Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 200402 |
| Name | oriT_ICEVchChn1307  |
| Organism | Vibrio cholerae O1 strain ICDC-1307 SXT element |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | KJ817376 (98002..98300 [-], 299 nt) |
| oriT length | 299 nt |
| IRs (inverted repeats) | 234..242, 254..262 (AAAGCCAAA..TTTGGCTTT) 45..50, 52..57 (CAAACG..CGTTTG) 7..12, 26..31 (TTTGGC..GCCAAA) |
| Location of nic site | _ |
| Conserved sequence flanking the nic site |
_ |
| Note | Predicted by oriTfinder 2.0 |
oriT sequence
Download Length: 299 nt
>oriT_ICEVchChn1307
GCTCTGTTTGGCGGCTGGTGACCTAGCCAAAAAAATTGAGACGCCAAACGTCGTTTGCATTCTGGCCTGAACTTGCCAAACGGTTTGTATCTTCATGGCGATACGTCTTTTTAGGTGTTTTTAAGTGAAATCAGCCTGTATCCCTTGTCGGGTATGGGATTGAGCGAGTCGATTTATATCGAGACGCCAAACAGTGATTGTGACGGCAGTTTTACGTTTGGCGTTTCGATCCAAAAGCCAAACGGATAGTGGTTTTGGCTTTAGGGGTTAATTGGATGGGGAAATTGGTTTGGTAGAAA
GCTCTGTTTGGCGGCTGGTGACCTAGCCAAAAAAATTGAGACGCCAAACGTCGTTTGCATTCTGGCCTGAACTTGCCAAACGGTTTGTATCTTCATGGCGATACGTCTTTTTAGGTGTTTTTAAGTGAAATCAGCCTGTATCCCTTGTCGGGTATGGGATTGAGCGAGTCGATTTATATCGAGACGCCAAACAGTGATTGTGACGGCAGTTTTACGTTTGGCGTTTCGATCCAAAAGCCAAACGGATAGTGGTTTTGGCTTTAGGGGTTAATTGGATGGGGAAATTGGTTTGGTAGAAA
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 14429 | GenBank | AKA21244 |
| Name | traI_-_ICEVchChn1307 |
UniProt ID | _ |
| Length | 716 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 716 a.a. Molecular weight: 79739.87 Da Isoelectric Point: 5.3647
>AKA21244.1 Conjugative transfer protein TraI, relaxase [Vibrio cholerae O1]
MFKNLFFQAKALPELSSQLDAEIPRYPPFLKGLPAASPEDLQSTQDELIAKLRQILGFNQRDFQRLIQPC
IDHLAAYVHLLPASEHHHHSGAGGLLRHSLEVAFWAAQAAEGIIFVASGTPVEKKELEPRWRVAAALGGL
FHDIGKPVSDLSITDEDGRYQWNPFLQTLSQWATNNRIERYFIRWRDGRCKRHEQFSILVLNRVMTPELL
AWLTQPGPEILQAMLEAIGNTDPEHVLSKLVIEADQTSVQRDLKAQRISVDDNALGVPVERYLLDAMRRL
LASSQWLVNQRDARVWVRKSNQSTNLYLVWKSAAKDIIELLAKDKIPGIPRDPDTLADILIERGLATKSG
SNERYESLAPEVLIKDDKPIWLPMLHISETDLLFSSNVPSGVTLFSKPEWEATQQTQAEPQSRSSEHPGL
SEASSSIEHSSSAQSPSTNSSEQDDELRHASDVNNPQATENAPGDECEKPNNSYDGAIADNVNQQNEAAL
NLPESLAWLPEASSALVVVGEQVLIRYPDAVRPWCAPRKLLAELSRLDWLELDPANPTRKARTVTTNDGV
QEQGLLLKVSISKRLIALIDISKQDTEPATAIQNEEALQRPSRTKTTNAQAKEPATRAERKQKPIAPNAK
SSTDPKYVQRQQMVNFVKDLPILLTDGDYPDVDHSADGIRVTIQTLRQVANAHGIPAGQLLRGISASDEC
QFDEGETVLFTAHAKR
MFKNLFFQAKALPELSSQLDAEIPRYPPFLKGLPAASPEDLQSTQDELIAKLRQILGFNQRDFQRLIQPC
IDHLAAYVHLLPASEHHHHSGAGGLLRHSLEVAFWAAQAAEGIIFVASGTPVEKKELEPRWRVAAALGGL
FHDIGKPVSDLSITDEDGRYQWNPFLQTLSQWATNNRIERYFIRWRDGRCKRHEQFSILVLNRVMTPELL
AWLTQPGPEILQAMLEAIGNTDPEHVLSKLVIEADQTSVQRDLKAQRISVDDNALGVPVERYLLDAMRRL
LASSQWLVNQRDARVWVRKSNQSTNLYLVWKSAAKDIIELLAKDKIPGIPRDPDTLADILIERGLATKSG
SNERYESLAPEVLIKDDKPIWLPMLHISETDLLFSSNVPSGVTLFSKPEWEATQQTQAEPQSRSSEHPGL
SEASSSIEHSSSAQSPSTNSSEQDDELRHASDVNNPQATENAPGDECEKPNNSYDGAIADNVNQQNEAAL
NLPESLAWLPEASSALVVVGEQVLIRYPDAVRPWCAPRKLLAELSRLDWLELDPANPTRKARTVTTNDGV
QEQGLLLKVSISKRLIALIDISKQDTEPATAIQNEEALQRPSRTKTTNAQAKEPATRAERKQKPIAPNAK
SSTDPKYVQRQQMVNFVKDLPILLTDGDYPDVDHSADGIRVTIQTLRQVANAHGIPAGQLLRGISASDEC
QFDEGETVLFTAHAKR
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4CP
| ID | 16956 | GenBank | AKA21230 |
| Name | traC_-_ICEVchChn1307 |
UniProt ID | _ |
| Length | 799 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 799 a.a. Molecular weight: 90157.73 Da Isoelectric Point: 5.9727
>AKA21230.1 IncF plasmid conjugative transfer pilus assembly protein TraC [Vibrio cholerae O1]
MKASLYSGQRASELLPVLAYSDDEQLFFMEDQSVGFGFLCDPLPGGDESVADRVNVLLNNDWPKDTLLQF
GLYASPDIQTDLQRMMGLRHRQSDPLLRASIRKRADFLDGGTVQPIEESTQTQVRNFQLIVTCKLPLESP
IPTERELSRASALRASFSQALATVGFRVTEMTDRNWLAALSAQLNWGKDASWRNPSPIRSEADKPLREQV
LDYDRAIKVDSQGLMLGDYRVKTLSFKRLPERIWFGHAASFAGDMMTGSRGLRGSFLLNVTIHFPSAEAM
RSRLETKRQWAVNQAYGPMLKFVPVLAAKKKGFDVLFEALQEGDRPIRANMTLTLFSPTEEASISSVSNA
RTYFKELGFELMEDKYFCLPIFLNALPFGADRQAMNDLFRFKTMATRHVIPLLPLFADWKGTGTPVINFV
SRNGQIMSVSLYDSGSNYNCCIAAQSGSGKSFLVNEIISSYLSEGGQCWVIDVGRSYEKLCEVYDGEFLQ
FGRDSGICLNPFEIVEDYDEEADVLVGLLAAMAAPTQSLTDFQMANLKRQTRELWEKKGRAMLVDDVAEA
LKNHDDRRVQDVGEQLYPFTTQGEYGRFFNGHNNIRFKNRFTVLELEELKGRKHLQQVVLLQLIYQIQQE
MYLGERDRRKIVFIDEAWDLLTQGDVGKFIETGYRRFRKYGGSAVTVTQSVNDLYDSPTGKAIAENSANM
YLLGQKAETINALKKEGRLPLGEGGYEYLKTVHTVTGVYSEIFFITEMGTGIGRLIVDPFHKLLYSSRAE
DVNAIKQLTRKGLSVADAISQLLKERGYE
MKASLYSGQRASELLPVLAYSDDEQLFFMEDQSVGFGFLCDPLPGGDESVADRVNVLLNNDWPKDTLLQF
GLYASPDIQTDLQRMMGLRHRQSDPLLRASIRKRADFLDGGTVQPIEESTQTQVRNFQLIVTCKLPLESP
IPTERELSRASALRASFSQALATVGFRVTEMTDRNWLAALSAQLNWGKDASWRNPSPIRSEADKPLREQV
LDYDRAIKVDSQGLMLGDYRVKTLSFKRLPERIWFGHAASFAGDMMTGSRGLRGSFLLNVTIHFPSAEAM
RSRLETKRQWAVNQAYGPMLKFVPVLAAKKKGFDVLFEALQEGDRPIRANMTLTLFSPTEEASISSVSNA
RTYFKELGFELMEDKYFCLPIFLNALPFGADRQAMNDLFRFKTMATRHVIPLLPLFADWKGTGTPVINFV
SRNGQIMSVSLYDSGSNYNCCIAAQSGSGKSFLVNEIISSYLSEGGQCWVIDVGRSYEKLCEVYDGEFLQ
FGRDSGICLNPFEIVEDYDEEADVLVGLLAAMAAPTQSLTDFQMANLKRQTRELWEKKGRAMLVDDVAEA
LKNHDDRRVQDVGEQLYPFTTQGEYGRFFNGHNNIRFKNRFTVLELEELKGRKHLQQVVLLQLIYQIQQE
MYLGERDRRKIVFIDEAWDLLTQGDVGKFIETGYRRFRKYGGSAVTVTQSVNDLYDSPTGKAIAENSANM
YLLGQKAETINALKKEGRLPLGEGGYEYLKTVHTVTGVYSEIFFITEMGTGIGRLIVDPFHKLLYSSRAE
DVNAIKQLTRKGLSVADAISQLLKERGYE
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
| ID | 16957 | GenBank | AKA21243 |
| Name | traD_-_ICEVchChn1307 |
UniProt ID | _ |
| Length | 606 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 606 a.a. Molecular weight: 67039.87 Da Isoelectric Point: 6.7825
>AKA21243.1 IncF plasmid conjugative transfer protein TraD [Vibrio cholerae O1]
MKENAYEMPWRTNYEAMAAAGWLVGATGAIAAEMLTELPPEPFWWMTGISSGMALYRLPEAYRLYKLQKG
LKGKPLAFMALSHLQKVMAKHPDELWLGYGFEWDQRHAQRAYEILKRDKQTLLNQGHGKQMGSTWIHGVE
PKEEDVYQPVGHTEGHTLIVGTTGAGKTRCFDAMITQAILRNEAVIIIDPKGDKELKDNAQRACIAAGSP
ERFVYFHPGFPEHSVRLNPLRNFNRGTEIASRIAALIPSETGADPFKAFGQMALNNIVQGLLLTSQRPDL
KTLRRFLEGGPEGLVVKAVTAWGEQVYPNFSVEIKRFTEKANTLAKQAMAMLLFYYERIQPVAANTDLEG
LLSMFEHDRTHYSKMVASLMPVLNMLTSSELGPLLSPIANDVNDSRLITDSGRIINNAQVAYIGLDSLTD
AMVGSAIGSLLLSDLTAVAGDRYNYGVDNRPVNIFIDEAAEVVNDPFIQLLNKGRGAKMRCVIATQTFAD
FAARTGSEAKARQVLGNINNLIALRVMDAETQQYITDNLPKTRLQYIMQTQGMSSNSDSPALFTGNHGER
LMEEEGDMFPPQLLGQLPNLEYIAKLSGGRVIKGRIPILTSSTQAA
MKENAYEMPWRTNYEAMAAAGWLVGATGAIAAEMLTELPPEPFWWMTGISSGMALYRLPEAYRLYKLQKG
LKGKPLAFMALSHLQKVMAKHPDELWLGYGFEWDQRHAQRAYEILKRDKQTLLNQGHGKQMGSTWIHGVE
PKEEDVYQPVGHTEGHTLIVGTTGAGKTRCFDAMITQAILRNEAVIIIDPKGDKELKDNAQRACIAAGSP
ERFVYFHPGFPEHSVRLNPLRNFNRGTEIASRIAALIPSETGADPFKAFGQMALNNIVQGLLLTSQRPDL
KTLRRFLEGGPEGLVVKAVTAWGEQVYPNFSVEIKRFTEKANTLAKQAMAMLLFYYERIQPVAANTDLEG
LLSMFEHDRTHYSKMVASLMPVLNMLTSSELGPLLSPIANDVNDSRLITDSGRIINNAQVAYIGLDSLTD
AMVGSAIGSLLLSDLTAVAGDRYNYGVDNRPVNIFIDEAAEVVNDPFIQLLNKGRGAKMRCVIATQTFAD
FAARTGSEAKARQVLGNINNLIALRVMDAETQQYITDNLPKTRLQYIMQTQGMSSNSDSPALFTGNHGER
LMEEEGDMFPPQLLGQLPNLEYIAKLSGGRVIKGRIPILTSSTQAA
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 33067..52931
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| Locus_29 | 28306..28908 | + | 603 | AKA21221 | hypothetical protein | - |
| Locus_30 | 29017..29691 | + | 675 | AKA21222 | Extracellular deoxyribonuclease Dns | - |
| Locus_31 | 29756..30274 | - | 519 | AKA21223 | plasmid-related regulatory protein | - |
| Locus_32 | 30294..32567 | - | 2274 | AKA21224 | plasmid-related membrane protein | - |
| Locus_33 | 33067..36759 | - | 3693 | AKA21225 | IncF plasmid conjugative transfer protein TraN | traN |
| Locus_34 | 36762..37790 | - | 1029 | AKA21226 | IncF plasmid conjugative transfer pilus assembly protein TraU | traU |
| Locus_35 | 37774..38898 | - | 1125 | AKA21227 | IncF plasmid conjugative transfer pilus assembly protein traW | traW |
| Locus_36 | 38909..39421 | - | 513 | AKA21228 | Conjugative signal peptidase TrhF | - |
| Locus_37 | 39405..39752 | - | 348 | AKA21229 | hypothetical protein | - |
| Locus_38 | 39745..42144 | - | 2400 | AKA21230 | IncF plasmid conjugative transfer pilus assembly protein TraC | virb4 |
| Locus_39 | 42144..42836 | - | 693 | AKA21231 | Thiol:disulfide involved in conjugative transfer | trbB |
| Locus_40 | 42968..43906 | - | 939 | AKA21232 | Ync protein | - |
| Locus_41 | 43899..44732 | - | 834 | AKA21233 | Ynd protein | - |
| Locus_42 | 44910..45296 | - | 387 | AKA21234 | Conjugative transfer protein TraA | - |
| Locus_43 | 45293..45943 | - | 651 | AKA21235 | Conjugative transfer protein TraV | traV |
| Locus_44 | 45940..47229 | - | 1290 | AKA21236 | IncF plasmid conjugative transfer pilus assembly protein TraB | traB |
| Locus_45 | 47232..48128 | - | 897 | AKA21237 | IncF plasmid conjugative transfer pilus assembly protein TraK | traK |
| Locus_46 | 48112..48738 | - | 627 | AKA21238 | IncF plasmid conjugative transfer pilus assembly protein TraE | traE |
| Locus_47 | 48735..49016 | - | 282 | AKA21239 | IncF plasmid conjugative transfer pilus assembly protein TraL | traL |
| Locus_48 | 49305..49892 | + | 588 | AKA21240 | orf49 | - |
| Locus_49 | 49919..50554 | - | 636 | AKA21241 | hypothetical protein | tfc7 |
| Locus_50 | 50541..51101 | - | 561 | AKA21242 | Conjugative transfer protein 234 | - |
| Locus_51 | 51111..52931 | - | 1821 | AKA21243 | IncF plasmid conjugative transfer protein TraD | virb4 |
| Locus_52 | 52980..55130 | - | 2151 | AKA21244 | Conjugative transfer protein TraI, relaxase | - |
| Locus_53 | 55252..55416 | + | 165 | AKA21245 | hypothetical protein | - |
| Locus_54 | 55379..57514 | - | 2136 | AKA21246 | putative DNA helicase | - |
Host bacterium
| ID | 357 | Element type | ICE (Integrative and conjugative element) |
| Element name | ICEVchChn1307 | GenBank | KJ817376 |
| Element size | 104025 bp | Coordinate of oriT [Strand] | 98002..98300 [-] |
| Host bacterium | Vibrio cholerae O1 strain ICDC-1307 SXT element | Coordinate of element | 1..104025 |
Cargo genes
| Drug resistance gene | sul2, aph(3'')-Ib, aph(6)-Id, tet(A), floR |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |