Table 1

Gene functions of the Vibrio phage ϕpp2
Feature ID Start Stop nt (bp) aa Function Match to Color
fig 75320.3.peg.1 41 973 933 311 RNaseH ribonuclease KVP40 & T4 G*
fig 75320.3.peg.3 1318 1611 294 98 late promoter transcription accessory protein KVP40 Y
fig 75320.3.peg.6 3216 3761 546 182 Frd dihydrofolate reductase KVP40 & T4 G
fig 75320.3.peg.7 3758 4477 720 240 ATP-dependent Clp protease proteolytic subunit (EC3.4.21.92) KVP40 Y
fig 75320.3.peg.8 4544 5644 1101 367 Phage recombination protein KVP40 & T4 G
fig 75320.3.peg.10 6060 7343 1284 428 DNA primase-helicase subunit KVP40 & T4 G
fig 75320.3.peg.12 7583 9418 1836 612 Ribonucleotide reductase of class III (anaerobic), large subunit (EC 1.17.4.2) KVP40 & T4 G
fig 75320.3.peg.15 10506 10982 477 159 Ribonucleotide reductase of class III (anaerobic), activating protein (EC 1.97.1.4) KVP40 & T4 G
fig 75320.3.peg.16 10982 11506 525 175 putative serine/threonine protein phosphatase KVP40 Y
fig 75320.3.peg.18 12420 13244 825 275 98.1% KVP40 DNA helicase, phage-associated KVP40 Y
fig 75320.3.peg.19 13244 13720 477 159 gp61.1 conserved hypothetical KVP40 & T4 G
fig 75320.3.peg.20 13801 14859 1059 353 DNA primase (EC 2.7.7.-)/DNA helicase (EC 3.6.1.-). Phage-associated KVP40 & T4 G
fig 75320.3.peg.21 14859 15356 498 166 Deoxyuridine 5'-triphosphate nucleotidohydrolase (EC 3.6.1.23) KVP40 Y
fig 75320.3.peg.23 15589 16281 693 231 exonuclease A KVP40 & T4 G
fig 75320.3.peg.31 18182 19081 900 300 Thymidylate synthase (EC 2.1.1.45) KVP40 G
fig 75320.3.peg.42 23359 24024 666 222 NAD-dependent protein deacetylase of SIR2 family KVP40 Y
fig 75320.3.peg.43 24180 25973 1794 598 DNA gyrase subunit B (EC 5.99.13) KVP40 & T4 G
fig 75320.3.peg.49 27350 28078 729 243 Ser/Tar protein phosphatase family protein KVP40 Y
fig 75320.3.peg.55 30282 31625 1344 448 DNA ligase KVP40 & T4 G
fig 75320.3.peg.60 36003 36242 240 80 glutaredoxin KVP40 Y
fig 75320.3.peg.61 36301 37197 897 299 Phage capsid vertex protein (T4-like gp24) KVP40 & T4 G
fig 75320.3.peg.62 37206 37718 513 171 T4-like phage RNA polymerase sigma factor for late transcription # T4-like phage gp55#T4GC0140 KVP40 & T4 G
fig 75320.3.peg.68 41040 41504 465 155 gp30.3 KVP40 & T4 G
fig 75320.3.peg.69 41509 41994 486 162 Putative 5'(3')-deoxyribonucleotidase (EC 3.1.3.-) KVP40 Y
fig 75320.3.peg.70 41991 43031 1041 347 Phage recombination-related endonuclease Gp47 KVP40 & T4 G
fig 75320.3.peg.72 43248 45485 2238 746 recombination endonuclease subunit KVP40 & T4 G
fig 75320.3.peg.75 46247 46912 666 222 27.11% T4 Sliding clamp DNA polymerase accessory protein, phage associated # Gp45 T4 DG
fig 75320.3.peg.76 46983 47939 957 319 Replication factor C small subunit/Phage DNA polymerase clamp loader subunit # T4-like phage gp44 # T4 GC0157 KVP40 & T4 G
fig 75320.3.peg.77 47950 48438 489 163 31.11% T4 Phage DNA polymerase clamp loader (fig|10665.1.peg.49) T4 DG
fig 75320.3.peg.78 48473 48853 381 127 RegA translaticnal repressor of early genes KVP40 & T4 G
fig 75320.3.peg.79 49482 48856 627 209 MobE homing endonuclease T4 R
fig 75320.3.peg.81 50130 52682 2553 851 DNA polymerase KVP40 & T4 G
fig 75320.3.peg.83 53047 54192 1146 382 Rn1A KVP40 & T4 G
fig 75320.3.peg.88 55585 56742 1158 386 3'-phosphatase, 5'-polynucleotide kinase, phage-associated #T4-like phage Pset #T4 GC1648 KVP40 & T4 G
fig 75320.3.peg.116 69766 70218 453 151 CMP/dCMP deaminase, zinc-binding KVP40 & T4 G
fig 75320.3.peg.117 70273 71199 927 309 NADPH-dependent 7-cyano-7-deazaguanine reductase (EC 1.7.1.-) KVP40 Y
fig 75320.3.peg.118 71268 71942 675 225 GTP cyclohydrolase I (EC 3.5.4.16) type 1 KVP40 Y
fig 75320.3.peg.119 72615 71914 702 234 Phage-associated homing endonuclease T4 R
fig 75320.3.peg.121 74083 74991 909 303 NADPH-dependent 7-cyano-7-deazaguanine reductase (EC 1.7.1.-) KVP40 Y
fig 75320.3.peg.122 75047 75763 717 239 Queuosine Biosynthesis QueC ATPase KVP40 Y
fig 75320.3.peg.124 76380 76655 276 92 32.1% T4 Phage tail fibers T4 DG
fig 75320.3.peg.127 77160 77498 339 113 Phage capsid and scaffold KVP40 Y
fig 75320.3.peg.129 78455 77946 510 170 gp49 recombination endonuclease VII KVP40 & T4 G
fig 75320.3.peg.131 78799 79806 1008 336 RNA ligase, phage-associated KVP40 & T4 G
fig 75320.3.peg.141 83194 85263 2070 690 Phage rIIA lysis inhibitor KVP40 & T4 G
fig 75320.3.peg.142 85256 86293 1038 346 rIIB protector from prophage-induced early lysis KVP40 & T4 G
fig 75320.3.peg.148 89179 90216 1041 347 NrdC 1 1 conserved hypothetical protein. KVP40 & T4 G
fig 75320.3.peg.151 90946 92211 1266 422 Dda DNA helicase KVP40 & T4 G
fig 75320.3.peg.157 94752 95777 1026 342 Nicotinamide-nucleotide adenylyltransferase, NadM family (EC 2.7.7.1)/ADP-ribose pyrophosphatase KVP40 Y
fig 75320.3.peg.188 105782 106366 585 195 Thymidine kinase (EC 2.7.1.21) KVP40 & T4 G
fig 75320.3.peg.201 111295 111711 417 139 endonuclease KVP40 & T4 G
fig 75320.3.peg.208 113557 114537 981 327 Nicotinamide-nucleotide adenylyltransferase, NadR family (EC 2.7.7.1)/Ribosyln:cotinamide kinase (EC 2.7.1.22) KVP40 Y
fig 75320.3.peg.212 115492 116157 666 222 Ribosyl nicotinamide transporter, PnuC-like KVP40 Y
fig 75320.3.peg.249 130608 131138 531 177 Cell wall mannoprotein with similarity to Tir1p, Tir2p, Tir3p, and Tir4p; expressed under anaerobic conditions, comp KVP40 Y
fig 75320.3.peg.255 134377 135366 990 330 moa A/nifB/pqqE family protein KVP40 Y
fig 75320.3.peg.256 136483 135359 1125 375 moa A/nifB/pqqE family protein KVP40 Y
fig 75320.3.peg.260 138690 140183 1494 498 Nicotinamide phosphoritosyltransferase (EC 2.4.2.12) KVP40 Y
fig 75320.3.peg.268 144971 143919 1053 351 moaA/nifB/pqqE family protein KVP40 Y
fig 75320.3.peg.273 147028 149253 2226 742 Ribonucleotide reductase of class Ia (aerobic), alpha subunit (EC 1.17.4.1) KVP40 & T4 G
fig 75320.3.peg.274 149293 149964 672 224 Phage-associated homing endonuclease T4 R
fig 75320.3.peg.275 149957 151081 1125 375 Ribonucleotide reductase of class Ia (aerobic), beta subunit (EC 1.17.4.1) KVP40 & T4 G
fig 75320.3.peg.276 151083 151382 300 100 NrdC thioredoxin KVP40 & T4 G
fig 75320.3.peg.279 152313 153317 1005 335 Thioredoxin, phage-associated KVP40 & T4 G
fig 75320.3.peg.280 153363 154649 1287 429 gp52 topoisomerase II medium subunit KVP40 & T4 G
fig 75320.3.peg.282 154900 155781 882 294 Queuosine Biosynthesis QueE Radical SAM KVP40 Y
fig 75320.3.peg.293 160936 161235 300 100 anti-sigma70 protein KVP40 Y
fig 75320.3.peg.296 165535 162206 3330 1110 Phage tail fibers (Match to KVP40 peg.297) KVP40 Y
fig 75320.3.peg.297 168882 165607 3276 1092 tail fiber fragment KVP40 Y
fig 75320.3.peg.322 184667 184212 456 152 gp57B conserved hypothetical protein KVP40 & T4 G
fig 75320.3.peg.324 185581 184943 639 213 dNMP kinase KVP40 & T4 G
fig 75320.3.peg.325 186347 185814 534 178 gp3 tail completion and health stabilizer protein KVP40 & T4 G
fig 75320.3.peg.328 189332 188484 849 283 Phage baseplate hub KVP40 & T4 G
fig 75320.3.peg.329 190090 189344 747 249 Phage baseplate-tail tube initiator KVP40 Y
fig 75320.3.peg.330 190507 190094 414 138 55.97% T4 Phage DNA end protector during packaging T4 DG
fig 75320.3.peg.331 191144 190689 456 152 Phage head completion protein KVP40 & T4 G
fig 75320.3.peg.332 191211 192350 1140 380 Phage baseplate tail tube cap KVP40 & T4 G
fig 75320.3.peg.333 192350 192928 579 193 Phage baseplate wedge KVP40 & T4 G
fig 75320.3.peg.335 194207 195466 1260 420 Phage baseplate hub KVP40 & T4 G
fig 75320.3.peg.337 195956 196252 297 99 PAAR KVP40 & T4 G
fig 75320.3.peg.340 197717 198136 420 140 Phage baseplate wedge KVP40 & T4 G
fig 75320.3.peg.341 198223 200181 1959 653 Phage baseplate wedge KVP40 & T4 G
fig 75320.3.peg.342 200181 203678 3498 1166 Phage baseplate wedge initiator KVP40 & T4 G
fig 75320.3.peg.343 203680 204702 1023 341 Phage baseplate wedge KVP40 & T4 G
fig 75320.3.peg.344 204758 205714 957 319 gp9 KVP40 & T4 G
fig 75320.3.peg.345 205724 207970 2247 749 Phage baseplate wedge KVP40 & T4 G
fig 75320.3.peg.348 210191 211612 1422 474 prophage LambdaSa04, minor structural protein, putative KVP40 & T4 G
fig 75320.3.peg.349 211911 213590 1680 560 Phage neck whiskers KVP40 & T4 G
fig 75320.3.peg.350 213601 214524 924 308 Phage neck protein KVP40 & T4 G
fig 75320.3.peg.351 214528 215364 837 279 Phage neck protein KVP40 & T4 G
fig 75320.3.peg.352 215593 216726 1134 378 tail health stabilizer and completion protein KVP40 & T4 G
fig 75320.3.peg.354 217441 217989 549 183 Phage terminase, small subunit KVP40 & T4 G
fig 75320.3.peg.355 217949 219751 1803 601 Phage terminase, large subunit KVP40 & T4 G
fig 75320.3.peg.356 219798 221813 2016 672 Phage tail health monomer KVP40 & T4 G
fig 75320.3.peg.357 221864 222364 501 167 Phage tail fibers KVP40 & T4 G
fig 75320.3.peg.358 222404 223951 1548 516 portal vertex protein of head KVP40 & T4 G
fig 75320.3.peg.360 224131 224622 492 164 Phage capsid and scaffold KVP40 & T4 G
fig 75320.3.peg.361 224625 225266 642 214 Phage prohead core scaffold protein and protease KVP40 & T4 G
fig 75320.3.peg.362 225299 226141 843 281 Phage scaffold prohead core protein KVP40 & T4 G
fig 75320.3.peg.363 226212 227756 1545 515 Phage major capsid protein KVP40 & T4 G
    fig 75320.3.peg.364
    228910
    227813
    1098
    366
    PSI-BLAST tRNA nucleotidyltransferase (Acinetobacter baumannii & Pseudomonas fluorescens)
    KVP40 & T4
    G
fig 75320.3.peg.367 230824 231315 492 164 Inh KVP40 & T4 G
fig 75320.3.peg.377 236908 238431 1524 508 DNA helicase, phage-associated KVP40 & T4 G
fig 75320.3.peg.381 239752 239339 414 138 UvsY recombination, repair and ssDNA binding protein KVP40 Y
fig 75320.3.peg.383 246382 242612 3771 1257 gp34 long tail fiber, proximal subunit KVP40 Y

The legends in the last column represented by G, Y, P and R correspond to the real color shown in Genome map of the Vibrio phage ϕpp2 (Figure 3). G (green arrows in Figure 3) indicates the gene functions were matched to both Enterobacteria phage T4 and Vibrio phage KVP40. Shallow lines with Y (yellow and ticks on the circle in Figure 3) indicate the gene functions fitted to KVP40 only. Bold P and italic bold R (purple and red bars in Figure 3) represent the genes which only aligned well with T4; additionally, the italic bold R (red bars with the number in Figure 3) indicates the PEG numbers of potential HE. The underlining (cyan in Figure 3) demonstrates one gene that matched to assorted bacteria.

Lin and Lin

Lin and Lin BMC Genomics 2012 13:224   doi:10.1186/1471-2164-13-224

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