Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 200140 |
| Name | oriT_ICEVpaCan1  |
| Organism | Vibrio parahaemolyticus strain S107-1 |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | CP028481 (75795..76093 [-], 299 nt) |
| oriT length | 299 nt |
| IRs (inverted repeats) | 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_ICEVpaCan1
GCTCTGTTTGGCGGCGGATGACTGAGCCAAAAAAATCGAGACGCCAAACGTCGTTTGCATTCTGGCCTGAACTTGCCAAACGGTTTGTATTTTCATGGCAATACGTCTTTTTAGGCGTTTTTAAGTGAAATCGGCCTGTATCCCTTGTCAGGTATGGGATTGCGCGAGTTGATTTATATCGAGACGCCAAACAGTGATTGTTACGGCAGTTTTACGTTTGGCGTTTCGATCCAAAAGCCAAACGGATAGTGGTTTTGGCTTTTGGGGTTAATTGGATGGGGAAATTGGTTTGGTAGAAA
GCTCTGTTTGGCGGCGGATGACTGAGCCAAAAAAATCGAGACGCCAAACGTCGTTTGCATTCTGGCCTGAACTTGCCAAACGGTTTGTATTTTCATGGCAATACGTCTTTTTAGGCGTTTTTAAGTGAAATCGGCCTGTATCCCTTGTCAGGTATGGGATTGCGCGAGTTGATTTATATCGAGACGCCAAACAGTGATTGTTACGGCAGTTTTACGTTTGGCGTTTCGATCCAAAAGCCAAACGGATAGTGGTTTTGGCTTTTGGGGTTAATTGGATGGGGAAATTGGTTTGGTAGAAA
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 14293 | GenBank | AVW96083 |
| Name | TraI_2_DA442_13700_ICEVpaCan1 |
UniProt ID | _ |
| Length | 716 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 716 a.a. Molecular weight: 79895.99 Da Isoelectric Point: 5.4225
>AVW96083.1 phosphohydrolase [Vibrio parahaemolyticus]
MFKKLFFQAKALPELSSQLDADIPRYPPFLKGLPAASPEDLQSTQEELIAKLRQVLGFNQRDFQRLIQPC
IDHLAAYVHLLPASEHHHHSGAGGLLRHSLEVAFWAAQAAEGIIFVASGTPVEKKELEPRWRVAAALGGL
FHDIGKPVSDLSITDEDGRYQWNPFLETLSQWTSNNSIERYFIRWRDGRCKRHEQFSILVLNRVMTPELL
AWLTQPGPEILQAMLEAIGNTDPEHVLSKLVIEADQTSVQRDLKAQRISVDDNALGVPVERYLLDAMRRL
LASSQWLVNQRDARVWIRKSNQSTHLYLVWKSAAKDIIDLLAKDKIPGIPRDPDTLADILIERGLATKSA
SNDRYESLAPEVLIKDDKPIWLPMLHISEADLLFSSNVPSGVTLFSKPEWEATQQTQAEPQSRSREQPGL
SEASSSIEHSSSTESPSTKPSDQDDELRHASDVNHLQENENVPGDGCEKPHHSYDADIANNANQHDAEAL
NLPESLAWLPEASSALVVVGEQVLIRYPDAVRHWCAPRKLLAELSRLDWLELDPANPTRKARTVTMNDGA
QEQGLLLKVSISKGLIALIDISKQDEESVTAIQNEEALPRPSRTETTNAQAKELATRAERKQKPIAPNAN
SSTDPKHAQRQQMVNFVKDLPILLTDGDYPDVDHSADGIRVTIQTLRQVANQHGIPAGQLLRGISASDQC
QFDEGETVLFTAHAKR
MFKKLFFQAKALPELSSQLDADIPRYPPFLKGLPAASPEDLQSTQEELIAKLRQVLGFNQRDFQRLIQPC
IDHLAAYVHLLPASEHHHHSGAGGLLRHSLEVAFWAAQAAEGIIFVASGTPVEKKELEPRWRVAAALGGL
FHDIGKPVSDLSITDEDGRYQWNPFLETLSQWTSNNSIERYFIRWRDGRCKRHEQFSILVLNRVMTPELL
AWLTQPGPEILQAMLEAIGNTDPEHVLSKLVIEADQTSVQRDLKAQRISVDDNALGVPVERYLLDAMRRL
LASSQWLVNQRDARVWIRKSNQSTHLYLVWKSAAKDIIDLLAKDKIPGIPRDPDTLADILIERGLATKSA
SNDRYESLAPEVLIKDDKPIWLPMLHISEADLLFSSNVPSGVTLFSKPEWEATQQTQAEPQSRSREQPGL
SEASSSIEHSSSTESPSTKPSDQDDELRHASDVNHLQENENVPGDGCEKPHHSYDADIANNANQHDAEAL
NLPESLAWLPEASSALVVVGEQVLIRYPDAVRHWCAPRKLLAELSRLDWLELDPANPTRKARTVTMNDGA
QEQGLLLKVSISKGLIALIDISKQDEESVTAIQNEEALPRPSRTETTNAQAKELATRAERKQKPIAPNAN
SSTDPKHAQRQQMVNFVKDLPILLTDGDYPDVDHSADGIRVTIQTLRQVANQHGIPAGQLLRGISASDQC
QFDEGETVLFTAHAKR
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4CP
| ID | 16572 | GenBank | AVW96068 |
| Name | traC_DA442_13615_ICEVpaCan1 |
UniProt ID | _ |
| Length | 799 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 799 a.a. Molecular weight: 90167.75 Da Isoelectric Point: 5.9743
>AVW96068.1 type IV secretion system protein TraC [Vibrio parahaemolyticus]
MKASLYSGQRASELLPVLAYSDDEQLFFMEDQSVGFGFLCDPLPGGDESVADRVNVLLNNDWPKDTLLQF
GLYASPDIQTDLQRMMGLRHRQSDPLLRASIRKRADFLEGGTVQPIEESTQTQVRNFQLIVTCKLPLESP
IPTERELSRASALRASFSQALATVGFRVTEMTDRNWLAALSAQLNWGKDASWRNPSPIRSEADKPLREQV
LDYDRAIKVDSQGLMLGDYRVKTLSFKRLPERIWFGHAASFAGDMMTGSRGLRGSFLLNVTIHFPSAEAI
RSRLETKRQWAVNQAYGPMLKFVPVLAAKKKGFDVLFEALQEGDRPIRANMTLTLFSPTEEASISSVSNA
RTYFKELGFELMEDKYFCLPIFLNALPFGADRQAMNDLFRFKTMATRHVIPLLPLFADWKGTGTPVINFV
SRNGQIMSVSLYDSGSNYNCCIAAQSGSGKSFLVNEIISSYLSEGGQCWVIDVGRSYEKLCEVYDGEFLQ
FGRDSGICLNPFEIVEDYDEEADVLVGLLAAMAAPTQSLTDFQMANLKRQTRELWEKKGRAMLVDDVAEA
LKNHEDRRVQDVGEQLYPFTTQGEYGRFFNGHNNIRFKNRFTVLELEELKGRKHLQQVVLLQLIYQIQQE
MYLGERDRRKIVFIDEAWDLLTQGDVGKFIETGYRRFRKYGGSAVTVTQSVNDLYDSPTGKAIAENSANM
YLLGQKAETINALKKEGRLPLGEGGYEYLKTVHTVTGVYSEIFFITEMGTGIGRLIVDPFHKLLYSSRAE
DVNAIKQLTRKGLSVADAISQLLKERGYE
MKASLYSGQRASELLPVLAYSDDEQLFFMEDQSVGFGFLCDPLPGGDESVADRVNVLLNNDWPKDTLLQF
GLYASPDIQTDLQRMMGLRHRQSDPLLRASIRKRADFLEGGTVQPIEESTQTQVRNFQLIVTCKLPLESP
IPTERELSRASALRASFSQALATVGFRVTEMTDRNWLAALSAQLNWGKDASWRNPSPIRSEADKPLREQV
LDYDRAIKVDSQGLMLGDYRVKTLSFKRLPERIWFGHAASFAGDMMTGSRGLRGSFLLNVTIHFPSAEAI
RSRLETKRQWAVNQAYGPMLKFVPVLAAKKKGFDVLFEALQEGDRPIRANMTLTLFSPTEEASISSVSNA
RTYFKELGFELMEDKYFCLPIFLNALPFGADRQAMNDLFRFKTMATRHVIPLLPLFADWKGTGTPVINFV
SRNGQIMSVSLYDSGSNYNCCIAAQSGSGKSFLVNEIISSYLSEGGQCWVIDVGRSYEKLCEVYDGEFLQ
FGRDSGICLNPFEIVEDYDEEADVLVGLLAAMAAPTQSLTDFQMANLKRQTRELWEKKGRAMLVDDVAEA
LKNHEDRRVQDVGEQLYPFTTQGEYGRFFNGHNNIRFKNRFTVLELEELKGRKHLQQVVLLQLIYQIQQE
MYLGERDRRKIVFIDEAWDLLTQGDVGKFIETGYRRFRKYGGSAVTVTQSVNDLYDSPTGKAIAENSANM
YLLGQKAETINALKKEGRLPLGEGGYEYLKTVHTVTGVYSEIFFITEMGTGIGRLIVDPFHKLLYSSRAE
DVNAIKQLTRKGLSVADAISQLLKERGYE
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
| ID | 16573 | GenBank | AVW96082 |
| Name | t4cp2_DA442_13695_ICEVpaCan1 |
UniProt ID | _ |
| Length | 606 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 606 a.a. Molecular weight: 67112.94 Da Isoelectric Point: 6.4435
>AVW96082.1 conjugal transfer protein [Vibrio parahaemolyticus]
MKENAYEMPWRTNYEAMAAAGWLVGATGAIAAEMLTELPPEPFWWMTGISSGMAMYRLPEAYRLYKLQKG
LKGKPLDFMALAHLQKVMAKHPDDLWLGYGFEWDQRHAQRAYEILKRDKQTLLNQGYGKQMGSTWIHGVE
PKEEDVYQPVGHTEGHTLIVGTTGAGKTRCFDAMITQAILRNEAVIIIDPKGDKELKDNAQRACIAAGSP
ERFVYFHPGFPEHSVRLNPLRNFNRGTEIASRIAALIPSETGADPFKAFGQMALNNIVQGLLLTSQRPDL
KTLRRFLEGGPEGLVVKAVTAWGEQVYPNFSVEIKRFTEKANTLAKQAMAMLLFYYERIQPVAANTDLEG
LLSMFEHDRTHYSKMVASLMPVLNMLTSSELGPLLSPIANDVDDSRLITDSGRIINNAQVAYIGLDSLTD
AMVGSAIGSLLLSDLTAVAGDRYNYGVENRPVNIFIDEAAEVVNDPFIQLLNKGRGAKMRCVIATQTFAD
FAARTGSEAKARQVLGNINNLIALRVMDAETQQYITDNLPKTRLQYIMQTQGMSSNSDSPALFTGNHGER
LMEEEGDMFPPQLLGQLPNLEYIAKLSGGRVIKGRIPILTSSTQAA
MKENAYEMPWRTNYEAMAAAGWLVGATGAIAAEMLTELPPEPFWWMTGISSGMAMYRLPEAYRLYKLQKG
LKGKPLDFMALAHLQKVMAKHPDDLWLGYGFEWDQRHAQRAYEILKRDKQTLLNQGYGKQMGSTWIHGVE
PKEEDVYQPVGHTEGHTLIVGTTGAGKTRCFDAMITQAILRNEAVIIIDPKGDKELKDNAQRACIAAGSP
ERFVYFHPGFPEHSVRLNPLRNFNRGTEIASRIAALIPSETGADPFKAFGQMALNNIVQGLLLTSQRPDL
KTLRRFLEGGPEGLVVKAVTAWGEQVYPNFSVEIKRFTEKANTLAKQAMAMLLFYYERIQPVAANTDLEG
LLSMFEHDRTHYSKMVASLMPVLNMLTSSELGPLLSPIANDVDDSRLITDSGRIINNAQVAYIGLDSLTD
AMVGSAIGSLLLSDLTAVAGDRYNYGVENRPVNIFIDEAAEVVNDPFIQLLNKGRGAKMRCVIATQTFAD
FAARTGSEAKARQVLGNINNLIALRVMDAETQQYITDNLPKTRLQYIMQTQGMSSNSDSPALFTGNHGER
LMEEEGDMFPPQLLGQLPNLEYIAKLSGGRVIKGRIPILTSSTQAA
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 2653672..2675748
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| DA442_13560 | 2649091..2649909 | - | 819 | AVW96058 | phage recombination protein Bet | - |
| DA442_13565 | 2649989..2650408 | - | 420 | AVW96059 | single-stranded DNA-binding protein | - |
| DA442_13570 | 2650424..2650750 | - | 327 | AVW96060 | plasmid-related protein | - |
| DA442_13575 | 2651118..2651720 | + | 603 | AVW96061 | hypothetical protein | - |
| DA442_13580 | 2651931..2652254 | + | 324 | AVW96062 | XRE family transcriptional regulator | - |
| DA442_13585 | 2652248..2653564 | + | 1317 | AVW96063 | toxin HipA | - |
| DA442_13590 | 2653672..2657364 | - | 3693 | AVW96064 | conjugal transfer protein TraN | traN |
| DA442_13595 | 2657367..2658395 | - | 1029 | AVW96065 | conjugal transfer protein TraU | traU |
| DA442_13600 | 2658379..2659503 | - | 1125 | AVW96066 | pilus assembly protein | traW |
| DA442_13605 | 2659514..2659933 | - | 420 | AVW96838 | S26 family signal peptidase | - |
| DA442_13610 | 2660010..2660357 | - | 348 | AVW96067 | plasmid-related protein | - |
| DA442_13615 | 2660350..2662749 | - | 2400 | AVW96068 | type IV secretion system protein TraC | virb4 |
| DA442_13620 | 2662749..2663441 | - | 693 | AVW96069 | disulfide isomerase | trbB |
| DA442_13625 | 2663768..2664721 | + | 954 | AVW96070 | hypothetical protein | - |
| DA442_13630 | 2665149..2665685 | + | 537 | AVW96071 | hypothetical protein | - |
| DA442_13635 | 2665840..2666106 | + | 267 | AVW96072 | DUF1778 domain-containing protein | - |
| DA442_13640 | 2666097..2666603 | + | 507 | AVW96073 | N-acetyltransferase | - |
| DA442_13645 | 2666644..2667030 | - | 387 | AVW96074 | hypothetical protein | - |
| DA442_13650 | 2667027..2667677 | - | 651 | AVW96075 | type IV conjugative transfer system protein TraV | traV |
| DA442_13655 | 2667674..2668963 | - | 1290 | AVW96076 | conjugal transfer protein TraB | traB |
| DA442_13660 | 2668966..2669862 | - | 897 | AVW96839 | hypothetical protein | traK |
| DA442_13665 | 2669846..2670472 | - | 627 | AVW96077 | pilus assembly protein | traE |
| DA442_13670 | 2670469..2670750 | - | 282 | AVW96078 | type IV conjugative transfer system protein TraL | traL |
| DA442_13675 | 2670984..2671274 | + | 291 | AVW96079 | addiction module antidote protein, HigA family | - |
| DA442_13680 | 2671476..2672582 | - | 1107 | AVW96840 | DUF4172 domain-containing protein | - |
| DA442_13685 | 2672736..2673371 | - | 636 | AVW96080 | conjugal transfer protein | tfc7 |
| DA442_13690 | 2673358..2673918 | - | 561 | AVW96081 | conjugative transfer protein | - |
| DA442_13695 | 2673928..2675748 | - | 1821 | AVW96082 | conjugal transfer protein | virb4 |
| DA442_13700 | 2675796..2677946 | - | 2151 | AVW96083 | phosphohydrolase | - |
Host bacterium
| ID | 142 | Element type | ICE (Integrative and conjugative element) |
| Element name | ICEVpaCan1 | GenBank | CP028481 |
| Element size | 3445421 bp | Coordinate of oriT [Strand] | 75795..76093 [-] |
| Host bacterium | Vibrio parahaemolyticus strain S107-1 | Coordinate of element | 2625296..2706787 |
Cargo genes
| Drug resistance gene | - |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |