Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 113552 |
| Name | oriT_pAR-0424-1  |
| Organism | Shigella flexneri strain AR-0424 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_CP044156 (77209..77560 [-], 352 nt) |
| oriT length | 352 nt |
| IRs (inverted repeats) | 192..198, 206..212 (TATAAAA..TTTTATA) 104..109, 119..124 (TTTAAA..TTTAAA) 93..98, 106..111 (GATTTA..TAAATC) 40..47, 50..57 (GCAAAAAC..GTTTTTGC) 4..11, 16..23 (TTGGTGGT..ACCACCAA) |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 352 nt
>oriT_pAR-0424-1
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACACTACGCAAAAACAAGTTTTTGCTGATTTATCTTTAATATCATTGAGTTGTATTTGTGGATTTATATTGTTTAAATCTGATTTTTTTAAAGCAGCGTCGTTAACGCAGCTACAGCAACGCGCCGACACCGCTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGTCAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCACTATGAATTCTAGTGTTTCGAAATTAACTTTGTTTTATGTTTAAAAAAGGTAATATCTA
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACACTACGCAAAAACAAGTTTTTGCTGATTTATCTTTAATATCATTGAGTTGTATTTGTGGATTTATATTGTTTAAATCTGATTTTTTTAAAGCAGCGTCGTTAACGCAGCTACAGCAACGCGCCGACACCGCTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGTCAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCACTATGAATTCTAGTGTTTCGAAATTAACTTTGTTTTATGTTTAAAAAAGGTAATATCTA
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
T4CP
| ID | 10041 | GenBank | WP_151106457 |
| Name | traD_F4V36_RS23800_pAR-0424-1 |
UniProt ID | _ |
| Length | 759 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 759 a.a. Molecular weight: 86492.44 Da Isoelectric Point: 5.2345
>WP_151106457.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Shigella]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILIGLVLWVKISWQTFINGCIYWWCTSLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVSTGKSEVIRRLANYAR
KRGDMVVIYDRSCEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNVANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVVSMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVLNTRAFFRSPSHQIA
EFAAGEIGEKEHLKASLQYSYGADPVRDGVSTGKEMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQTRPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEDVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPQQSQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPEEEM
EQQLPPGISESGEVVDMAAYEAWQQENHPDIQQHMQRREEVNINVHRERGEDVEPGDDF
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILIGLVLWVKISWQTFINGCIYWWCTSLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVSTGKSEVIRRLANYAR
KRGDMVVIYDRSCEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNVANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVVSMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVLNTRAFFRSPSHQIA
EFAAGEIGEKEHLKASLQYSYGADPVRDGVSTGKEMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQTRPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEDVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPQQSQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPEEEM
EQQLPPGISESGEVVDMAAYEAWQQENHPDIQQHMQRREEVNINVHRERGEDVEPGDDF
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
| ID | 10042 | GenBank | WP_000069772 |
| Name | traC_F4V36_RS23905_pAR-0424-1 |
UniProt ID | _ |
| Length | 876 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 876 a.a. Molecular weight: 99344.15 Da Isoelectric Point: 6.4096
>WP_000069772.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANKSIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAA
ATQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASFHGAKITTQTVDAQAFIEIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLNVRADYLTLGLRENGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPEMSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFKGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAGSPTIRSRLDEMIVLLDQY
TANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRTLKKLNVIDEGW
RLLDFKNRKVGEFIQKGYRTCRRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY
NQLFPDQFQPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRREG
LSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA
MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANKSIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAA
ATQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASFHGAKITTQTVDAQAFIEIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLNVRADYLTLGLRENGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPEMSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFKGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAGSPTIRSRLDEMIVLLDQY
TANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRTLKKLNVIDEGW
RLLDFKNRKVGEFIQKGYRTCRRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY
NQLFPDQFQPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRREG
LSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 48676..78131
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| F4V36_RS23800 | 48676..50955 | - | 2280 | WP_151106457 | type IV conjugative transfer system coupling protein TraD | prgC |
| F4V36_RS23805 | 51006..51743 | - | 738 | WP_012881122 | hypothetical protein | - |
| F4V36_RS23810 | 51946..52677 | - | 732 | WP_012881123 | conjugal transfer complement resistance protein TraT | - |
| F4V36_RS23815 | 52691..53200 | - | 510 | WP_000628111 | conjugal transfer entry exclusion protein TraS | - |
| F4V36_RS23820 | 53197..56022 | - | 2826 | WP_033807963 | conjugal transfer mating-pair stabilization protein TraG | traG |
| F4V36_RS23825 | 56019..57391 | - | 1373 | Protein_69 | conjugal transfer pilus assembly protein TraH | - |
| F4V36_RS23830 | 57378..57770 | - | 393 | WP_000659962 | F-type conjugal transfer protein TrbF | - |
| F4V36_RS23835 | 57751..58098 | - | 348 | WP_071571857 | P-type conjugative transfer protein TrbJ | - |
| F4V36_RS23840 | 58028..58572 | - | 545 | Protein_72 | type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB | - |
| F4V36_RS23845 | 58559..58843 | - | 285 | WP_000624107 | type-F conjugative transfer system pilin chaperone TraQ | - |
| F4V36_RS23850 | 58924..59259 | + | 336 | WP_001620807 | hypothetical protein | - |
| F4V36_RS23855 | 59240..59581 | - | 342 | WP_000556795 | conjugal transfer protein TrbA | - |
| F4V36_RS23860 | 59595..60338 | - | 744 | WP_001030371 | type-F conjugative transfer system pilin assembly protein TraF | traF |
| F4V36_RS23865 | 60331..60588 | - | 258 | WP_033807961 | conjugal transfer protein TrbE | - |
| F4V36_RS23870 | 60615..62519 | - | 1905 | WP_225620370 | type-F conjugative transfer system mating-pair stabilization protein TraN | traN |
| F4V36_RS23875 | 62755..63135 | - | 381 | WP_001462111 | hypothetical protein | - |
| F4V36_RS23880 | 63132..63770 | - | 639 | WP_033807960 | type-F conjugative transfer system pilin assembly protein TrbC | trbC |
| F4V36_RS23885 | 63779..64084 | - | 306 | WP_000224418 | hypothetical protein | - |
| F4V36_RS23890 | 64114..65106 | - | 993 | WP_000830849 | conjugal transfer pilus assembly protein TraU | traU |
| F4V36_RS23895 | 65103..65735 | - | 633 | WP_001203720 | type-F conjugative transfer system protein TraW | traW |
| F4V36_RS23900 | 65732..66118 | - | 387 | WP_000214084 | type-F conjugative transfer system protein TrbI | - |
| F4V36_RS23905 | 66115..68745 | - | 2631 | WP_000069772 | type IV secretion system protein TraC | virb4 |
| F4V36_RS23910 | 68871..69218 | - | 348 | WP_000836682 | hypothetical protein | - |
| F4V36_RS23915 | 69246..69464 | - | 219 | WP_033807959 | hypothetical protein | - |
| F4V36_RS23920 | 69563..70036 | - | 474 | WP_033807958 | hypothetical protein | - |
| F4V36_RS23925 | 70029..70442 | - | 414 | WP_000549589 | hypothetical protein | - |
| F4V36_RS23930 | 70435..70656 | - | 222 | WP_001278683 | conjugal transfer protein TraR | - |
| F4V36_RS23935 | 70791..71306 | - | 516 | WP_000809881 | type IV conjugative transfer system lipoprotein TraV | traV |
| F4V36_RS23940 | 71303..71623 | - | 321 | WP_012881128 | conjugal transfer protein TrbD | - |
| F4V36_RS23945 | 71610..72200 | - | 591 | WP_000002784 | conjugal transfer pilus-stabilizing protein TraP | - |
| F4V36_RS23950 | 72190..73617 | - | 1428 | WP_033807957 | F-type conjugal transfer pilus assembly protein TraB | traB |
| F4V36_RS23955 | 73617..74345 | - | 729 | WP_001230769 | type-F conjugative transfer system secretin TraK | traK |
| F4V36_RS23960 | 74332..74898 | - | 567 | WP_000399780 | type IV conjugative transfer system protein TraE | traE |
| F4V36_RS23965 | 74920..75231 | - | 312 | WP_000012113 | type IV conjugative transfer system protein TraL | traL |
| F4V36_RS23970 | 75246..75605 | - | 360 | WP_001098994 | type IV conjugative transfer system pilin TraA | - |
| F4V36_RS23975 | 75639..75866 | - | 228 | WP_000589556 | conjugal transfer relaxosome protein TraY | - |
| F4V36_RS23980 | 75986..76633 | - | 648 | WP_000332523 | transcriptional regulator TraJ family protein | - |
| F4V36_RS23985 | 76825..77208 | - | 384 | WP_001151529 | conjugal transfer relaxosome DNA-binding protein TraM | - |
| F4V36_RS23990 | 77541..78131 | + | 591 | WP_000252683 | transglycosylase SLT domain-containing protein | virB1 |
| F4V36_RS23995 | 78428..79249 | - | 822 | WP_001234445 | DUF932 domain-containing protein | - |
| F4V36_RS24000 | 79360..79656 | - | 297 | WP_001272251 | hypothetical protein | - |
Host bacterium
| ID | 13987 | GenBank | NZ_CP044156 |
| Plasmid name | pAR-0424-1 | Incompatibility group | - |
| Plasmid size | 79831 bp | Coordinate of oriT [Strand] | 77209..77560 [-] |
| Host baterium | Shigella flexneri strain AR-0424 |
Cargo genes
| Drug resistance gene | erm(B), mph(A), sul1, qacE, aadA5, blaTEM-1B |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |