Table 2.
Comparison of ΦSH19 proteins with those of Vi01 and SboM-AG3
| CDS | ΦSH19 coordinates & amino acid length | Predicted MW |
Pfam domain | Amino acid ID with Vi01 | Amino acid ID with SboM-AG3 |
|---|---|---|---|---|---|
| RIIA | 1-2742 (913) | 104,992 | None | 98% | 54% |
| RIIB | 2775-4358 (527) | 58,980 | None | 97% | 69% |
| Putative tail fibre | 5502-6311 (269) | 27,826 | Ig-like I-set domain (CL0011) | 86% | 86% |
| DNA topoisomerase II | 8523-10,436 (637) | 71,862 | HATPase c (CL0025) & DNA gyrase B | 96% | 90% |
| DNA topoisomerase II (medium subunit) | 10,357-11,769 (470) | 53,939 | DNA topoisomerase IV | 88% | 88% |
| Conserved uncharacterized protein | 13,309-13,929 (206) | 23,005 | Putative Macro domain of ADP-ribose binding module (CL0233) | 92% | 74% |
| DexA exonuclease | 14,263-14,895 (210) | 24,438 | None | 95% | 93% |
| dCMP deaminase | 18,704-19,225 (173) | 19,460 | dCMP cytosine deaminase 1 family-cytidine & deoxycytidylate deaminase Zn-binding domain (CL0109) | 97% | 62% |
| Conserved uncharacterized protein | 19,227-19,634 (135) | 15,378 | Bacterial membrane-flanked domain (DUF304) | 93% | 88% |
| Head completion protein | 19,845-20,465c (206) | 24,189 | None | 92% | 74% |
| Putative homing endonuclease | 20,465-21,205c (246) | 28,205 | GIY-YIG catalytic domain (CL0418) | No match | 34% |
| T4-like baseplate tail tube cap | 21,259-22,227 (322) | 36,142 | T4 tail cap family | 100% | 94% |
| Baseplate wedge subunit | 22,240-22,797 (185) | 21,574 | Phage Gp53 family | 97% | 80% |
| Loader of T4-like helicase | 26,134-26,796c (220) | 26,253 | T4 helicase N family | 99% | 79% |
| DNA ligase | 27,281-28,708c (475) | 53,501 | ATP-dependent DNA ligase domain (CL0078) | 95% | 83% |
| DNA primase-helicase subunit | 31,451-32,875c (474) | 54,192 | DnaB-like helicase N & C terminal domains | 98% | 88% |
| UvsX (RecA-like protein) | 33,189-34,274c (361) | 40,791 | RecA bacterial DNA recombination proteins (CL0023) | 72% | 78% |
| dUTPase | 34,789-35,340c (183) | 21,114 | dUTPase 2 family(CL0231) | 69% | 63% |
| Thymidylate synthase | 35,903-36,943c (346) | 39,216 | Thymidylate synthase family | 93% | 77% |
| DNA end protector | 39,924-40,268c (234) | 28,347 | None | 100% | 91% |
| Baseplate tail tube | 40,488-41,624 (378) | 42,658 | Phage T4 Gp19 family | 98% | 90% |
| ssDNA binding protein | 41,652-42,683c (343) | 38,896 | Gp3 DNA binding protein-like domain | 98% | 77% |
| Late promoter transcription factor | 43,029-43,331c (100) | 11,175 | None | 100% | 70% |
| Regulatory protein (FmdB family) | 43,264-43,509c (81) | 8732 | CXXC CXXC SSSS family containing a Zn ribbon domain (CL0167) | 96% | 88% |
| Putative uncharacterized protein | 43,875-44,396c (203) | 23,739 | RuvC family (crossover junction endoribonuclease RuvC) | 100% | 83% |
| Baseplate hub subunit | 45,471-46,274 (267) | 30,186 | T4 baseplate family | 96% | 67% |
| Tail-associated lysozyme | 46,781-48,406 (541) | 59,023 | Gp5 OB family & CHAP domain (CL0125) associated with peptidoglycan hydrolysis | 98% | 87% |
| Baseplate wedge protein | 48,471-48,851 (126) | 14,124 | GPW Gp25 family (gene 25-like lysozyme) | 97% | 87% |
| NrdB | 50,229-51,332c (367) | 42,209 | Ribonucleotide reductase small chain domain (CL0044) | 99% | 89% |
| NrdA | 51,403-53,730c (775) | 88,137 | ATP-cone domain, ribonucleotide reductase IgN all alpha domain & IgC barrel domain | 94% | 89% |
| PhoH-like phosphate starvation-inducible protein | 53,764-54,603c (279) | 31,567 | PhoH-like protein family (CL0023) | 100% | 88% |
| Peptidoglycan binding protein | 54,711-55,505c (264) | 28,815 | Peptidoglycan binding protein domain (CL0244) & protein of unknown function (DUF3380) | 98% | 86% |
| DNA primase subunit | 56,712-57,776c (354) | 41,386 | None | 97% | 77% |
| Conserved uncharacterized protein | 63,656-64,273c (205) | 22,902 | T4 RegB endoribonuclease family (CL0037) | 98% | 79% |
| NrdA.1 | 64,978-65,313c (336) | 12,934 | None | 94% | 92% |
| Recombination endonuclease subunit | 65,622-67,955c (777) | 88,531 | None | 98% | 72% |
| Recombination protein subunit | 67,958-69,073c (371) | 43,030 | None | 98% | 91% |
| σ factor for late transcription | 69,060-69,854c (264) | 30,775 | None | 90% | 77% |
| Putative homing endonuclease | 69,854-70,576c (240) | 27,188 | None | No match | 36% |
| RNase H | 70,587-71,114c (175) | 19,878 | RNase H domain (CL0219) | 97% | 71% |
| ATP-dependent helicase | 71,921-73,522c (533) | 60,690 | None | 99% | 86% |
| DNA binding protein | 73,778-74,056c (92) | 9728 | Bacterial DNA-binding protein domain | 100% | 86% |
| Conserved uncharacterized protein | 74,140-74,931c (263) | 28,556 | SPFH domain/Band 7 family (CL0433) | 98% | No match |
| Superinfection exclusion protein | 75,137-75,457c (106) | 12,562 | None | 95% | No match |
| ImpD | 75,736-76,407c (223) | 25,665 | None | 95% | 74% |
| Acyl carrier protein | 80,335-80,687c (110) | 12,162 | Phosphoantetheine (PP)-binding family (CL0314) | 92% | 61% |
| Conserved uncharacterized protein | 84,506-84,925c (139) | 15,622 | Protein of unknown function (DUF3268) | 90% | 84% |
| Putative RegA translational repressor | 89,926-90,390c (154) | 18,078 | Bacteriophage translational regulator | 99% | 90% |
| Clamp loader for DNA polymerase | 90,420-90,842c (140) | 16,200 | None | 98% | 76% |
| Gp44 sliding clamp holder | 90,847-91,836c (329) | 37,214 | ATPase family (CL0023) | 99% | 87% |
| Gp45 sliding clamp holder | 91,914-92,582c (222) | 24,510 | Gp45 sliding clamp C terminal | 99% | 82% |
| Putative type III restriction enzyme (RE) | 93,293-94,792 (499) | 57,802 | Type III RE subunit (CL0023) & helicase conserved C terminal domain (CL0023) | 95% | 81% |
| Conserved uncharacterized protein | 94,822-95,568c (248) | 28,911 | PD-(D/E)XK nuclease superfamily | 97% | 86% |
| Putative UvsY | 95,568-96,023c (151) | 17,991 | UvsY protein family (recombination, repair, & ssDNA binding protein | 93% | 85% |
| Tail completion protein | 96,062-96,559c (165) | 18,542 | T4 Gp19 family | 98% | 80% |
| Major capsid protein | 101,588-102,910c (440) | 48,059 | Gp23 major capsid protein family | 98% | 94% |
| Prohead core scaffold protein | 103,002-103,841c (279) | 30,898 | None | 96% | 74% |
| Prohead protease | 103,888-104,556c (222) | 24,482 | Peptidase U9 family (CL0201) | 99% | 92% |
| Portal vertex protein of the head | 105,102-106,784c (560) | 63,094 | T4 Gp20 family | 99% | 81% |
| Tail tube protein | 106,852-107,385c (177) | 19,912 | T4 Gp19 family | 100% | 98% |
| GIY-YIG endonuclease | 107,416-107,874c (152) | 17,316 | GIY-YIG catalytic domain endonuclease family (CL0418) | 95% | 32% |
| Tail sheath protein | 107,933-109,828c (631) | 68,439 | Phage sheath 1 family | 98% | 92% |
| Large terminase subunit | 109,881-112,091c (736) | 84,547 | Terminase 6 family | 95% | 85% |
| Small terminase subunit | 112,072-112,752c (226) | 24,825 | DNA packaging family (terminase DNA packaging enzyme) | 98% | 74% |
| Proximal tail sheath stabilization | 112,755-113,453c (232) | 26,979 | None | 98% | 80% |
| Gp14 neck protein | 113,456-114,097c (213) | 24,759 | T4 neck protein family | 100% | 82% |
| Gp13 neck protein | 114,400-115,209c (269) | 31,142 | None | 99% | 87% |
| Tail spike 1 | 120,710-122,641c (643) | 68,851 | None | 67% (res. 1-171 only) | 62% (res. 1-190 only) |
| Tail spike 2 | 122,702-124,876c (724) | 78,194 | Pectate lyase C (CL0268) | 86% (res. 1-276 only) | 73% (res. 1-161 only) |
| Tail spike 3 | 124,992-127,088c (698) | 75,785 | P22 tail spike family | 86% (res. 1-154 only) | 46% (res. 1-179 only) |
| Haemolysin-type calcium binding protein | 127,168-130,209c (1013) | 108,436 | None | 81% (res. 1-418 only) | 63% (res. 1-404 only) |
| Baseplate wedge subunit | 132,287-134,080c (597) | 66,068 | None | 98% | 79% |
| DNA polymerase | 145,442-148,438 (998) | 116,583 | DNA polymerase family B exonuclease domains (CL0194 & CL0219) | 98% | 86% |
| Putative uncharacterized protein | 148,776-149,615 (279) | 32,346 | NT5C family 5' nucleotidase deoxypyrimidine (CL0137) | 97% | 80% |