TABLE 1.

Regions of homology in the SM1 genome

ORFStartStopMWpIPutative functionBest matcha,bOther BLAST homologiesb
1123010343.69.4IntegraseIntegrase, S. pneumoniae phage MM1, CAB96616 (79%) L. lactis phage bIL312, NP_076801 (38%); S. pyogenes M1 GAS, NP_269567 (35%); S. agalactiae 2603V/R phage LambdaSa1, NP_687574 (37%)
21791135116.510.7 L. lactis phage TPW22, AAF12708 (72%) Clostridium acetobutylicum, NP_348535 (53%)
32184180415.05.6 S. pyogenes MGAS315, NP_665260 (45%) S. pyogenes phage φNIH1.1, NP_438116 (44%); S. agalactiae 2603V/R, NP_688872 (44%); S. pneumoniae phage MM1, NP_150135 (38%)
42541218813.34.9RepressorRepressor, S. pneumoniae MM1 NP_150136 (55%) S. pyogenes MGAS315, NP_664488 (50%); S. pyogenes MGAS8232, NP_606594 (50%); S. agalactiae 2603V/R phage LambdaSa2, NP_688871 (50%); Listeria innocua phage A118, NP_471937 (46%); S. pyogenes phage φNIH1.1, NP_438117 (44%); Listeria monocytogenes phage 2389, NP_511010 (44%); Enterococcus faecalis V583, NP_816474 (44%)
5282929574.86.2
6297231848.25.1
73840316026.16.3
8389541047.88.7RepressorCro homolog S. agalactiae 2603V/R, NP_688867 (80%) S. pyogenes phage 315.1, NP_664490 (50%); S. pyogenes MGAS8232, NP_606596 (50%)
9410843057.35.1
10431644685.74.5
115081442225.35.7 S. pyogenes SSI-1, NP_802143 (60%). S. pyogenes MGAS315, NP_664778 (60%)
12513853688.86.4
13539055185.05.0
146158548126.15.4 S. pyogenes MGAS8232, NP_607411 (37%)
156213693227.25.9AntirepressorAntirepressor protein, S. agalactiae 2603V/R phage LambdaSa2, NP_688866 (77%) S. pyogenes MGAS8232, AAL97097 (72%); N. gonorrhoeae, CAC28354 100% identity over the first 128 amino acids
167015728710.69.4 S. pneumoniae phage MM1, NP_150139 (82%)
177337759410.15.4 S. thermophilus phage Sfi21, NP_597801 (41%)
187610803816.64.8
198058885530.66.0Replication initiationDnaD homolog, C. acetobutylicum, NP_348556 (60%) S. aureus phage phi 11, NP_803268 (49%); Orf 20 S. aureus phage φPV83, NP_061610 (45%)
20884390015.85.1
218995976529.85.8HelicaseDnaC homolog orf 5, S. thermophilus phage 7201, NP_038305 (43%)Orf 12 L. lactis phage rlt, NP_695040 (36%); DnaC L. lactis phage bIL309, NP_076710 (33%); DnaC L. lactis phage bIL286, NP_076651 (33%)
22101121058518.05.6 E. faecalis V583, NP_817053 (47%)lin1252, L. innocua, NP_470589 (46%); S. pyogenes phage 315.3, NP_664935 (43%)
23105851194354.39.7lin1253, L. innocua, NP_470590 (41%) S. pyogenes phage 315.3, NP_664934 (40%); E. faecalis V583, NP_817052 (37%)
24119631228912.34.4 S. pneumoniae phage MM1, NP_150152 (80%)
25123231258310.24.2
26125801292113.48.7Potential HNH nuclease Microbulbifer degradans 2-40, ZP_00066196 (50%)
27129181317810.09.4 S. thermophilus phage Sfi21, NP_597808 (37%) S. agalactiae 2603V/R, NP_688856 (37%); S. thermophilus phage DT1, NP_049431 (36%)
28131751359116.09.7
2913674139259.79.2 S. pneumoniae phage MM1, NP_758428 (73%) S. agalactiae 2603V/R, NP_688855 (69%); S. pyogenes phage MGAS8232, NP_607814 (60%); S. pyogenes phage φNIH1.1, NP_438130 (60%)
3013903140675.86.1—/PICK>
31140871451216.75.8 S. pyogenes phage 315.5, NP_665134 (52%) S. pyogenes phage φNIH1.1, NP_438135 (49%); S. pyogenes phage 315.2, NP_664754 (49%); S. thermophilus phage O1205, NP_695102 (43%)
32146251519121.89.5Integrase/recombinaseRecombinase S. pyogenes phage 315.1, NP_664508 (53%) S. pyogenes phage MGAS8232, NP_606615 (52%); site-specific recombinase, S. agalactiae 2603V/R phage LambdaSa2, NP_688849 (45%)
33150431574713.110.0Potential HNH nuclease S. pyogenes phage MGAS8232, NP_607557 (68%)Orf 3, L. lactis phage φ31, AAC39305 (68%); Orf 26, L. lactis phage rlt, NP_695054 (68%); S. pyogenes phage 315.3, NP_664927 (67%)
34159881722045.05.5ORF5, L. lactis phage φ31, AAC39307 (71%)Structural protein, L. lactis phage rlt, NP_695055 (70%); S. agalactiae 2603V/R, NP_687610 (64%); putative structural protein, S. pyogenes MGAS8232, NP_607555 (63%)
3517210184246.16.7 S. agalactiae 2603V/R, NP_687611 (66%) S. pyogenes MGAS8232, NP_607554 (52%); S. pyogenes SSI-1, NP_802006 (52%); Orf 28 L. lactis phage rlt, NP_695056 (48%); N. gonorrhoeae, AAD31039 (43%)
3618411185906.54.6 N. meningitidis Z2491, NP_283152 (74%)
3718753190049.59.2 E. faecalis V583, NP_815180 (51%)Lin0103, L. innocua, NP_469449 (50%); L. lactis phage ul36, NP_663675 (40%)
38190682044751.76.0TerminaseTerminase (Orf 29), L. lactis phage rlt, NP_695057 (73%) S. pyogenes MGAS8232, NP_607550 (70%); putative terminase S. pyogenes phage 315.3, NP_664919 (70%); S. agalactiae 2603V/R, NP_687612 (68%)
39205972103116.15.0 S. agalactiae 2603V/R, NP_687613 (51%) S. pyogenes MGAS315, NP_664918 (50%); Orf 30, L. lactis phage rlt, NP_695058 (43%)
40210442194632.85.2Major capsid ProteinPutative structural protein, phage-associated S. pyogenes M1 GAS NP_269540 (62%)Putative structural protein, phage-associated S. pyogenes MGAS8232, NP_607548 (62%); structural protein L. lactis phage rlt, NP_695059 (55%); S. agalactiae 2603V/R phage LambdaSa1, NP_687614 (62%)
4121949221708.04.3 S. pyogenes, NP_269539 (38%)Orf 32, L. lactis phage rlt, NP_695060 (33%)
42221912258614.55.5ORF33, L. lactis phage rlt, NP_695061 (75%) S. pyogenes SSI-1, NP_802015 (70%); S. agalactiae 2603V/R, NP_687616 (68%); S. pyogenes MGAS315.2, NP_664915 (62%)
43225732291112.76.6ORF34, L. lactis phage rlt, NP_695062 (66%) S. pyogenes M1 GAS, NP_269537 (65%); S. agalactiae 2603V/R, NP_687617 (64%); S. pyogenes SSI-1, NP_802016 (63%)
4422904231408.610.1 S. pyogenes phage315.3, NP_664913 (62%) S. pyogenes MGAS8232, NP_607544 (62%); S. agalactiae 2603V/R, NP_687618 (62%); Orf 35 L. lactis phage rlt, NP_695063 (57)
45231412347612.65.2 S. pyogenes M1 GAS, NP_269535 (62%) S. pyogenes MGAS8232, NP_607543 (61%); Orf 36, L. lactis phage rlt, NP_695064 (61%)
46234922404319.45.0Major tail proteinStructural protein, S. agalactiae 2603V/R phage LambdaSa1, NP_687620 (62%)Structural protein, L. lactis phage rlt, NP_695065 (61%); putative structural protein, phage-associated S. pyogenes phage 315.3, NP_664911 (61%); putative structural protein, phage-associated S. pyogenes M1 GAS, NP_269534 (59%)
47240462435711.69.4 S. agalactiae 2603V/R, NP_687621 (50%) S. pyogenes M1 GAS, NP_269533 (48%); Orf 38, L. lactis phage rlt, NP_695066 (47%)
48243722475214.34.6 S. pyogenes phage 315.3, NP_664909 (55%) S. pyogenes M1 GAS, NP_269532 (55%); S. agalactiae 2603V/R, NP_687622 (53%); Orf 39, L. lactis phage rlt, NP_695067 (51%)
492475227775107.44.8Putative platelet binding protein PblA; tail tape measure protein S. agalactiae 2603V/R phage LambdaSa1, NP_687623 (57%) L. lactis phage rlt ORF40, NP_695068 (60%); S. pyogenes phage 315.3, NP_664908 (49%); tape measure protein, L. lactis bacteriophage TP901-1, NP_112708 (33%); putative tape measure protein, L. lactis phage rlt ORF 42, NP_695070 (30%)
50277752847026.18.4 S. pyogenes phage 315.3, NP_664907 (37%) S. pyogenes MGAS8232, NP_607535 (37%); S. pyogenes M1 GAS, NP_269530 (36%)
512846731655121.08.1Putative platelet binding protein Pb1B; tail fiber protein S. pyogenes MGAS8232, NP_607534 (43%) S. pyogenes phage 315.3, NP_664906 (43%); S. pyogenes M1 GAS, NP_269529 (43%)
5231652318617.74.9
53318513249824.14.8 S. pyogenes SSI-1, NP_802386 (30%) S. pyogenes phage 315.1, NP_664532 (30%); S. pyogenes MGAS8232, NP_606638 (37%)
54325153293115.68.8 S. agalactiae 2603V/R phage LambdaSa1, NP_688829 (37%) L. casei phage A2, NP_680498 (33%); S. pneumoniae phage Dp-1, CAB07984 (31%)
55329183325012.35.6HolinPutative holin, S. pneumoniae phage VO1, CAD35392 (84%)Putative holin 2, S. pneumoniae phage MM1, NP_150181 (75%); putative holin, S. agalactiae 2603V/R phage LambdaSa2, NP_688828 (65%); putative holin, S. pyogenes phage 315.5, NP_665111 (50%)
56332533414034.34.7Lysin N-Acetylmuramoyl-l-alanine amidase, S. pneumoniae phage Dp-1, CAB07986 (72%)Putative lysin, S. agalactiae 2603V/R phage LambdaSa1, NP_687631 (69%); S. agalactiae 2603V/R phage LambdaSa2, NP_688827 (68%)
  • a Dashes indicate no significant homologies.

  • b Numbers in parentheses indicate the percent identity.