Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 101670 |
| Name | oriT_p2018n8361554_7  |
| Organism | Escherichia coli strain COL4 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | NZ_JACYGC010000011 (78802..79153 [+], 352 nt) |
| oriT length | 352 nt |
| IRs (inverted repeats) | 255..262, 271..278 (ACCGCTAG..CTAGCGGT) 192..198, 206..212 (TATAAAA..TTTTATA) 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_p2018n8361554_7
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATAGAGAGTTATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAAGCGGTGTCGGCGCGGCTACAACAACGCGCCGACACCGCTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCATTATGAATTTTAGTGTTTCGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA
AGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATAGAGAGTTATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAAGCGGTGTCGGCGCGGCTACAACAACGCGCCGACACCGCTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCGTCCCTGTTTGCATTATGAATTTTAGTGTTTCGAAATTAACTTTATTTTATGTTCAAAAAAGGTAATCTCTA
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Auxiliary protein
| ID | 572 | GenBank | WP_001151524 |
| Name | WP_001151524_p2018n8361554_7 |
UniProt ID | A0A5W2DT22 |
| Length | 127 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
Auxiliary protein sequence
Download Length: 127 a.a. Molecular weight: 14517.48 Da Isoelectric Point: 5.0516
>WP_001151524.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MAKVNLYISNDAYEKINAIIEKRRQEGAREKDVSFSATASMLLELGLRVHEAQMERKESAFNQTEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPKNDDE
MAKVNLYISNDAYEKINAIIEKRRQEGAREKDVSFSATASMLLELGLRVHEAQMERKESAFNQTEFNKLL
LECVVKTQSSVAKILGIESLSPHVSGNPKFEYANMVEDIREKVSSEMERFFPKNDDE
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | A0A5W2DT22 |
| ID | 573 | GenBank | WP_001369361 |
| Name | WP_001369361_p2018n8361554_7 |
UniProt ID | B7LI64 |
| Length | 133 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
Auxiliary protein sequence
Download Length: 133 a.a. Molecular weight: 15409.70 Da Isoelectric Point: 9.9240
>WP_001369361.1 MULTISPECIES: conjugal transfer relaxosome DNA-bindin protein TraY [Gammaproteobacteria]
MLLKRFGTRSATGKMVKLKLPVDVESLLIEASNRSGRSRSFEAVIRLKDHLHRYPKFNRAGNIYGKSLVK
YLTMRLDDETNQLLIAAKNRSGWCKTDEAADRVIDHLIKFPDFYNSEIFREADKEEDITFNTL
MLLKRFGTRSATGKMVKLKLPVDVESLLIEASNRSGRSRSFEAVIRLKDHLHRYPKFNRAGNIYGKSLVK
YLTMRLDDETNQLLIAAKNRSGWCKTDEAADRVIDHLIKFPDFYNSEIFREADKEEDITFNTL
Protein domains
Predicted by InterproScan.
Protein structure
| Source | ID | Structure |
|---|---|---|
| AlphaFold DB | B7LI64 |
T4CP
| ID | 1119 | GenBank | WP_115186477 |
| Name | traD_IYY09_RS25205_p2018n8361554_7 |
UniProt ID | _ |
| Length | 726 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 726 a.a. Molecular weight: 82537.11 Da Isoelectric Point: 5.0524
>WP_115186477.1 type IV conjugative transfer system coupling protein TraD [Escherichia coli]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTENPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQTEQPQQPQQPQQ
PQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQENHPDIQQ
QMQRREEVNINVHRERGEDVEPGDDF
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTENPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQTEQPQQPQQPQQ
PQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQQENHPDIQQ
QMQRREEVNINVHRERGEDVEPGDDF
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
| ID | 1120 | GenBank | WP_194846446 |
| Name | traC_IYY09_RS25650_p2018n8361554_7 |
UniProt ID | _ |
| Length | 875 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 875 a.a. Molecular weight: 99116.78 Da Isoelectric Point: 5.7326
>WP_194846446.1 type IV secretion system protein TraC [Escherichia coli]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAAA
TQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASITTQTVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNVADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFLGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAESPTIRSRLDEMIVLLDQYT
ANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGIPLCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMKAAA
TQFPLPEGMNLPLTLRHYRVFISYCSPSKKKSRADILEMENLVKIIRASLQGASITTQTVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNVADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFLGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAESPTIRSRLDEMIVLLDQYT
ANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 78231..94516
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| IYY09_RS25540 | 73686..73919 | + | 234 | WP_000005990 | DUF905 family protein | - |
| IYY09_RS25545 | 73947..74144 | + | 198 | Protein_79 | hypothetical protein | - |
| IYY09_RS25550 | 74199..74633 | + | 435 | WP_097560612 | conjugation system SOS inhibitor PsiB | - |
| IYY09_RS25555 | 74630..75392 | + | 763 | Protein_81 | plasmid SOS inhibition protein A | - |
| IYY09_RS25560 | 75361..75549 | - | 189 | WP_001299721 | hypothetical protein | - |
| IYY09_RS26155 | 75571..75720 | + | 150 | Protein_83 | plasmid maintenance protein Mok | - |
| IYY09_RS25565 | 75662..75787 | + | 126 | WP_001372321 | type I toxin-antitoxin system Hok family toxin | - |
| IYY09_RS26160 | 76007..76237 | + | 231 | WP_071586998 | hypothetical protein | - |
| IYY09_RS26165 | 76235..76407 | - | 173 | Protein_86 | hypothetical protein | - |
| IYY09_RS26170 | 76477..76683 | + | 207 | WP_000547968 | hypothetical protein | - |
| IYY09_RS25570 | 76708..76995 | + | 288 | WP_000107535 | hypothetical protein | - |
| IYY09_RS25575 | 77113..77934 | + | 822 | WP_001234426 | DUF932 domain-containing protein | - |
| IYY09_RS25580 | 78231..78821 | - | 591 | WP_001376243 | transglycosylase SLT domain-containing protein | - |
| IYY09_RS25585 | 79154..79537 | + | 384 | WP_001151524 | conjugal transfer relaxosome DNA-binding protein TraM | - |
| IYY09_RS25590 | 79724..80413 | + | 690 | WP_000283385 | conjugal transfer transcriptional regulator TraJ | - |
| IYY09_RS25595 | 80512..80907 | + | 396 | WP_001309237 | conjugal transfer relaxosome DNA-bindin protein TraY | - |
| IYY09_RS25600 | 80940..81305 | + | 366 | WP_000994779 | type IV conjugative transfer system pilin TraA | - |
| IYY09_RS25605 | 81320..81631 | + | 312 | WP_000012106 | type IV conjugative transfer system protein TraL | traL |
| IYY09_RS25610 | 81653..82219 | + | 567 | WP_000399792 | type IV conjugative transfer system protein TraE | traE |
| IYY09_RS25615 | 82206..82934 | + | 729 | WP_001230787 | type-F conjugative transfer system secretin TraK | traK |
| IYY09_RS25620 | 82934..84361 | + | 1428 | WP_000146685 | F-type conjugal transfer pilus assembly protein TraB | traB |
| IYY09_RS25625 | 84351..84941 | + | 591 | WP_001376242 | conjugal transfer pilus-stabilizing protein TraP | - |
| IYY09_RS25630 | 84928..85125 | + | 198 | WP_001324648 | conjugal transfer protein TrbD | - |
| IYY09_RS25635 | 85137..85388 | + | 252 | WP_001038342 | conjugal transfer protein TrbG | - |
| IYY09_RS25640 | 85385..85900 | + | 516 | WP_000809838 | type IV conjugative transfer system lipoprotein TraV | traV |
| IYY09_RS25645 | 86035..86256 | + | 222 | WP_001278689 | conjugal transfer protein TraR | - |
| IYY09_RS25650 | 86416..89043 | + | 2628 | WP_194846446 | type IV secretion system protein TraC | virb4 |
| IYY09_RS25655 | 89040..89426 | + | 387 | WP_000214082 | type-F conjugative transfer system protein TrbI | - |
| IYY09_RS25660 | 89423..90055 | + | 633 | WP_001203720 | type-F conjugative transfer system protein TraW | traW |
| IYY09_RS25665 | 90052..91044 | + | 993 | WP_000830839 | conjugal transfer pilus assembly protein TraU | traU |
| IYY09_RS25670 | 91053..91691 | + | 639 | WP_000777692 | type-F conjugative transfer system pilin assembly protein TrbC | trbC |
| IYY09_RS25675 | 91688..93496 | + | 1809 | WP_000821840 | type-F conjugative transfer system mating-pair stabilization protein TraN | traN |
| IYY09_RS25680 | 93523..93780 | + | 258 | WP_000864318 | conjugal transfer protein TrbE | - |
| IYY09_RS25685 | 93773..94516 | + | 744 | WP_001030385 | type-F conjugative transfer system pilin assembly protein TraF | traF |
| IYY09_RS25690 | 94530..94871 | + | 342 | WP_000556795 | conjugal transfer protein TrbA | - |
| IYY09_RS25695 | 94852..95187 | - | 336 | WP_097427752 | toxin ArtA | - |
Host bacterium
| ID | 2114 | GenBank | NZ_JACYGC010000011 |
| Plasmid name | p2018n8361554_7 | Incompatibility group | IncFII |
| Plasmid size | 95662 bp | Coordinate of oriT [Strand] | 78802..79153 [+] |
| Host baterium | Escherichia coli strain COL4 |
Cargo genes
| Drug resistance gene | sitABCD |
| Virulence gene | afaC-I, iucA, iucB, iucC, iutA |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |