TABLE 2.
Features of bacteriophage phiIPLA88 ORFs, gene products, and functional assignments
| ORF | Position (nt) |
Length (nt) | No. of amino acids | Size (kDa [pI]) | Predictive function | Closest hit (e value) | % Amino acid identity (% similarity) | Accession no. | Predicted domain (protein ID) (e value)a | |
|---|---|---|---|---|---|---|---|---|---|---|
| From | To | |||||||||
| 1 | 1065 | 1 | 1,065 | 354 | 41.0 (9.63) | Integrase | S. aureus RF122 (0.0) | 99 (99) | YP_417222.1 | Phage integrase (PF00589) (2.2e−14) |
| 2 | 1639 | 1124 | 516 | 171 | 19.2 (8.98) | Hypothetical protein | S. aureus RF122 (6e−93) | 100 (100) | YP_417221.1 | Prokar_Lipoprotein(PS51257) (0.0) |
| 3 | 2143 | 1643 | 501 | 166 | 19.2 (9.58) | Putative excisionase | S. aureus RF122 (9e−89) | 100 (100) | YP_417220.1 | |
| 4 | 2834 | 2196 | 639 | 212 | 24.2 (5.67) | Mutated repressor | S. aureus phiNM (3e−107) | 98 (99) | YP_873953.1 | HTH (PF01381) (1.7e−14); Peptidase_S24 (PF00717) (0.00011) |
| 5 | 3025 | 3279 | 255 | 84 | 10 (9.03) | Cro | S. aureus phiNM (4e−37) | 97 (100) | YP_873954.1 | HTH (PF01381) (1.8e−13) |
| 6 | 4050 | 3460 | 591 | 196 | 22.3 (6.23) | Hypothetical protein | S. aureus RF122 (2e−107) | 100 (100) | YP_417216.1 | Transmembrane region |
| 7 | 4107 | 4856 | 750 | 249 | 28.5 (9.79) | Antirepressor | S. aureus RF122 (4e−144) | 100 (100) | YP_417215.1 | ANT (PF03374) (2.5e−102); AntA (PF08346) (3.8e−31) |
| 8 | 4872 | 5087 | 216 | 71 | 8.7 (9.70) | Hypothetical protein | S. aureus RF122 (4e−34) | 100 (100) | YP_417214.1 | DUF771 (PF05595) (3.3e−6) |
| 9 | 5102 | 5272 | 171 | 56 | 6.4 (8.60) | Hypothetical protein | S. aureus RF122 (5e−24) | 100 (100) | YP_417213.1 | DUF1270 (PF06900) (5.0e−34) |
| 10 | 5277 | 5591 | 315 | 104 | 12.4 (9.60) | Hypothetical protein | S. aureus RF122 (6e−53) | 100 (100) | YP_417212.1 | |
| 11 | 5656 | 5958 | 303 | 100 | 11.1 (4.48) | Hypothetical protein | S. aureus RF122 (8e−49) | 100 (100) | YP_417211.1 | |
| 12 | 5963 | 6223 | 261 | 86 | 10.1 (4.40) | Hypothetical protein | S. aureus φPVL108 (4e−46) | 94 (96) | YP_918906.1 | DUF1108 (PF06531)(6.2e−60) |
| 13 | 6233 | 6454 | 222 | 73 | 8.6 (5.42) | Hypothetical protein | S. aureus RF122 (4e−35) | 100 (100) | YP_417209.1 | |
| 14 | 6447 | 7067 | 621 | 206 | 23.5 (5.65) | Topoisomerase | S. aureus RF122 (6e−119) | 100 (100) | YP_417208.1 | DUF1071 (PF06378) (2.7e−12) |
| 15 | 7070 | 7495 | 426 | 141 | 15.8 (5.24) | ssDNA binding protein | S. aureus RF122 (9e−76) | 100 (100) | YP_417207.1 | SSB (PF00436) (1.6e−29) |
| 16 | 7509 | 8180 | 672 | 223 | 26 (6.60) | Hypothetical protein | S. aureus RF122 (8e−131) | 100 (100) | YP_417206.1 | DUF968 (PF06147) (0.0) |
| 17 | 8177 | 8932 | 756 | 251 | 29.4 (8.37) | DNA replication protein | S. aureus RF122 (1e−145) | 100 (100) | YP_417205.1 | DnaD and phage-associated region (IPR006343) (3.6e−10) |
| 18 | 8932 | 9288 | 357 | 118 | 13.7 (5.74) | Hypothetical protein | S. aureus RF122 (1e−64) | 100 (100) | YP_417204.1 | |
| 19 | 9285 | 10526 | 1,242 | 413 | 47.4 (5.14) | DNA helicase | S. aureus RF122 (0.0) | 100 (100) | YP_417203.1 | DnaB_C (PF03796) (7.2e−51) |
| 20 | 10523 | 10738 | 216 | 71 | 8.5 (5.13) | Hypothetical protein | S. aureus RF122 (1e−34) | 100 (100) | YP_417202.1 | |
| 21 | 10741 | 10962 | 222 | 73 | 8.5 (4.83) | Hypothetical protein | S. aureus RF122 (2e−35) | 100 (100) | YP_417201.1 | |
| 22 | 10973 | 11377 | 405 | 134 | 16.1 (9.79) | Hypothetical protein | S. aureus RF122 (1e−72) | 100 (100) | YP_417200.1 | DUF1064 (PF06356) (2.7e−86) |
| 23 | 11382 | 11567 | 186 | 61 | 7.2 (4.06) | Hypothetical protein | S. aureus φ29 (5e−25) | 93 (96) | YP_240593.1 | |
| 24 | 11568 | 11930 | 363 | 120 | 14.5 (10.42) | Hypothetical protein | S. aureus RF122 (2e−65) | 100 (100) | YP_417199.1 | PVL_ORF50 (PF07768)(1.5e-65) |
| 25 | 11930 | 12184 | 255 | 84 | 9.6 (4.99) | Hypothetical protein | S. aureus RF122 (8e−44) | 100 (100) | YP_417198.1 | |
| 26 | 12184 | 12432 | 249 | 82 | 9.8 (5.90) | Hypothetical protein | S. aureus RF122 (9e−42) | 100 (100) | YP_417197.1 | Phage_Orf51 (PF06194)(3.1e−59) |
| 27 | 12441 | 12677 | 237 | 78 | 9.6 (10.17) | Hypothetical protein | S. aureus RF122 (3e−39) | 100 (100) | YP_417196.1 | |
| 28 | 12737 | 12991 | 255 | 84 | 9.5 (3.95) | Hypothetical protein | S. aureus RF122 (3e−40) | 100 (100) | YP_417195.1 | DUF1024 (PF06260)(1.3e−51) |
| 29 | 12978 | 13139 | 162 | 53 | 6.1 (3.30) | Hypothetical protein | S. aureus phage 71 (1e−19) | 98 (98) | YP_240445.1 | |
| 30 | 13139 | 13675 | 537 | 178 | 20.6 (4.36) | dUTPase | S. aureus RF122 (6e−100) | 100 (100) | YP_417194.1 | dUTPase_2 (PF08761)(6.5e−6) |
| 31 | 13712 | 13957 | 246 | 81 | 9.5 (10.08) | Hypothetical protein | S. aureus RF122 (1e−35) | 100 (100) | YP_417193.1 | Transmembrane regions |
| 32 | 13954 | 14160 | 207 | 68 | 7.7 (7.31) | Hypothetical protein | S. aureus RF122 (6e−32) | 98 (100) | YP_417192.1 | DUF1381 (PF07129) (2.2e−43) |
| 33 | 14157 | 14330 | 174 | 57 | 6.5 (4.05) | Transcriptional activator | S. aureus RF122 (4e−25) | 100 (100) | YP_417191.1 | RinB (PF06116) (4.5e−38) |
| 34 | 14492 | 14911 | 420 | 139 | 16.1 (9.52) | Transcriptional activator | S. aureus RF122 (5e−72) | 100 (100) | YP_417190.1 | Phage transcriptional activator RinA (IPR006523) (2.1e−32) |
| 35 | 15099 | 15593 | 495 | 164 | 18.9 (6.24) | Terminase small subunit | S. aureus RF122 (3e−93) | 100 (100) | YP_417189.1 | Terminase_2 (PF03592) (1.3e−39) |
| 36 | 15596 | 16885 | 1,290 | 429 | 50.2 (9.33) | Terminase large subunit | S. aureus RF122 (0.0) | 100 (100) | YP_417188.1 | Terminase_3 (PF04466) (2.2e−11) |
| 37 | 16896 | 18437 | 1,542 | 513 | 59.6 (4.60) | Portal protein | S. aureus RF122 (0.0) | 100 (100) | YP_417187.1 | Phage_prot_Gp6 (PF05133) (2.8e−100) |
| 38 | 18319 | 18504 | 186 | 61 | 7.1 (11.05) | Hypothetical protein | Staphylococcus φ80α (2e−24) | 98 (98) | YP_001285357.1 | |
| 39 | 18549 | 19433 | 885 | 294 | 33.9 (9.38) | Head morphogenesis protein | S. aureus RF122 (1e−173) | 100 (100) | YP_417186.1 | Phage_Mu_F (PF04233) (5.1e−06) |
| 40 | 19506 | 19676 | 171 | 56 | 6.5 (9.70) | Hypothetical protein | S. aureus φ53 (5e−22) | 92 (94) | YP_239646.1 | |
| 41 | 19811 | 20425 | 615 | 204 | 23.6 (4.92) | Scaffold protein | S. aureus RF122 (4e−109) | 99 (100) | YP_417185.1 | |
| 42 | 20439 | 21413 | 975 | 324 | 36.6 (4.93) | Major head protein | S. aureus RF122 (3e−171) | 100 (100) | YP_417184.1 | Major capsid protein gp5superfamily (SSF56563)(2.8e-26) |
| 43 | 21435 | 21722 | 288 | 95 | 10.9 (5.21) | Hypothetical protein | S. aureus RF122 (9e−47) | 100 (100) | YP_417183.1 | |
| 44 | 21731 | 22063 | 333 | 110 | 12.8 (5.08) | DNA packaging protein | S. aureus RF122 (8e−56) | 100 (100) | YP_417182.1 | |
| 45 | 22362 | 22709 | 348 | 115 | 13.4 (5.60) | Head to tail joining protein | S. aureus RF122 (3e−62) | 100 (100) | YP_417180.1 | TP901-1_ORF40 (PF07772) (1.1e−38) |
| 46 | 22721 | 23104 | 384 | 127 | 14.7 (4.21) | Hypothetical protein | S. aureus RF122 (8e−70) | 100 (100) | YP_417179.1 | |
| 47 | 23122 | 23703 | 582 | 193 | 21.2 (4.55) | Major tail protein | S. aureus RF122 (4e−109) | 100 (100) | YP_417178.1 | Phage_tail_2 (PF06199)(4.1e−84) |
| 48 | 23765 | 24130 | 366 | 121 | 13.1 (4.30) | Hypothetical protein | S. aureus RF122 (4e−60) | 100 (100) | YP_417177.1 | |
| 49 | 24160 | 24504 | 345 | 114 | 13.5 (4.41) | Minor structural protein | φ11 (7e−60) | 100 (100) | NP_803294.1 | |
| 50 | 24521 | 27988 | 3,468 | 1,155 | 125.6 (10.37) | Tape measure protein | S. aureus φNM (0.0) | 98 (99) | YP_874001.1 | TMP (PF05017) (0.089); WD_REPEATS_1 (PS00678); transmembrane regions |
| 51 | 28001 | 28948 | 948 | 315 | 37 (7.28) | Minor tail protein | S. aureus RF122 (0.0) | 100 (100) | NP_803296.1 | WD_REPEATS_1 (PS00678) |
| 52 | 28957 | 30858 | 1,902 | 633 | 71.1 (6.96) | Putative anti-receptor protein | S. aureus RF122 (0.0) | 99 (100) | YP_417173.1 | Phage minor structural protein, N-terminal (IPR007119)(0.024); SGNH hydrolaseIPR13830 (1.1e−24) |
| 53 | 30873 | 32783 | 1,911 | 636 | 73.3 (6.64) | Minor structural protein | S. aureus RF122 (0.0) | 98 (99) | YP_417172.1 | |
| 54 | 32783 | 34606 | 1,824 | 607 | 66.5 (4.62) | Minor tail protein | S. aureus RF122 (0.0) | 99 (99) | YP_417171.1 | |
| 55 | 34606 | 34983 | 378 | 125 | 14.1 (4.30) | Hypothetical protein | S. aureus φ85 (2e−59) | 92 (95) | YP_239743.1 | |
| 56 | 34984 | 35166 | 183 | 60 | 7.2 (6.69) | Hypothetical protein | S. aureus φ29 (9e−29) | 98 (98) | YP_240554.1 | Phage uncharacterized protein XkdX (IPR010022) (3.3e-22) |
| 57 | 35207 | 35506 | 300 | 99 | 12.0 (10.23) | Hypothetical protein | S. aureus φNM (2e−35) | 89 (94) | YP_874008.1 | Transmembrane region |
| 58 | 35643 | 37547 | 1,905 | 634 | 72.5 (9.78) | Hydrolase | S. aureus RF122 (0.0) | 99 (99) | YP_417168.1 | CHAP (PF05257) (1.5e−30); LYZ2 (SM00047) (1e−51) |
| 59 | 37660 | 39573 | 1,914 | 637 | 71.8 (6.48) | Tail fiber protein | S. aureus RF122 (0.0) | 99 (99) | YP_417167.1 | Collagen alpha chain (PTHR10499) (0.00037) |
| 60 | 39624 | 40061 | 438 | 145 | 15.6 (4.52) | Holin | S. aureus RF122 (7e−79) | 100 (100) | YP_417166.1 | Transmembrane regions Phage_holin_1 (PF04531) (9.1e−50) |
| 61 | 40042 | 41487 | 1,446 | 481 | 53.7 (8.71) | Amidase | S. aureus RF122 (0.0) | 100 (100) | YP_417165.1 | Amidase_2 (PF01510) (2.5e−38); SH3b (SM00287) (1.4e−12); CHAP (PF05257) (4.7e−47) |
a
ID, identifier; HTH, helix-turn-helix; PVL, Panton-Valentine leukocidin; SSB, single-stranded DNA binding protein.