Table 4.
Features of phage TP-778L orfs and putative functions of their products.
| Orf (gene) | DNA-frame | Start | Stop | Size (aa) | SD sequence AAGGAGGTa | Predicted function/best match BLASTp result | E-value | Match identity (%) | References, acc. no. |
|---|---|---|---|---|---|---|---|---|---|
| 1 (int) | −3 | 420 | 1 | 139 | TTGGGGGAttaaataaATG | Putative integrase/ | 2e-90 | 99 | Desiere et al., 1998, NP_049990 |
| Streptococcus thermophilus phage Sfi21, integrase / | |||||||||
| 359 | |||||||||
| 2 (ltp) | −1 | 952 | 524 | 142 | TGGTAGGAaattttATG | Putative superinfection exclusion lipoprotein/ | 3e-79 | 93 | Neve et al., 1998, AAC03455 |
| Streptococcus thermophilus phage TP-J34/ | |||||||||
| 142 | |||||||||
| 3 | −2 | 1400 | 1032 | 122 | AAGGAAAAgtgagaatttATG | Putative metallo- proteinase motif/ Streptococcus thermophilus phage Sfi21, cI- like repressor/ | 4e-81 | 96 | Desiere et al., 1998, NP_049992 |
| 122 | |||||||||
| 4 (crh) | −2 | 1772 | 1407 | 121 | AAGGAGAAagatATG | Putative CI- repressor/ | 1e-80 | 100 | Neve et al., 1998, AAC03457 |
| Streptococcus thermophilus phage TP-J34, putative cI-repressor homolog/ | |||||||||
| 121 | |||||||||
| 5 (cro) | +3 | 1941 | 2144 | 67 | GAGGAGAAacaaaATG | Putative Cro protein/ | 3e-41 | 99 | Neve et al., 1998, AAC03458 |
| Streptococcus thermophilus phage TP-J34, Cro-like regulatory protein/ | |||||||||
| 67 | |||||||||
| 6 (ant) | +1 | 2197 | 2913 | 238 | AGAAAGGAtaatacATG | Putative antirepressor/ | 2e-175 | 99 | Neve et al., 1998, AAC03459 |
| Streptococcus thermophilus phage TP-J34, P1-antirepressor homolog / | |||||||||
| 238 | |||||||||
| 7 | +3 | 2934 | 3215 | 93 | ATAGGGGTtgaaaaagactATG | -/ | 1e-61 | 100 | Neve et al., 1998, AAC03460 |
| Streptococcus thermophilus phage TP-J34, hypothetical protein/ 93 | |||||||||
| 8 | +2 | 3275 | 3538 | 87 | AAGGAATTaaaATG | -/ | 6e-57 | 100 | Desiere et al., 1998, NP_597801 |
| Streptococcus thermophilus phage Sfi21 Orf87, hypothetical protein Sfi21p33/ | |||||||||
| 87 | |||||||||
| 9 | +1 | 3556 | 3693 | 46 | AAAGAGGAgaaacaaaATG | -/ | 4e-26 | 100 | This study |
| Streptococcus thermophilus phage TP-J34, hypothetical protein/ 46 | |||||||||
| 10 | +2 | 3932 | 4405 | 157 | AAGGAGTAtaccataaaatATG | -/ | 4e-88 | 84 | Guglielmotti et al., 2009, YP_003344879 |
| Streptococcus thermophilus phage ALQ13.2, hypothetical protein/ 157 | |||||||||
| 11 | +1 | 4402 | 5103 | 233 | AAGGAGAAaccttaacataagATG | -/ | 3e-168 | 99 | Levesque et al., 2005, YP_238517 |
| Streptococcus thermophiles phage, putative replication initiation protein/ | |||||||||
| 233 | |||||||||
| 12 | +2 | 5060 | 6472 | 470 | AAAGGGGTgtaaggtagATG | -/ | 0.0 | 99 | Deveau et al., 2008, YP_001686831 |
| Streptococcus thermophilus phage 858 Orf 37, putative helicase/ | |||||||||
| 470 | |||||||||
| 13 | +2 | 6479 | 6952 | 157 | TTGGAGATaaaaaaacATG | -/ | 3e-108 | 97 | Deveau et al., 2008, YP_001686832 |
| Streptococcus thermophilus phage 858 Orf 38/ | |||||||||
| 157 | |||||||||
| 14 | +3 | 6957 | 7772 | 271 | TTTGCCATtctaagactATG | -/ | 0.0 | 99 | Deveau et al., 2008, YP_001686833 |
| Streptococcus thermophilus phage 858 Orf 39, primase-polymerase domain/ 271 | |||||||||
| 15 | +1 | 7741 | 9297 | 518 | AAGGAGTTagatactaaacATG | Putative primase/ | 0.0 | 92 | Geng et al., 2011, YP_006561246 |
| Streptococcus phage YMC-2011, putative primase / | |||||||||
| 519 | |||||||||
| 16 | +1 | 9541 | 9861 | 106 | AGAAAGGTaaattttaaGTG | -/ | 1e-65 | 92 | Deveau et al., 2008, YP_001686835 |
| Streptococcus thermophilus phage 858 Orf 41, VRR_NUC domain/ | |||||||||
| 106 | |||||||||
| 17 | +2 | 9845 | 10081 | 78 | AAGGAAGCtttggatatagtaaATG | -/ | 7e-42 | 87 | Guglielmotti et al., 2009, YP_003347446 |
| Streptococcus thermophilus phage Abc2, hypothetical protein/ | |||||||||
| 78 | |||||||||
| 18 | +3 | 10098 | 10253 | 51 | AAGATGGTagagttATG | -/ | 1e-23 | 84 | Desiere et al., 1998, NP_049960 |
| Streptococcus thermophilus phage Sfi19 Orf 51; hypothetical protein Sfi19p40/ | |||||||||
| 51 | |||||||||
| 19 | +3 | 10254 | 10835 | 193 | GAGGTGGAataaGTG | -/ | 9e-58 | 69 | Guglielmotti et al., 2009, YP_003347451 |
| Streptococcus thermophilus phage Abc2, hypothetical protein/ | |||||||||
| 166 | |||||||||
| 20 | +3 | 10836 | 11348 | 170 | GAAGAGGTtgaataaATG | Putative DNA-binding protein/ | 6e-111 | 91 | Mills et al., 2011, YP_002925093 |
| Streptococcus thermophilus phage 5093, DNA binding protein, HTH_XRE/ | |||||||||
| 170 | |||||||||
| 21 | +1 | 11317 | 11634 | 105 | AGGGAAGAtagtaaATG | -/ | 1e-65 | 95 | This study |
| Streptococcus thermophilus phage TP-J34, hypothetical protein/ | |||||||||
| 105 | |||||||||
| 22 | +2 | 11636 | 12079 | 147 | GTAGAGGTaattaagATG | -/ | 2e-103 | 99 | This study |
| Streptococcus thermophilus phage TP-J34, hypothetical / | |||||||||
| 147 | |||||||||
| 23 | +1 | 12085 | 12795 | 236 | GTGGGGGCgtaggattcATG | / | 7e-161 | 94 | Stanley et al., 2000, NP_038319 |
| Streptococcus thermophilus phage 7201 Orf 18/ | |||||||||
| 235 | |||||||||
| 24 | +2 | 13232 | 13645 | 137 | AGAGAGGGcagaaaaATG | Putative transcriptional regulator/ | 2e-94 | 99 | This study |
| Streptococcus thermophilus phage TP-J34 Orf27, transcriptional regulator ArpU family/ | |||||||||
| 137 | |||||||||
| 25 (terS) | +2 | 13766 | 14278 | 170 | TTTGAGTTgtctttttttgattatgaaATG | Putative terminase small subunit/ | 7e-85 | 86 | Levesque et al., 2005, YP_001686797 |
| Streptococcus thermophilus phage 2972, terminase small subunit/ | |||||||||
| 150 | |||||||||
| 26 (terL) | +3 | 14265 | 15500 | 411 | AAGGAGCTgttagcgATG | Putative terminase large subunit/ | 0.0 | 97 | This study |
| Streptococcus thermophilus phage TP-J34 Orf29, putative terminase large subunit / | |||||||||
| 411 | |||||||||
| 27 | +2 | 15506 | 17014 | 502 | TAGGAGGAatgATG | Putative portal protein/ | 0.0 | 97 | Deveau et al., 2008, YP_001686800 |
| Streptococcus thermophilus phage 858 orf6, putative portal protein/ | |||||||||
| 502 | |||||||||
| 28 | +1 | 17011 | 17904 | 297 | GAGAGGGTtatgaATG | Putative head protein/ | 0.0 | 96 | Levesque et al., 2005, YP_238489 |
| Streptococcus thermophilus phage 2972, head protein/ | |||||||||
| 297 | |||||||||
| 29 | +3 | 18096 | 18677 | 193 | TAGGAGAAcaaaATG | Putative scaffold protein/ | 7e-130 | 96 | Levesque et al., 2005, YP_238490 |
| Streptococcus thermophilus phage 2972, scaffold protein/ | |||||||||
| 193 | |||||||||
| 30 | +1 | 18697 | 19056 | 119 | AAGGAAATtttaaATG | Putative head protein/ | 6e-75 | 97 | Levesque et al., 2005, YP_238491 |
| Streptococcus thermophilus phage 2972, head protein/ | |||||||||
| 119 | |||||||||
| 31 | +1 | 19075 | 20121 | 348 | GAGGAGGAacattaaaacATG | Putative capsid protein/ | 0.0 | 98 | Guglielmotti et al., 2009, YP_003344853 |
| Streptococcus thermophilus phage ALQ13, capsid/ | |||||||||
| 348 | |||||||||
| 32 | +3 | 20133 | 20294 | 53 | TAAGAGGTactgatATG | -/ | 5e-19 | 98 | Guglielmotti et al., 2009, YP_003344854 |
| Streptococcus thermophilus phage ALQ13, hypothetical protein/ | |||||||||
| 53 | |||||||||
| 33 | +2 | 20309 | 20647 | 112 | AGTGAGGTatggcgtgATG | -/ | 3e-70 | 94 | Stanley et al., 1997, NP_695111 |
| Streptococcus thermophilus phage 01205 Orf 33, hypothetical protein/ | |||||||||
| 122 | |||||||||
| 34 | +1 | 20644 | 20958 | 104 | GGTgaggtgctatttctATG | -/ | 7e-62 | 94 | Levesque et al., 2005, YP_238495 |
| Streptococcus thermophilus phage 2972, hypothetical protein / | |||||||||
| 104 | |||||||||
| 35 | +2 | 20960 | 21304 | 114 | AAGGTGaTgaaataacATG | -/ | 4e-72 | 94 | Lucchini et al., 1999, NP_056684 |
| Streptococcus thermophilus phage Sfi11 Orf 114, hypothetical protein/ | |||||||||
| 114 | |||||||||
| 36 | +1 | 21289 | 21687 | 132 | GAAGAGATggcgaaATG | -/ | 1e-84 | 95 | Guglielmotti et al., 2009, YP_003344858 |
| Streptococcus thermophilus phage ALQ13, hypothetical protein/ | |||||||||
| 128 | |||||||||
| 37 | +2 | 21701 | 22210 | 169 | AATTAGGAGGAaaaaATG | Putative tail protein/ | 9e-115 | 98 | Levesque et al., 2005, YP_238498 |
| Streptococcus thermophilus phage 2972, tail protein/ | |||||||||
| 169 | |||||||||
| 38 | +3 | 22287 | 22640 | 117 | TAGGAGTAaacaaacaATG | -/ | 6e-78 | 99 | Levesque et al., 2005, YP_238499 |
| Streptococcus thermophilus phage 2972, hypothetical protein / | |||||||||
| 117 | |||||||||
| 39 | +2 | 22703 | 23020 | 105 | GAGGAGTTaatcactaatgccATG | -/ | 2e-65 | 99 | Levesque et al., 2005, YP_238500 |
| Streptococcus thermophilus phage 2972, hypothetical protein / | |||||||||
| 105 | |||||||||
| 40 (tmp) | +3 | 23010 | 27563 | 1517 | AGAGAGGGgcttgctagATG | Putative tape measure protein/ | 0.0 | 90 | Stanley et al., 2000 NP_695118 |
| Streptococcus thermophilus phage O1205, putative tail protein/ | |||||||||
| 1517 | |||||||||
| 41 | +2 | 27563 | 29101 | 512 | TGCGAGGTctaaattaATG | Putative tail protein/ | 0.0 | 89 | Lucchini et al., 1999, NP_056690 |
| Streptococcus thermophilus phage Sfi11, putative minor structural protein/ | |||||||||
| 511 | |||||||||
| 42 | +1 | 29101 | 35163 | 2020 | AAGGTGGAtttaATG | Putative host specificity protein/ | 0.0 | 88 | Deveau et al., 2008, YP_001686815 |
| Streptococcus thermophilus phage 858 Orf21,prophage tail protein / | |||||||||
| 1006 | |||||||||
| 43 | +1 | 35164 | 37185 | 673 | TAGGAGGTttttaaTTG | Putative tail protein/ | 0.0 | 89 | Deveau et al., 2008, YP_001686816 |
| Streptococcus thermophilus phage 858 Orf22/ | |||||||||
| 673 | |||||||||
| 44 | +1 | 37201 | 37548 | 115 | AAGAAGGAaaattcATG | -/ | 6e-73 | 96 | This study |
| Streptococcus thermophilus phage TP-J34, hypothetical protein/ | |||||||||
| 133 | |||||||||
| 45 | +2 | 37568 | 37714 | 48 | AAAGAGGAaaaagatATG | -/ | 2e-24 | 100 | This study |
| Streptococcus thermophilus phage TP-J34, hypothetical protein/ | |||||||||
| 48 | |||||||||
| 46 | +1 | 37732 | 38055 | 107 | TAGGAGGGatgtgttATG | -/ | 2e-71 | 100 | This study |
| Streptococcus thermophilus phage TP-J34, hypothetical protein/ | |||||||||
| 107 | |||||||||
| 47 (hol) | +3 | 38064 | 38306 | 80 | TGAGAGGAtaaataacaatATG | Putative holin/ | 7e-44 | 93 | Guglielmotti et al., 2009, YP_003347430 |
| Streptococcus thermophilus phage Abc2, holin/ 80 | |||||||||
| 48 (lys) | +1 | 38308 | 39153 | 281 | AAGGAAGGaaaatagtATG | Putative lysin/ | 8e-181 | 90 | This study |
| Streptococcus thermophilus phage TP-J34, putative lysin/ | |||||||||
| 281 | |||||||||
| 49 | +1 | 39499 | 39720 | 73 | AAGATTGAaaacaaactagacgacATG | -/ | 5e-46 | 100 | Neve et al., 1998, AAC03448 |
| Streptococcus thermophilus phage TP-J34/ | |||||||||
| 73 | |||||||||
| 50 | +3 | 40419 | 40715 | 98 | AGAGAGGTaaaaagaaATG | -/ | 2e-38 | 66 | WP_009730541 |
| Streptococcus sp. F0441, hypothetical protein/ | |||||||||
| 101 | |||||||||
| 51 | +2 | 40778 | 41200 | 140 | AAGGAAGTatATG | -/ | 5e-85 | 90 | Desiere et al., 1998, NP_049988 |
| Streptococcus thermophilus phage Sfi21, hypothetical protein / | |||||||||
| 140 | |||||||||
| 52 | +3 | 41202 | 41624 | 140 | AAAGATGTaatctaaaATG | -/ | 1e-81 | 87 | Desiere et al., 1998, NP_049989 |
| Streptococcus thermophilus phage Sfi21, hypothetical protein / | |||||||||
| 140 |
ada Silva Oliveira et al., 2004.