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Table 3 Sequence analysis of the 10243 bp fragment further upstream of gtrIC cluster

From: Shigella flexneri serotype 1c derived from serotype 1a by acquisition of gtrIC gene cluster via a bacteriophage

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
  1. aThe position relative to the 10,244 bp fragment is indicated
  2. bNA, not applicable
  3. ’Partial open reading frame
  4. cOn the basis of nucleotide sequence homology, percentage and E-value of BlastN database search
  5. Note: all nt positions include the stop codon, while the aa length does not include the stop codon