S. thermophilus DT1 | 42 (154) | AAD21922 |
a
Boyce et al. (8) designation for previously identified ORFs.
b
The stop position includes the stop codon.
c
The sequence shown includes the putative start codon and the immediate upstream 20 nucleotides. The putative RBS is shown in uppercase letters.
d
The protein sequences in the databases which show homology with the respective BK5-T ORFs are shown. Empty cells indicate that no significant homologies were observed; experimentally determined functions are indicated after a dash.