TABLE 1.
Characteristics of ST104 ORFs and deduced proteins
| ORF | Gene | Directiona | Start position | Stop position | Product length (amino acids) | Function of deduced protein | Accession no. and sequence similarity | % Identityb |
|---|---|---|---|---|---|---|---|---|
| ORF1 | gtrc | − | 17 | 1474 | 485 | O-antigen conversion | AAF74999; glucosyl transferase, phage P22 (S. enterica) | 92 (485) |
| AAL15475; glucosyl transferase; phage ST64T (S. enterica) | 93 (485) | |||||||
| ORF2 | gtrB | − | 1464 | 2396 | 310 | O-antigen conversion | AAF75000; bactoprenol glucosyltransferase, phage P22 (S. enterica) | 99 (310) |
| AAL15476; bactoprenol glucosyltransferase, phage ST64T (S. enterica) | 100 (310) | |||||||
| ORF3 | gtrA | − | 2393 | 2755 | 120 | O-antigen conversion | AAF75001; translocase, phage P22 (S. enterica) | 100 (120) |
| AAL15477; translocase, phage ST64T (S. enterica) | 100 (120) | |||||||
| ORF4 | int | − | 3104 | 4267 | 387 | Integrase | AAF75002; integrase, phage P22 (S. enterica) | 97 (387) |
| AAL15478; integrase, phage ST64T (S. enterica) | 98 (387) | |||||||
| ORF5 | xis | − | 4144 | 4494 | 116 | Excisionase | AAF75003; excisionase, phage P22 (S. enterica) | 97 (116) |
| AAL15479; excisionase, phage ST64T (S. enterica) | 97 (116) | |||||||
| ORF6 | − | 4706 | 4990 | 94 | AAD25409; hypothetical protein, phage 933W (E. coli) | 97 (94) | ||
| ORF7 | − | 4983 | 5267 | 94 | BAA84361; hypothetical protein, prophagte VT2-Sa (E. coli) | 28 (73) | ||
| ORF8 | − | 5267 | 6058 | 263 | AAK28855; hypothetical protein, phage HK620 (E. coli) | 88 (130) | ||
| AAD25483; hypothetical protein, phage 933W (E. coli) | 38 (316) | |||||||
| AAF75008; Ead, phage P22 (S. enterica) | 47 (122) | |||||||
| AAF75006; Eaa, phage P22 (S. enterica) | 39 (78) | |||||||
| AAL15482; Eaa2, phage ST64T (S. enterica) | 37 (79) | |||||||
| ORF9 | − | 6128 | 6637 | 169 | AAK28856; hypothetical protein, phage HK620 (E. coli) | 49 (169) | ||
| AAF75010; Eae, phage P22 (S. enterica) | 62 (86) | |||||||
| ORF10 | − | 6634 | 6804 | 56 | AAK28857; hypothetical protein, phage HK620 (E. coli) | 75 (56) | ||
| AAN52173; ORF56; phage ST64 (S. enterica) | 89 (56) | |||||||
| AAF75011; ORF56, phage P22 (S. enterica) | 60 (55) | |||||||
| ORF11 | abc2 | − | 6815 | 7108 | 97 | Anti-RecBCD protein | AAF7512; anti-Rec protein Abc2, phage P22 (S. enterica) | 71 (97) |
| AAL15488; anti-Rec protein Abc2, phage ST64T (S. enterica) | 72 (97) | |||||||
| ORF12 | abc1 | − | 7155 | 7439 | 94 | Anti-RecBCD protein | AAF75013; anti-Rec protein Abc1, phage P22 (S. enterica) | 97 (94) |
| AAL15489; anti-Rec protein Abc1, phage ST64T (S. enterica) | 97 (94) | |||||||
| ORF13 | erf | − | 7439 | 8146 | 235 | Recombination protein | AAF75014; recombination protein Erf, phage P22 (S. enterica) | 75 (71) |
| AAL15490; ORF235, phage ST64T (S. enterica) | 95 (235) | |||||||
| ORF14 | arf | − | 8143 | 8286 | 47 | Recombination protein | AF217253; recombination protein Arf, phage P22 (S. enterica) | 87 (47) |
| ORF15 | kil | − | 8276 | 8464 | 62 | Unknown | AAF75016; Kil, phage P22 (S. enterica) | 78 (62) |
| ORF16 | c3 | − | 8445 | 8603 | 52 | Regulatory protein | AAF75017; regulatory protein C3, phage P22 (S. enterica) | 75 (52) |
| AAL15492; regulatory protein C3, phage ST64T (S. enterica) | 93 (45) | |||||||
| ORF17 | 17 | − | 8688 | 9002 | 104 | Superinfection exclusion protein | AAF75018; superinfection exclusion protein, phage P22 (S. enterica) | 91 (103) |
| AAL15493; superinfection exclusion protein, phage ST64T (S. enterica) | 99 (104) | |||||||
| ORF18 | − | 9278 | 9565 | 95 | AAF75020; ORF78, phage P22 (S. enterica) | 46 (48) | ||
| ORF19 | − | 9599 | 10243 | 214 | AAL15494; ORF232, phage ST64T (S. enterica) | 76 (213) | ||
| ORF20 | ral | − | 10327 | 10521 | 64 | Antirestriction protein | AAF75021; antirestriction protein Ral, phage P22 (S. enterica) | 96 (63) |
| AAL15495; antirestriction protein Ral, phage ST64T (S. enterica) | 98 (64) | |||||||
| ORF21 | sieB | + | 10735 | 11322 | 195 | Superinfection exclusion protein | AAF75022; superinfection protein, phage P22 (S. enterica) | 88 (192) |
| ORF22 | 24 | − | 11335 | 11637 | 100 | Antitermination protein | AAF75023; antitermination protein, phage P22 (S. enterica) | 98 (100) |
| AAL15496; antitermination protein, phage ST64T (S. enterica) | 96 (75) | |||||||
| ORF23 | − | 12244 | 13323 | 359 | CAB39294; hypothetical protein, phage 933W (E. coli) | 34 (357) | ||
| ORF24 | c2 | − | 13488 | 14177 | 229 | Regulatory protein | CAA34222; regularoty protein CI, phage HK022 (E. coli) | 41 (234) |
| ORF25 | cro | + | 14288 | 14503 | 71 | Antirepressor | AAD25431; regulatory protein Cro, phage 933W (E. coli) | 32 (61) |
| ORF26 | c1 | + | 14614 | 14895 | 93 | Transcriptional activator | AAL15499; regulatory protein C1, phage ST64T (S. enterica) | 100 (93) |
| AAF75026; transcriptional protein, phage P22 (S. enterica) | 49 (93) | |||||||
| ORF27 | + | 14930 | 15091 | 53 | AAf31131; gp53, phage HK97 (E. coli) | 100 (53) | ||
| ORF28 | 18 | + | 15078 | 15899 | 273 | DNA replication protein | AAF31132; gp54, prophage HK97 (E. coli) | 98 (273) |
| AAF75028; DNA replication protein, phage P22 (S. enterica) | 51 (259) | |||||||
| ORF29 | 12 | + | 15896 | 17272 | 458 | Helicase | AAF75029; helicase, phage P22 (S. enterica) | 98 (458) |
| ORF30 | + | 17269 | 17538 | 89 | BAA84311; ORF28, phage VT2-Sa (E. coli) | 95 (89) | ||
| ORF31 | ninB | + | 17612 | 18049 | 145 | Unknown | AAF75030; NinB, phage P22 (S. enterica) | 97 (145) |
| AAL15506; NinB, phage ST64T (S. enterica) | 46 (102) | |||||||
| ORF32 | ninD | + | 18046 | 18219 | 57 | Unknown | AAF75031; NinD, phage P22 (S. enterica) | 96 (57) |
| AAL15507; NinD, phage ST64T (S. enterica) | 96 (57) | |||||||
| ORF33 | ninE | + | 18186 | 18362 | 58 | Unknown | AAF75032; NinE, phage P22 (S. enterica) | 98 (58) |
| AAL15508; NinE, phage ST64T (S. enterica) | 98 (58) | |||||||
| ORF34 | ninX | + | 18359 | 18706 | 115 | Unknown | AAF75033; NinX, phage P22 (S. enterica) | 57 (125) |
| AAL15509; NinX, phage ST64T (S. enterica) | 100 (115) | |||||||
| ORF35 | ninF | + | 18699 | 18875 | 58 | Unknown | AAF75034; NinF, phage P22 (S. enterica) | 96 (58) |
| AAL15510; NinF, phage ST64T (S. enterica) | 85 (57) | |||||||
| ORF36 | ninG | + | 18868 | 19479 | 203 | Unknown | AAF75035; NinG, phage P22 (S. enterica) | 94 (203) |
| ORF37 | ninY | + | 19476 | 19700 | 74 | Unknown | AAF75036; NinY, phage P22 (S. enterica) | 97 (74) |
| ORF38 | ninH | + | 19697 | 19900 | 67 | Unknown | AAF75037; NinH, phage P22 (S. enterica) | 98 (67) |
| AAL15514; NinH, phage ST64T (S. enterica) | 98 (67) | |||||||
| ORF39 | ninZ | + | 19881 | 20060 | 59 | Unknown | CAA55166; NinZ, phage P22 (S. enterica) | 89 (59) |
| AAL15515; NinZ, phage ST64T (S. enterica) | 93 (59) | |||||||
| ORF40 | 23 | + | 20057 | 20830 | 257 | Antitermination protein | AAG55478; antitermination protein, phage CP-933W (E. coli) | 43 (272) |
| AAA96595; antitermination protein, phage lambda (E. coli) | 42 (256) | |||||||
| AAF75038; antitermination protein, phage P22 (S. enterica) | 39 (256) | |||||||
| ORF41 | 13 | + | 21261 | 21464 | 67 | Holin | CAA09709; holin, phage PS119 (S. enterica) | 100 (67) |
| ORF42 | 19 | + | 21436 | 21939 | 167 | Lysozyme | CAA09710; lysozyme, phage PS119 (S. enterica) | 100 (167) |
| AAF75040; lysozyme, phage P22 (S. enterica) | 35 (131) | |||||||
| ORF43 | 15 | + | 21936 | 22403 | 155 | Endopeptidase | CAA09711; endopeptidase, phage PS119 (S. enterica) | 100 (155) |
| AAF75041; endopeptidase, phage P22 (S. enterica) | 55 (156) | |||||||
| AAL15519; endopeptidase, phage ST64T (S. enterica) | 39 (151) | |||||||
| ORF44 | + | 22156 | 22362 | 68 | BAB34244; putative lipoprotein precursor (E. coli) | 95 (68) | ||
| ORF45 | + | 22616 | 23146 | 176 | CAA33655; KilA, phage P1 (E. coli) | 31 (104) | ||
| ORF46 | + | 23369 | 23611 | 80 | AAL15520; ORF118, phage ST64T (S. enterica) | 100 (80) | ||
| AAF7506; ORF80, phage P22 (S. enterica) | 42 (80) | |||||||
| AAK28888; HkbM, prophage HK620 (E. coli) | 43 (80) | |||||||
| ORF47 | + | 23615 | 24004 | 129 | AAL15521; ORF129, phage ST64T (S. enterica) | 100 (117) | ||
| ORF48 | + | 24004 | 24408 | 134 | AAL15522; ORF134, phage ST64T (S. enterica) | 100 (134) | ||
| ORF49 | 3 | + | 24412 | 24900 | 162 | Terminase (small subunit) | AAF75043; terminase small subunit, phage P22 (S. enterica) | 96 (162) |
| AAL11524; terminase small subunit, phage ST64T (S. enterica) | 100 (162) | |||||||
| ORF50 | 2 | + | 24878 | 26377 | 499 | Terminase (large subunit) | AAF75044; terminase large subunit, phage P22 (S. enterica) | 99 (441) |
| AAL15523; terminase large subunit, phage ST64T (S. enterica) | 99 (499) | |||||||
| ORF51 | 1 | + | 26377 | 28554 | 725 | Portal protein | AAF75045; portal protein, phage P22 (S. enterica) | 98 (705) |
| AAL15525; portal protein, phage ST64T (S. enterica) | 99 (725) | |||||||
| ORF52 | 8 | + | 28568 | 29479 | 303 | Scaffolding protein | AAF75046; scaffolding protein, phage P22 (S. enterica) | 99 (303) |
| AAL15526; scaffolding protein, phage ST64T (S. enterica) | 99 (303) | |||||||
| ORF53 | 5 | + | 29479 | 30771 | 430 | Coat protein | AAF75047; coat protein, phage P22 (S. enterica) | 99 (430) |
| AAL15527; coat protein, phage ST64T (S. enterica) | 100 (430) | |||||||
| ORF54 | + | 30812 | 31372 | 186 | AAL15528; ORF186, phage ST64T (S. enterica) | 95 (186) | ||
| AAF75048; ORF69, phage P22 (S. enterica) | 36 (44) | |||||||
| ORF55 | 4 | + | 31356 | 31856 | 166 | DNA stabilization | AAF75049; DNA-stabilizing protein, phage P22 (S. enterica) | 99 (166) |
| AAL15529; DNA-stabilizing protein, phage ST64T (S. enterica) | 96 (166) | |||||||
| ORF56 | 10 | + | 31816 | 33234 | 472 | Packaged DNA stabilization | AAF75050; packaged DNA stabilization protein, phage P22 (S. enterica) | 95 (472) |
| AAL15530; packaged DNA stabilization protein, phage ST64T (S. enterica) | 98 (472) | |||||||
| ORF57 | 26 | + | 33238 | 33939 | 233 | Packaged DNA stabilization | AAF75051; packaged DNA stabilization protein, phage P22 (S. enterica) | 80 (233) |
| AAL15531; packaged DNA stabilization protein, phage ST64T (S. enterica) | 54 (233) | |||||||
| ORF58 | 14 | + | 33939 | 34394 | 151 | Unknown | AAF75052; gp14, phage P22 (S. enterica) | 92 (151) |
| AAL15532; gp14, phage ST64T (S. enterica) | 98 (151) | |||||||
| ORF59 | 7 | + | 34397 | 35086 | 229 | DNA transfer protein | AAF75053; DNA transfer protein, phage P22 (S. enterica) | 96 (229) |
| AAL15533; DNA transfer protein, phage ST64T (S. enterica) | 61 (230) | |||||||
| ORF60 | 20 | + | 35097 | 36533 | 478 | DNA transfer protein | AAF75054; DNA transfer protein, phage P22 (S. enterica) | 78 (495) |
| AAL15534; DNA transfer protein, phage ST64T (S. enterica) | 58 (449) | |||||||
| ORF61 | 16 | + | 36533 | 38509 | 658 | DNA transfer protein | AAL15535; DNA transfer protein, phage ST64T (S. enterica) | 100 (658) |
| AAF75055; DNA transfer protein, phage P22 (S. enterica) | 31 (618) | |||||||
| ORF62 | + | 38642 | 38941 | 99 | ZP00032952; hypothetical protein (Burkholderia fungorum) | 42 (87) | ||
| ORF63 | mnt | − | 38962 | 39210 | 82 | Regulatory protein | AAL15536; regulatory protein, phage ST64T (S. enterica) | 100 (82) |
| AAF75057; regulatory protein, phage P22 (S. enterica) | 60 (81) | |||||||
| ORF64 | 9 | + | 39346 | 41349 | 667 | Tailspike protein | AAF75060; tailspike protein, phage P22 (S. enterica) | 98 (667) |
| AAL15537; tailspike protein, phage ST64T (S. enterica) | 99 (667) |
a
A plus sigin indicates rightward orientation of the gene, and a minus sign indicates leftward orientation of the gene.
b
Each value in parentheses is the number of amino acids from which the sequence identity is calculated. The GenBank database was used for homology searches.