Table 3 Sequence analysis of the 10243 bp fragment further upstream of gtrIC cluster
ORF (gene name) or feature | Nt positiona | Gene size (bp) | No of amino acids encoded | Database search results | ||||
|---|---|---|---|---|---|---|---|---|
Feature or protein (Saiz, aa) | Source (accession no.) | Identity (%) | Positive (%) | BlastP E value | ||||
orf 1’ (ndpA or yejK) | Complement (1..332) | 332 of 1007 | 111 | Nucleoid-associated protein ndpA (335aa) | Shigella flexneri K-272 (EGK22467.1) | 110/110 (100 %) | 110/110 (100 %) | 7e-72 |
DNA-associated protein (335aa) | Escherichia coli BL21(DE3)(YP_002999856.1) | 110/110 (100 %) | 110/110 (100 %) | 8e-72 | ||||
Nucleoid-associated protein NdpA (335aa) | Shigella boydii Sb227 (YP_408543.1) | 110/110 (100 %) | 110/110 (100 %) | 8e-72 | ||||
Shigella boydii CDC 3083-94 | ||||||||
Nucleoid-associated protein YejK (335aa) | (YP_001879481.1) | 110/110 (100 %) | 110/110 (100 %) | 8e-72 | ||||
orf 2 | 331..477 | 147 | 48 | Hypothetical prot. HMPREF9346_02485, (48aa) | Escherichia coli MS 119–7 (ZP_07102777.1) | 48/48 (100 %) | 48/48 (100 %) | 7e-26 |
Hypothetical prot. HMPREF9552_01955, (48aa) | Escherichia coli MS 198-1(ZP_07116146.1) | 48/48 (100 %) | 48/48 (100 %) | 7e-26 | ||||
Hypothetical prot. HMPREF9547_02658, (48aa) | Escherichia coli MS 175–1 (ZP_07169115.1) | 48/48 (100 %) | 48/48 (100 %) | 7e-26 | ||||
Putative ABC transporter permease protein,(303aa) | Streptomyces roseosporus | 13/25 (52 %) | 17/25 (68 %) | 8.6 | ||||
NRRL11379(ZP_04709202.1) | ||||||||
ABC transporter permease protein, (303aa) | Streptomyces roseosporus NRRL | 13/25 (52 %) | 17/25 (68 %) | 8.6 | ||||
15998(ZP_06584909.1) | ||||||||
ABC transporter permease protein (303aa) | Streptomyces roseosporus NRRL | 13/25 (52 %) | 17/25 (68 %) | 8.6 | ||||
15998 (EFE75370.1) | ||||||||
orf 3 | Complement (377..493) | 117 | 38 | Hypothetical prot. ECSTEC7V_2603, (54aa) | Escherichia coli STEC_7v (EGE64095.1) | 38/38 (100 %) | 38/38 (100 %) | 4e-19 |
hypothetical prot. EcE24377A_2485, (39aa) | Escherichia coli E24377A (YP_001463540.1) | 38/38 (100 %) | 38/38 (100 %) | 9e-19 | ||||
Hypothetical protein EcHS_A2325, (39aa) | Escherichia coli HS (YP_001458987.1) | 38/38 (100 %) | 38/38 (100 %) | 9e-19 | ||||
Hypothetical protein SbBS512_E077(39aa) | Shigella boydii CDC 3083–94 (YP_001879480.1) | 38/38 (100 %) | 38/38 (100 %) | 9e-19 | ||||
orf 4 (yejL) | 514..741 | 228 | 75 | yejL gene product (75aa) | Shigella flexneri 2a str. 301(NP_708086.1) | 75/75 (100 %) | 75/75 (100 %) | 5e-46 |
Hypothetical protein S2403(75aa) | Shigella flexneri 2a str. 2457 T (NP_837801.1) | |||||||
Hypothetical protein SFV_2265 (75aa) | Shigella flexneri 5 str. 8401 (YP_689686.1) | |||||||
orf 5 (yejM) | 761..2521 | 1761 | 586 (2 domains detected) | yejM gene product (586aa) | Shigella flexneri 2a str. 301(NP_708087.1) | 586/586 (100 %) | 586/586 (100 %) | 0.0 |
Sulfatase (586aa) | Shigella flexneri 2a str. 2457 T (NP_837802.1) | |||||||
yejM gene product (586aa) | Shigella flexneri 2002017 (YP_005727919.1) | |||||||
tRNA-Pro | 2596..2669 | 74 | NA | tRNA-Pro (74 bp) | Escherichia coli str. K-12 substr. W3110 (NC_007779.1) | 74/74 (100 %)c | NA | 1e-30c |
orf 6 | Complement (1838..2164) | 327 | 108 | No significant homology | ||||
orf 7 (int) | 2879..4123 | 1245 | 414 | Prophage integrase (413aa) | Shigella boydii CDC 3083–94 (YP_001879477.1) | 412/412 (100 %) | 412/412 (100 %) | 0.0 |
Prophage CP4-57 integrase (414aa) | Escherichia coli TX1999 (EGX23085.1) | 408/414 (99 %) | 410/414 (99 %) | 0.0 | ||||
integrase (414aa) | Escherichia coli 042 (YP_006096729.1) | 403/414 (97 %) | 409/414 (99 %) | 0.0 | ||||
orf 8 | 4398..4589 | 192 | 63 | Putative prophage regulatory protein (63aa) | Escherichia coli 042 (YP_006096730.1) | 59/63 (94 %) | 63/63 (100 %) | 4e-35 |
Hypothetical prot. SbBS512_E0760 (51aa) | Shigella boydii CDC 3083–94 (YP_001879474.1) | 49/51 (96 %) | 51/51 (100 %) | 2e-27 | ||||
Transcriptional regulator, AlpA family (68aa) | Escherichia coli 53638 (ZP_03002982.1) | 43/61 (70 %) | 52/61 (85 %) | 2e-24 | ||||
CP4-57 regulatory protein (AlpA) family protein (68aa) | Escherichia coli UMNF18 (AEJ57337.1) | 42/61 (69 %) | 52/61 (85 %) | 3e-24 | ||||
orf 9 | 4816..5412 | 597 | 198 [F + 1] | Putative prophage protein (198aa) | Escherichia coli 042 (YP_006096731.1) | 165/198 (83 %) | 171/198 (86 %) | 4e-114 |
Putative prophage protein (198aa) | Escherichia coli DEC7A (EHV77794.1) | 151/198 (76 %) | 163/198 (82 %) | 7e-100 | ||||
Immunity region (569aa) | Escherichia coli STEC_94C | 78/153 (51 %) | 96/153 (63 %) | 2e-34 | ||||
orf 10 | 5235..5423 | 189 | 62 [F + 3] | Hypothetical prot. SbBS512_E0759 (62aa) | Shigella boydii CDC 3083–94 (YP_001879473.1) | 62/62 (100 %) | 62/62 (100 %) | 1e-37 |
Hypothetical protein SFK315_2596 (62aa) | Shigella flexneri K-315 (EIQ20710.1) | 61/62 (98 %) | 61/62 (98 %) | 4e-36 | ||||
Conserved hypothetical protein (62aa) | Escherichia albertii TW07627 (ZP_02901801.1) | 50/62 (81 %) | 53/62 (85 %) | 3e-29 | ||||
orf 11 | 5416..5601 | 186 | 61 | Hypothetical prot. SbBS512_E0758 (61aa) | Shigella boydii CDC 3083–94 (YP_001879472.1) | 61/61 (100 %) | 61/61 (100 %) | 3e-35 |
Putative prophage protein (61aa) | Escherichia coli 042 (YP_006096732.1) | 60/61 (98 %) | 60/61 (98 %) | 5e-34 | ||||
orf 12 | complement (5536..5949) | 414 | 137 | Hypothetical prot. ECe0006 (95aa) | Escherichia coli (ABM53624.1) | 43/92 (47 %) | 54/92 (59 %) | 6e-18 |
Hypothetical prot. c1494(95aa) | Escherichia coli CFT073 (NP_753403.1) | 44/93 (47 %) | 55/93 (59 %) | 9e-18 | ||||
Hypothetical prot. SBO_2130 (95aa) | Shigella boydii Sb227 (YP_408537.1) | 42/92 (46 %) | 53/92 (58 %) | 2e-17 | ||||
orf 13 | 5641..5940 | 300 | 99 | Hypothetical prot. SbBS512_E0757 (99aa) | Shigella boydii CDC 3083–94 (YP_001879471.1) | 99/99 (100 %) | 99/99 (100 %) | 2e-67 |
Hypothetical prot. EcoM_00008 (99aa) | Escherichia coli WV_060327(EFW72294.1) | 76/99 (77 %) | 82/99 (83 %) | 1e-47 | ||||
Hypothetical bacteriophage prot.(99aa) | Escherichia coli H299 (ZP_08382870.1) | 75/99 (76 %) | 81/99 (82 %) | 6e-47 | ||||
Hypothetical bacteriophage prot.(99aa) | Shigella dysenteriae 1012 (ZP_03066472.1) | 72/99 (73 %) | 79/99 (80 %) | 1e-44 | ||||
Bacteriophage protein (99aa) | Shigella flexneri 2a str. 301(NP_707045.1) | 67/99 (68 %) | 78/99 (79 %) | 1e-41 | ||||
orf 14 | 5937..8072 bacteriophage P4-DNA primease | 2136 | 711 | Hypothetical prot. SbBS512_E0756 (711aa) | Shigella boydii CDC 3083–94 (YP_001879470.1) | 711/711 (100 %) | 711/711 (100 %) | 0.0 |
Hypothetical prot. SFK315_2598 (711aa) | Shigella flexneri K-315 (EIQ20712.1) | 674/709 (95 %) | 691/709 (97 %) | 0.0 | ||||
Putative prophage protein(712aa) | Escherichia coli 042 (YP_006096734.1) | 630/712 (88 %) | 658/712 (92 %) | 0.0 | ||||
Putative prophage DNA primase (711aa) | Escherichia coli DEC7A,C,D,E, EPECa12(EHV77797.1,86415.1, 91550.1, EHW01270.1 EIQ62754.1) | 621/711 (87 %) | 652/711 (92 %) | 0.0 | ||||
DNA Primease, phage-associated (713aa) | Escherichia coli PA5 (ZP_02787536.1) | 563/713 (79 %) | 618/713 (87 %) | 0.0 | ||||
Putative prophage primase (693aa) | Escherichia coli 042 (YP_006096469.1) | 520/693 (75 %) | 579/693 (84 %) | 0.0 | ||||
orf 15’ | 8309..8500 | 192 | 64 | Putative single stranded DNA-binding protein (141aa) | Shigella boydii CDC 3083–94 (YP_001879469.1) | 64/64 (100 %) | 64/64 (100 %) | 3e-38 |
Putative single stranded DNA-binding protein of prophage (136aa) | Escherichia coli IAI39 (YP_002407987.1) | 59/64 (92 %) | 62/64 (97 %) | 9e-35 | ||||
Putative single-strand DNA binding prophage protein (141aa) | Escherichia coli 042 (ref|YP_006096735.1) | 60/64 (94 %) | 62/64 (97 %) | 1e-34 | ||||
orf 16 | 8580..8846 | 267 | 88 | transposase (88aa) | Escherichia coli CFT073 (NP_754364.1) | 86/88 (98 %) | 88/88 (100 %) | 2e-55 |
transposase (88aa) | Escherichia coli UTI89 (YP_541223.1) | 86/88 (98 %) | 86/88 (98 %) | 86/88 (98 %) | ||||
IS1400 transposase A (88aa) | Escherichia coli 536 (YP_669883.1) | |||||||
trp1400A gene product (95aa) | Erwinia billingiae Eb661(YP_003743077.1) | 81/88 (92 %) | 87/88 (99 %) | 3e-52 | ||||
IS1400 transposase A (95aa) | Yersinia enterocolitica subsp. enterocolitica 8081 (YP_001004058.1) | 80/88 (91 %) | 86/88 (98 %) | 6e-52 | ||||
orf 17 | 9212..9691 | 480 | 159 | Insertion element IS407 family protein(159aa) | Escherichia coli MS 107–1 (ZP_07096798.1) | 151/159 (95 %) | 156/159 (98 %) | 8e-109 |
transposase B (182aa) | Edwardsiella ictaluri 93–146 (YP_002932372.1) | 151/159 (95 %) | 152/159 (96 %) | 7e-108 | ||||
Integrase core domain-containing protein (236aa) | Escherichia fergusonii B253 (EGC09228.1) | 151/159 (95 %) | 156/159 (98 %) | 2e-107 | ||||
InsK (207aa) | Salmonella enterica subsp. enterica serovar Montevideo str. SARB31 (EHL38295.1) | 150/159 (94 %) | 155/159 (97 %) | 1e-106 | ||||
Transposase B (233aa) | Salmonella enterica subsp. enterica serovar Kentucky str. CDC 191 (ZP_03224077.1) | 151/159 (95 %) | 156/159 (98 %) | 2e-106 | ||||
IS1400 transposase B (159aa) | Escherichia coli 536 (YP_669884.1) | 148/159 (93 %) | 152/159 (96 %) | 2e-106 | ||||
orf 18 | 8580..9691 | 1112 | 370 | Putative transposase (370aa) | Salmonella enterica subsp. VII (CAX68025.1) | 351/370 (95 %) | 358/370 (97 %) | 0.0 |
Transposase (370aa) | Salmonella enterica subsp. enterica serovar Enteritidis str. P125109 (YP_002244693.1) | 350/370 (95 %) | 352/370 (95 %) | 0.0 | ||||
Transposase (370aa) | Salmonella enterica subsp. enterica serovar Gallinarum str. 287/91 (YP_002227530.1) | 349/370 (94 %) | 349/370 (94 %) | 0.0 | ||||
Orf19 | Complement (8843..9217) | 375 | 122 | Hypothetical prot. HMPREF9345_01631(122aa) | Escherichia coli MS 107–1 (ZP_07096799.1) | 108/122 (89 %) | 115/122 (94 %) | 1e-74 |
Hypothetical protein UUU_27350 (124aa) | Klebsiella pneumoniae subsp. pneumoniae DSM 30104 (EJK89616.1) | 100/124 (81 %) | 111/124 (90 %) | 5e-68 | ||||
orf 20’ | 10055..10156 | 102 | 34 | Transposase family protein (63aa) | Shigella flexneri J1713 (gb|EGM62085.1) | 34/34 (100 %) | 34/34 (100 %) | 1e-15 |
Transposase IS3/IS911 (40aa) | Shigella flexneri K-218 (EGK22768.1) | 34/34 (100 %) | 34/34 (100 %) | 1e-15 | ||||
ISEhe3 orfA (71aa) | Shigella sonnei 53G (YP_005457329.1) | 34/34 (100 %) | 34/34 (100 %) | 1e-15 | ||||
ISEhe3 orfA (92aa) | Shigella flexneri 5 str. 8401 (YP_688117.1) | 34/34 (100 %) | 34/34 (100 %) | 2e-15 | ||||
ISEhe3 orfA (92aa) | Shigella flexneri 2a str. 2457 T (NP_836231.1) | 34/34 (100 %) | 34/34 (100 %) | 2e-15 | ||||
orf 21’ | 10157..10243 | 87 | NA | Insertion sequence IS911 (1250 bp)c | Shigella dysenteriae (X17613.1) | 86/87 (99 %)c | NA | 2e-35c |