TABLE 1.

Analysis of predicted ORFs and proteins of SfV

>ORF (gene name)Gene coordinates and orientationGene productFunction (reference[s])Related phage and bacterial proteins
Size (aa)Molecular mass (kDa)pIdProtein(s) (size and origin)GenBank accession no.BlastP e value (% positives)c
168→56216417.910.4Small terminase subunitHypothetical protein Z1853 (118 aa: E coli O157:H7 prophage CP-933C)AE0053281e-10 (59)
Hypothetical protein (159 aa; Bacteriophage GMSE-1)AF3116591e-10 (46)
ORF9 (122 aa; H. influenzae)AF1982569e-10 (54)
2559→229257765.35.3Large terminase subunitYmfN (455 aa; E. coli)AE0002140.0 (97)
Terminase large subunit (563 aa; Pseudomonas phage D3)AF165214e-135 (62)
Terminase large subunit ECs1598 (553 aa; E. coli O157:H7)AP0025557e-67 (48)
32392→366642448.37.9Portal proteinORF25 (416 aa; Bacillus phage phi-105)AB0162827e-51 (55)
Phage phi-105 ORF25-like protein (ORF25 410 aa; H. influenzae)AF1982562e-37 (50)
Putative portal protein MIr8522 (410 aa; Mesorhizobium loti)AP0030142e-36 (50)
Putative portal protein ECs1592 (403 aa; E. coli O157:H7)AP0025551e-35 (47)
43659→426120022.74.9Capsid proteasePutative phage protein STM2236 (172 aa; S. enterica serovar Typhimurium LT2)AE0088007e-75 (90)
Putative protease ORF209 (209 aa); Lactobacillus casei bacteriophage A2AJ2517905e-24 (60)
Hypothetical protein Lin2577 (194 aa; Listeria innocua)AL5961725e-21 (54)
ORF41 (194 aa; phiPV83 prophage Staphylococcus aureus)AB0445542e-20 (55)
54272→650140945.85.1CapsidMajor capsid protein GP36 (392 aa; Bacteriophage phi-C31)AJ0065891e-14 (37)
Hypothetical protein CC2783 (341 aa; Caulobacter crescentus)AE0059436e-08 (38)
Phage major capsid protein GP36 (467 aa; Mesorhizobium loti)AP0030143e-06 (37)
65580→590310712.44.2UnknownHypothetical proteins Z1851 and ECs1594 (98 aa; E. coli O157:H7 prophages CP-933C and Sp7)aAE005328, AP00255552e-06 (48)
76014→63109811.47.9UnknownHypothetical protein 1752p (111 aa; Agrobacterium tumefaciens)AE0080261e-05 (42)
86285→679116819.712.6Unknown
96788→734818620.84.2Unknown
107357→7527566.410.1UnknownGp38 (67 aa; E. coli phage Mu)AF0839773e-06 (59)
Putative phage protein YPO1241 (64 aa; Yersinia pestis)AJ4141478e-06 (61)
117511→900749853.25.5Tail sheath proteinPutative phage tail sheath protein YPO1242 (502 aa; Yersinia pestis)AJ414147e-106 (60)
Mu-like tail sheath protein GpL (hypothetical protein HI1511, 487 aa; H. influenzae prophage)U328272e-80 (55)
Tail sheath protein GpL (490 aa; E. coli phage Mu)AF0839773e-72 (51)
129007→9363118UnknownHypothetical protein YPO1243 (122 aa; Yersinia pestis)AJ4141479e-10 (48)
139363→963289Unknown
149774→1160961165.310.0Tail proteinHypothetical protein STY4603 (926 aa; S. enterica subsp. enterica serovar Typhi)AL627283e-107 (56)
OrfG (396 aa; S. enterica subsp. enterica serovar Typhi)AF1538292e-52 (67)
Tape measure protein (937 aa; Lactococcus lactis phage TP901-1)AF2529675e-18 (39)
1511655→1299844748.55.6Tail/DNA circulation proteinDNA circulation protein (hypothetical protein HI1515; 455 aa; H. influenzae Rd prophage)U328272e-31 (46)
Putative DNA circulation protein ECs4983 (456 aa; E. coli O157:H7 prophage Sp16a [Mu-like])AP0025673e-21 (40)
Putative phage protein YPO1246 (468 aa; Yersinia pestis)AJ4141472e-19 (46)
DNA circulation protein N (64-kDa virion protein 495 aa; E. coli phage Mu)AF0839771e-16 (39)
1612995→1407435939.24.9Tail protein43-kDa tail protein P (379 aa; E. coli phage Mu)AF0839778e-45 (50)
Putative tail protein ECs4984 (374 aa; E. coli O157:H7 prophage Sp16a [Mu-like])AP0025674e-35 (44)
Putative phage tail protein YPO1247 (351 aa; Yersinia pestis)AJ4141472e-20 (44)
1714074→1462218219.66.5Tail protein (15)Putative phage baseplate assembly protein YPO1248 (198 aa; Yersinia pestis)AJ4141479e-17 (47)
Hypothetical protein ECs4985 (204 aa; E. coli O157:H7 prophage Sp16a [Mu-like])AP0025673e-14 (45)
Gp45 (197 aa; E. coli phage Mu)AF0839773e-12 (43)
1814622→1504714116.25.9Tail protein (15)Putative phage protein GP46 YPO1249 (151 aa; Yersinia pestis)AJ4141472e-13 (58)
Gp46 (145 aa; E. coli phage Mu)AF0839777e-12 (50)
Mu-like Gp46 protein (hypothetical protein HI1519; 135 aa; H. influenzae Rd)U328272e-10 (57)
1915034→1609235238.34.9Tail protein (15)YmfP (hypothetical protein b1152; 263 aa; E. coli prophage e14b)AE000214e-143 (96)
Mu-like Gp47 protein (hypothetical protein HI1520 355 aa; H. influenzae Rd prophage)U328275e-40 (46)
Hypothetical protein ECs4987 (361 aa; E. coli O157:H7 prophage Sp16a [Mu-like])AP0025671e-35 (43)
Gp47 (360 aa; E. coli phage Mu)AF0839773e-34 (44)
2016083→1666719421.64.9Tail protein (15)YmfQ (hypothetical protein b1153; 194 aa; E. coli prophage e14b)AE000214e-113 (98)
Putative phage protein YPO1251 (115 aa; Yersinia pestis)AJ4141471e-09 (49)
Hypothetical protein ECs4988 (186 aa; E. coli O157:H7 prophage Sp16a [Mu-like])AP0025671e-08 (42)
Hypothetical protein NMA1825 (188 aa; Neisseria meningitidis Z2491)AJ3912564e-08 (43)
Gp48 (180 aa; E. coli phage Mu)AF0839772e-07 (42)
2116671→1732121622.65.3UnknownOrf5′ (170 aa; S. flexneri cryptic prophage SfI)AF1395965e-92 (95)
YcfK (hypothetical protein b1154; 209 aa; E. coli prophage e14b)AE0002143e-53 (64)
YfdL (Hypothetical protein b2355; 172 aa; E. coli prophage KpLE1b)AE0003242e-37 (74)
Hypothetical protein Z0314 (236 aa; E. coli O157:H7 prophage CP-933H)AE0052031e-21 (59)
2217230→1773316718.94.6Tail fiber assembly proteinOrf4 (167 aa; Shigella flexneri cryptic prophage SfI)AF1395964e-85 (94)
Hypothetical protein P37 (155 aa; phage APSE-1)AF1578351e-18 (53)
Hypothetical protein YcdD (106 aa; S. enterica serovar Typhimurium)M553422e-12 (74)
Putative tail fiber assembly protein U (175 aa; E. coli phage Mu)AF0839773e-12 (75)
23 (gtrV)19111←1785841747.710.0Serotype-specific glucosyltransferase (4, 26, 27)GtrX (416 aa; S. flexneri bacterio phage SfX)L050019e-66 (55)
24 (gtrB)20031←1910830734.77.0Bactoprenol glucosyl; transferase (4, 26, 27)GtrBII (309 aa; S. flexneri phage SfII)AF021347e-170 (99)
GtrBI (306 aa; S. flexneri phage SfI)AF139596e-169 (98)
GtrBX (305 aa; S. flexneri phage SfX)AF056939e-167 (98)
GtrBIV (304 aa; S. flexneri prophage SfIV)AF288197e-163 (95)
Hypothetical protein b2351 (306 aa; E. coli prophage KpLE1b)AE000323e-162 (96)
25 (gtrA)20390←2002812013.210.4Flippase? (4, 26, 27)GtrAI (120 aa; S. flexneri phage SfI)AF1395964e-63 (99)
GtrAII (120 aa; S. flexneri phage SfII)AF0213475e-63 (99)
GtrAX (120 aa; S. flexneri phage SfX)AF0569391e-58 (94)
Hypothetical protein b2350 (120 aa; E. coli prophage KpLE1b)AE0003235e-58 (93)
26 (int)21815←2065238744.810.5Integrase (4, 26, 27)Int (387 aa; S. enterica serovar Typhimurium phage P22)AF2172530.0 (94)
Putative integrase Z0307 (324 aa; E. coli O157:H7 prophage CP-933H)AE005202e-177 (98)
Int (387 aa; E. coli prophage DLP12)AE000159e-168 (84)
27 (xis)22041→2169211613.010.2Excisionase (4, 26, 27)Xis, (116 aa; S. enterica serovar Typhimurium phage P22)AF2172531e-51 (89)
Xis (115 aa; E. coli strain 586)X166644e-18 (61)
Xis (115 aa; S. flexneri phage SfX)U820843e-17 (59)
2822347←2204210112.14.7UnknownHypothetical protein b2363 (101 aa; E. coli prophage KpLE1b)AE0003242e-51 (99)
Hypothetical protein ECs2756 (187 aa; E. coli O157:H7)AP0025593e-19 (78)
Hypothetical protein ECs1518 (195 aa; E. coli O157:H7 prophage CP-933N)AP0025553e-18 (76)
2922709←2234712013.74.6UnknownHypothetical protein b2362 (120 aa; E. coli prophage KpLE1b)AE0003242e-66 (97)
Hypothetical protein 1942p (226 aa; Agrobacterium tumefaciens)AE0080352e-12 (49)
Hypothetical protein CC1451 (250 aa; Caulobacter crescentus)AE0058191e-11 (46)
3023236←2270017820.35.1UnknownYfdR (hypothetical protein b2361 187 aa; E. coli prophage KpLE1b)AE0003241e-98 (99)
3124188←2336427430.54.8UnknownYfdQ (hypothetical protein b2360; 274 aa; E. coli prophage KpLE1b)AE000324e-150 (99)
Hypothetical protein XF1649 (273 aa; Xylella fastidiosa)AE0039912e-39 (56)
3224616←2425412013.15.9UnknownHypothetical protein b2359 (148 aa; E. coli prophage KpLE1b)AE0003241e-62 (99)
Hypothetical protein XF1650 (124 aa; Xylella fastidiosa)AE0039918e-17 (60)
3325513←252179811.24.9Unknown
34 (cl)26360←2568622425.16.7RepressorPutative repressor protein C2 (hypothetical protein b1145; 224 aa; E. coli prophage e14)AE000214e-131 (99)
Repressor protein cI (223 aa; Bordetella phage BP3p)AY0291858e-22 (48)
Repressor protein C2 (216 aa; S. enterica serovar Typhimurium phage P22)AF2172534e-16 (53)
35 (cro)26451→26651667.310.1RepressorHypothetical protein b1146 (165 aa; E. coli prophage e14)bAE0002149e-52 (94)
3626695→2724618320.14.7UnknownYmfL (hypothetical protein b1147; 189 aa; prophage e14)bAE0002148e-93 (93)
Orf33 (156 aa; Pseudomonas aeruginosa phage phi CTX)AB0085502e-04 (44)
3727243→2807927830.19.3Immunity regionHypothetical protein Orf179 (179 aa; S. flexneri)Z231018e-15 (58)
OrfB (118 or 119 aa; S. flexneri)Z231005e-11 (60)
Putative regulator/cI repressor Z0337 and ECs0300 (185 aa; E. coli O157:H7 prophages CP-9331 and Sp2 a [P4-like])AE005204 AP0025511e-09 (48)
3828072→28308788.911.4Unknown
3928305→2912327229.38.4Replication and originHypothetical protein Z1337 (400 aa; E. coli O157:H7 prophage CP-933M)AE0052884e-28 (49)
Hypothetical protein ECs1073 (363 aa; E. coli O157:H7)AP0025544e-28 (49)
YfdO (hypothetical protein b2358; 122 aa; E. coli prophage KpLE1b)AE0003242e-07 (87)
4029126→2961416218.710.5UnknownYfdM (hypothetical protein b2357; 164 aa; E. coli prophage KpLE b)AE0003241e-86 (96)
41 (dam)29614→3026721724.56.1DNA adenine methylase (Dam)YfdM (hypothetical protein b2356; 102 aa; E. coli prophage KpLE1b)AE0003244e-49 (100)
Putative DNA methyltransferase (hypothetical protein Z3349; 175 aa; E. coli O157:H7 prophage CP-933V)AE0054434e-05 (41)
ORF32 (175 aa; E. coli phage VT2-Sa)AP0003635e-05 (41)
Gp62 (175 aa; E. coli phage HK97)AF0695295e-05 (41)
4230264→3059010812.110.5Regulation?LexA repressor (205 aa; Providencia rettgeri), other LexA proteinsX709653e-13 (61)
4330587→3097612914.210.1Crossover junction endodeoxy ribonucleasePutative crossover junction endodeoxyribonuclease Z3115 and ECs2751 (119 aa; E. coli O157:H7 prophages CP-933U and Sp14 a [lambda-like])AE005421, AP0025591e-16 (58)
Putative endonuclease Z2057 and ECs1777 (119 aa; E. coli O157:H7 prophages CP-933O and Sp9 a [lambda-like])AE005344 AP0025563e-16 (54)
Putative endonuclease Z6061 and ECs2268 (119 aa; E. coli O157:H7 prophages CP-933P and Sp12 a [lambda-like])AE006460 AP0025571e-15 (56)
4430996→3180526930.29.6UnknownPhage-related protein XF2294 (242 aa; Xylella fastidiosa)AE0040418e-12 (50)
KilA (266 aa; E. coli phage PI)X156391e-10 (52)
Unknown protein HkbK (165 aa; E. coli phage HK620)AF3355382e-05 (46)
4531885→3280230534.57.4UnknownPutative cytoplasmic protein STM2240 (329 aa; S. enterica serovar Typhimurium LT2)AE008800e-163 (92)
Hypothetical protein b1560 (363 aa; E. coli)AE000253e-110 (68)
Hypothetical protein ECs2195 (360 aa; E. coli O157:H7 prophage Sp11 a)AP002557e-108 (68)
Hypothetical protein Z2100 (349 aa; E. coli O157:H7 prophage CP-933O)AE005347e-108 (68)
46 (Q)32816→3356825027.88.9Antitermination protein QPutative Q protein (hypothetical protein b1559, 260 aa; E. coli prophage Qin)AE000253e-137 (95)
Putative Q protein Z1345 and ECs1524 (273 aa; E. coli O157:H7 prophage CP-933M and Sp8 a)AE005288 AP0025556e-42 (54)
Putative antitermination protein STY1036 (265 aa; S. enterica subsp. enterica serovar Typhi)AL6272685e-34 (49)
4733818→34012647.45.0UnknownHypothetical protein Orf2 (65 aa; E. coli phage P27)AJ2493512e-27 (96)
Hypothetical protein Z2059 and ECs1779 (106 aa; E. coli O157:H7 prophages CP-933O and Sp9 a)AE005344 AP0025564e-27 (97)
Hypothetical protein Z2103 and ECs2192 (94/65 aa; E. coli O157:H7 prophages CP-933O and Sp1)aAE005347 AP0025573e-26 (96)
4834162→3521435040.38.6UnknownPutative Dam methylase Z2060 and ECs1780 (352 aa; E. coli O157:H7 prophage CP-933O and Sp9)aAE005344 AP0025561e-172 (90)
Hypothetical protein Orf3 (312 aa; E. coli phage P27)AJ249351e-155 (90)
Putative Dam methylase Gp52 (284 aa; E. coli phage N15)AF0645397e-81 (70)
49 (S)35291→3562611111.910.1HolinPutative bacteriophage protein STY2045 (113 aa; S. enterica subsp. enterica serovar Typhi)AL6272721e-53 (94)
Putative inner membrane protein STM2237 (109 aa; S. enterica serovar Typhimurium LT2)AE0088004e-37 (94)
Fels-1 prophage protein STM0906 (114 aa; S. enterica serovar Typhimurium LT2)AE0087383e-26 (65)
50 (R)35630→3610615817.710.0LysinPutative endolysin STY2044 (158 aa; S. enterica subsp. enterica serovar Typhi)AL6272721e-85 (97)
Putative endolysin Z1876 and ECs1622 (158 aa; E. coli O157:H7 prophages CP-933X and Sp8)aAE005330 AP0025551e-80 (94)
Lysin (158 aa; E. coli phage HK97)AF0695293e-79 (93)
Lysin (158 aa; E. coli phage HK022)AF0693084e-79 (93)
51 (Rz)36090→3648213014.59.2LysisPutative phage protein STY2043 (130 aa; Salmonella enterica subsp. enterica serovar Typhi)AL6272722e-53 (87)
Gp23 (119 aa; E. coli phage Mu)AF0839773e-06 (46)
Putative protein P14 (129 aa; phage APSE-1)AF1578352e-04 (44)
Hypothetical protein ECs4963 (85 aa; E. coli O157:H7 prophage Sp16a [Mu-like])AP0025670.005 (44)
52 (Rzl)36301→3663911212.410.6LysisPutative protein P16 (109 aa; phage APSE-1)AF1578356e-16 (66)
Hypothetical protein ECs4964 (148 aa; E. coli O157:H7 prophage Sp16a [Mu-like])AP0025673e-13 (54)
5336666→3701611613.110.7UnknownHypothetical protein Orf7 (116 aa; Xenorhabdus nematophilus)AJ1330221e-37 (70)
Hypothetical protein 19 (124 aa; Bacillus phage Phi-105)AB0162822e-12 (47)