Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 107526 |
| Name | oriT_p2246-CTXM  |
| Organism | Shigella boydii strain 2246 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_KX646543 (70587..70672 [-], 86 nt) |
| oriT length | 86 nt |
| IRs (inverted repeats) | 61..68, 73..80 (TTGGTGGT..ACCACCAA) 27..34, 37..44 (GCAAAAAC..GTTTTTGC) 8..14, 20..26 (TGATTTA..TAAATCA) |
| Location of nic site | 53..54 |
| Conserved sequence flanking the nic site |
TGTGTGGTGC |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 86 nt
>oriT_p2246-CTXM
AATTACATGATTTAAAACGTAAATCAGCAAAAACTTGTTTTTGCGTAGTGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTT
AATTACATGATTTAAAACGTAAATCAGCAAAAACTTGTTTTTGCGTAGTGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTT
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Auxiliary protein
| ID | 2319 | GenBank | WP_001354030 |
| Name | WP_001354030_p2246-CTXM |
UniProt ID | A0A734M5H3 |
| Length | 127 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
Auxiliary protein sequence
Download Length: 127 a.a. Molecular weight: 14508.47 Da Isoelectric Point: 4.7116
>WP_001354030.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MARVILYISNDVYDKVNAIVEQRRQEGARDKDISVSGTASMLLELGLRVYEAQMERKESAFNQTEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPKNDEE
MARVILYISNDVYDKVNAIVEQRRQEGARDKDISVSGTASMLLELGLRVYEAQMERKESAFNQTEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPKNDEE
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A734M5H3 |
| ID | 2320 | GenBank | WP_000089263 |
| Name | WP_000089263_p2246-CTXM |
UniProt ID | A0A3U3XJL9 |
| Length | 75 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
Auxiliary protein sequence
Download Length: 75 a.a. Molecular weight: 8541.74 Da Isoelectric Point: 8.6796
>WP_000089263.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Gammaproteobacteria]
MSRNIIRPAPGNKVLLVLDDATNHKLLGARERSGRTKTNEVLVRLRDHLNRFPDFYNLDAIKEGAEETDS
IIKDL
MSRNIIRPAPGNKVLLVLDDATNHKLLGARERSGRTKTNEVLVRLRDHLNRFPDFYNLDAIKEGAEETDS
IIKDL
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A3U3XJL9 |
T4CP
| ID | 5272 | GenBank | WP_000069777 |
| Name | traC_HPF80_RS00590_p2246-CTXM |
UniProt ID | _ |
| Length | 876 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 876 a.a. Molecular weight: 99195.86 Da Isoelectric Point: 6.1126
>WP_000069777.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANKSIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAA
ATQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASIATQTVDAQAFIDIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLNVRADYLTLGLRENGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAGSPTIRSRLDEMIVLLDQY
TANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGW
RLLDFKNRKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY
NQLYPDQFQPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEG
LSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA
MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANKSIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAA
ATQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASIATQTVDAQAFIDIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLNVRADYLTLGLRENGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAGSPTIRSRLDEMIVLLDQY
TANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGW
RLLDFKNRKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY
NQLYPDQFQPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEG
LSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
| ID | 5273 | GenBank | WP_125097878 |
| Name | traD_HPF80_RS00690_p2246-CTXM |
UniProt ID | _ |
| Length | 762 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 762 a.a. Molecular weight: 86727.59 Da Isoelectric Point: 5.1644
>WP_125097878.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILIGLVLWVKISWQTFINGCIYWWCTSLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGDPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEDVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPE
EEMEQQLPPGISESGEVVDMAAYEAWQQENHPDIQQHMQRREEVNINVHRERGEDVEPGDDF
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILIGLVLWVKISWQTFINGCIYWWCTSLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLASVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGDPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPEVASGEDVTQAEQPQQPQQPQQPQQ
PQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPQQPVSSVINDKKSDAGVSVPAGGIEQELKMKPE
EEMEQQLPPGISESGEVVDMAAYEAWQQENHPDIQQHMQRREEVNINVHRERGEDVEPGDDF
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 70019..101772
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| HPF80_RS00460 | 65400..65630 | + | 231 | WP_000218642 | hypothetical protein | - |
| HPF80_RS00465 | 65682..67043 | + | 1362 | WP_000170695 | DUF3560 domain-containing protein | - |
| HPF80_RS00470 | 67090..67653 | + | 564 | WP_001298559 | class I SAM-dependent methyltransferase | - |
| HPF80_RS00745 | 67739..68194 | - | 456 | Protein_90 | hypothetical protein | - |
| HPF80_RS00485 | 68494..68790 | + | 297 | WP_001272251 | hypothetical protein | - |
| HPF80_RS00490 | 68901..69722 | + | 822 | WP_001234445 | DUF932 domain-containing protein | - |
| HPF80_RS00495 | 70019..70609 | - | 591 | WP_000252683 | transglycosylase SLT domain-containing protein | virB1 |
| HPF80_RS00500 | 70944..71327 | + | 384 | WP_001354030 | conjugal transfer relaxosome DNA-binding protein TraM | - |
| HPF80_RS00505 | 71521..72153 | + | 633 | WP_171265063 | conjugal transfer transcriptional regulator TraJ | - |
| HPF80_RS00510 | 72242..73470 | + | 1229 | WP_088895425 | IS3-like element IS2 family transposase | - |
| HPF80_RS00515 | 73665..73892 | + | 228 | WP_000089263 | conjugal transfer relaxosome protein TraY | - |
| HPF80_RS00520 | 73925..74284 | + | 360 | WP_001098992 | type IV conjugative transfer system pilin TraA | - |
| HPF80_RS00525 | 74299..74610 | + | 312 | WP_000012113 | type IV conjugative transfer system protein TraL | traL |
| HPF80_RS00530 | 74632..75198 | + | 567 | WP_000399780 | type IV conjugative transfer system protein TraE | traE |
| HPF80_RS00535 | 75185..75913 | + | 729 | WP_001230772 | type-F conjugative transfer system secretin TraK | traK |
| HPF80_RS00540 | 75913..77364 | + | 1452 | WP_134265680 | F-type conjugal transfer pilus assembly protein TraB | traB |
| HPF80_RS00545 | 77354..77920 | + | 567 | WP_000896599 | conjugal transfer pilus-stabilizing protein TraP | - |
| HPF80_RS00550 | 77907..78227 | + | 321 | WP_001057307 | conjugal transfer protein TrbD | - |
| HPF80_RS00555 | 78224..78739 | + | 516 | WP_000809881 | type IV conjugative transfer system lipoprotein TraV | traV |
| HPF80_RS00560 | 78874..79095 | + | 222 | WP_001278683 | conjugal transfer protein TraR | - |
| HPF80_RS00565 | 79131..80099 | + | 969 | WP_000654804 | IS5-like element IS903B family transposase | - |
| HPF80_RS00570 | 80139..80567 | + | 429 | WP_089438737 | hypothetical protein | - |
| HPF80_RS00575 | 80560..81033 | + | 474 | WP_000549568 | hypothetical protein | - |
| HPF80_RS00580 | 81113..81331 | + | 219 | WP_000556745 | hypothetical protein | - |
| HPF80_RS00750 | 81359..81707 | + | 349 | Protein_111 | hypothetical protein | - |
| HPF80_RS00590 | 81833..84463 | + | 2631 | WP_000069777 | type IV secretion system protein TraC | virb4 |
| HPF80_RS00595 | 84460..84846 | + | 387 | WP_000214084 | type-F conjugative transfer system protein TrbI | - |
| HPF80_RS00600 | 84843..85475 | + | 633 | WP_094885485 | type-F conjugative transfer system protein TraW | traW |
| HPF80_RS00605 | 85472..86464 | + | 993 | WP_000830838 | conjugal transfer pilus assembly protein TraU | traU |
| HPF80_RS00610 | 86494..86799 | + | 306 | WP_000224416 | hypothetical protein | - |
| HPF80_RS00615 | 86808..87446 | + | 639 | WP_001080256 | type-F conjugative transfer system pilin assembly protein TrbC | trbC |
| HPF80_RS00620 | 87443..89293 | + | 1851 | WP_171265065 | type-F conjugative transfer system mating-pair stabilization protein TraN | traN |
| HPF80_RS00625 | 89320..89577 | + | 258 | WP_000864353 | conjugal transfer protein TrbE | - |
| HPF80_RS00630 | 89570..90313 | + | 744 | WP_001030371 | type-F conjugative transfer system pilin assembly protein TraF | traF |
| HPF80_RS00635 | 90327..90671 | + | 345 | WP_000556796 | conjugal transfer protein TrbA | - |
| HPF80_RS00640 | 90790..91074 | + | 285 | WP_000624194 | type-F conjugative transfer system pilin chaperone TraQ | - |
| HPF80_RS00645 | 91061..91606 | + | 546 | WP_000059831 | type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB | traF |
| HPF80_RS00755 | 91563..91658 | + | 96 | Protein_124 | conjugal transfer protein TrbJ | - |
| HPF80_RS00655 | 92397..92660 | + | 264 | WP_171265066 | conjugal transfer protein TrbJ | - |
| HPF80_RS00660 | 92641..93033 | + | 393 | WP_000660699 | F-type conjugal transfer protein TrbF | - |
| HPF80_RS00665 | 93020..94393 | + | 1374 | WP_000944331 | conjugal transfer pilus assembly protein TraH | traH |
| HPF80_RS00670 | 94390..97212 | + | 2823 | WP_001007039 | conjugal transfer mating-pair stabilization protein TraG | traG |
| HPF80_RS00675 | 97228..97713 | + | 486 | WP_000605870 | hypothetical protein | - |
| HPF80_RS00680 | 97762..98493 | + | 732 | WP_000782451 | conjugal transfer complement resistance protein TraT | - |
| HPF80_RS00685 | 98696..99433 | + | 738 | WP_000199905 | hypothetical protein | - |
| HPF80_RS00690 | 99484..101772 | + | 2289 | WP_125097878 | type IV conjugative transfer system coupling protein TraD | prgC |
Host bacterium
| ID | 7961 | GenBank | NZ_KX646543 |
| Plasmid name | p2246-CTXM | Incompatibility group | IncFII |
| Plasmid size | 111559 bp | Coordinate of oriT [Strand] | 70587..70672 [-] |
| Host baterium | Shigella boydii strain 2246 |
Cargo genes
| Drug resistance gene | erm(B), mph(A), cmlA1, qacE, blaCTX-M-14 |
| Virulence gene | - |
| Metal resistance gene | merR, merT, merP, merA, merD, merE |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |