Detailed information of oriT
oriT
The information of the oriT region
| oriTDB ID | 200138 |
| Name | oriT_ICEVchNep1  |
| Organism | Vibrio cholerae strain VC504 ICE element |
| Sequence Completeness | - |
| NCBI accession of oriT (coordinates [strand]) | KC886257 (5166..5464 [+], 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_ICEVchNep1
GCTCTGTTTGGCGGCTGGTGACCTAGCCAAAAAAATTGAGACGCCAAACGTCGTTTGCATTCTGGCCTGAACTTGCCAAACGGTTTGTATCTTCATGGCGATACGTCTTTTTAGGTGTTTTTAAGTGAAATCAGCCTGTATCCCTTGTCGGGTATGGGATTGAGCGAGTCGATTTATATCGAGACGCCAAACAGTGATTGTGACGGCAGTTTTACGTTTGGCGTTTCGATCCAAAAGCCAAACGGATAGTGGTTTTGGCTTTAGGGGTTAATTGGATGGGGAAATTGGTTTGGTAGAAA
GCTCTGTTTGGCGGCTGGTGACCTAGCCAAAAAAATTGAGACGCCAAACGTCGTTTGCATTCTGGCCTGAACTTGCCAAACGGTTTGTATCTTCATGGCGATACGTCTTTTTAGGTGTTTTTAAGTGAAATCAGCCTGTATCCCTTGTCGGGTATGGGATTGAGCGAGTCGATTTATATCGAGACGCCAAACAGTGATTGTGACGGCAGTTTTACGTTTGGCGTTTCGATCCAAAAGCCAAACGGATAGTGGTTTTGGCTTTAGGGGTTAATTGGATGGGGAAATTGGTTTGGTAGAAA
Visualization of oriT structure
oriT secondary structure
Predicted by RNAfold.
Download structure file
Relaxase
| ID | 14291 | GenBank | AHM25075 |
| Name | TraI_2_-_ICEVchNep1 |
UniProt ID | _ |
| Length | 716 a.a. | PDB ID | |
| Note | Predicted by oriTfinder 2.0 | ||
Relaxase protein sequence
Download Length: 716 a.a. Molecular weight: 80010.08 Da Isoelectric Point: 5.6098
>AHM25075.1 Conjugative transfer protein TraI, relaxase [Vibrio cholerae]
MFKNLFFQAKALPDLSSQLDAEIPRYPPFLKGLPAASPEDLQSTQDELIAKLRQVLGFNLRDFQRLIQPC
IDHLAAYVHLLPASEHHHHSGAGGLLRHSLEVAFWAAQAAEGIIFVASGTPVEKKELEPRWRVAAALGGL
FHDIGKPVSDLSITDEDGRYQWNPFLETLSQWATNNSIERYFIRWRDGRCKRHEQFSILVLNRVMTPELL
AWLTQPGPEILQAMLEAIGNTDPEHVLSKLVIEADQTSVQRDLKAQRISVDDNALGVPVERYLLDAMRRL
LASSQWLVNQRDARVWLRKSNQSTHLYLVWKSAAKDIIELLAKDKIPGIPRDPDTLADILIERGLATKSA
SNERYESLAPEVLIKDDKPIWLPMLHISEADLLFSSNVPSSVRLFSKSEWEATQQTQAEPQSRSSEHSDL
PEASSSIEHRKSTESPSTNSSEQDDELRHASDVNHLEENENVPGDGYEKPNNSYDGAISNNVNQHDAEAL
NLPESLVWLPEASSALVMVGEQVLIRYPDAVRHWCAPRKLLAELSRLDWLELDPANPTRKARTVTTKGGV
QEQGLLLKVSISKGLTSLIDLPKQDAESAAAIQNEEASQRPSRTKTTNAQAREPAKRAERKQKPIAPNAN
SSTDPKHAQRQQMVNFVKDLPILLTDGDYPDVDHSADGIRVTIQTLRQVAKEHGIPAGQLLRGISASDQC
QFDEGETVLFTAHAER
MFKNLFFQAKALPDLSSQLDAEIPRYPPFLKGLPAASPEDLQSTQDELIAKLRQVLGFNLRDFQRLIQPC
IDHLAAYVHLLPASEHHHHSGAGGLLRHSLEVAFWAAQAAEGIIFVASGTPVEKKELEPRWRVAAALGGL
FHDIGKPVSDLSITDEDGRYQWNPFLETLSQWATNNSIERYFIRWRDGRCKRHEQFSILVLNRVMTPELL
AWLTQPGPEILQAMLEAIGNTDPEHVLSKLVIEADQTSVQRDLKAQRISVDDNALGVPVERYLLDAMRRL
LASSQWLVNQRDARVWLRKSNQSTHLYLVWKSAAKDIIELLAKDKIPGIPRDPDTLADILIERGLATKSA
SNERYESLAPEVLIKDDKPIWLPMLHISEADLLFSSNVPSSVRLFSKSEWEATQQTQAEPQSRSSEHSDL
PEASSSIEHRKSTESPSTNSSEQDDELRHASDVNHLEENENVPGDGYEKPNNSYDGAISNNVNQHDAEAL
NLPESLVWLPEASSALVMVGEQVLIRYPDAVRHWCAPRKLLAELSRLDWLELDPANPTRKARTVTTKGGV
QEQGLLLKVSISKGLTSLIDLPKQDAESAAAIQNEEASQRPSRTKTTNAQAREPAKRAERKQKPIAPNAN
SSTDPKHAQRQQMVNFVKDLPILLTDGDYPDVDHSADGIRVTIQTLRQVAKEHGIPAGQLLRGISASDQC
QFDEGETVLFTAHAER
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
T4CP
| ID | 16568 | GenBank | AHM25076 |
| Name | t4cp2_-_ICEVchNep1 |
UniProt ID | _ |
| Length | 606 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 606 a.a. Molecular weight: 67115.98 Da Isoelectric Point: 6.5130
>AHM25076.1 IncF plasmid conjugative transfer protein TraD [Vibrio cholerae]
MKENAYEMPWRTNYEAMAAAGWLVGATGAIAAEMLTELPPEPFWWMTGISSGMALYRLPEAYRLYKLQMG
LKGKPLAFMELSHLQKVMAKHPDELWLGYGFEWDQRHAQRAYEILKRDKKTLLNQGHGKQMGSTWIHGVE
PKEEDVYQPVGHTEGHTLIVGTTGAGKTRCFDAMITQAILRNEAVIIIDPKGDKELKDNAQRACIAAGSP
ERFVYFHPGFPEHSVRLNPLRNFNRGTEIASRIAALIPSETGADPFKAFGQMALNNIVQGLLLTSQRPDL
KTLRRFLEGGPEGLVVKAVTAWGEQVYPNFSVEIKRFTEKANTLAKQAMAMLLFYYERIQPVAANTDLEG
LLSMFEHDRTHYSKMVASLMPVLNMLTSSELGPLLSPIANDVDDSRLITDSGRIINNAQVAYIGLDSLTD
AMVGSAIGSLLLSDLTAVAGDRYNYGVENRPVNIFIDEAAEVVNDPFIQLLNKGRGAKMRCVIATQTFAD
FAARTGSEAKARQVLGNINNLIALRVMDAETQQYITDNLPKTRLQYIMQTQGMSSNSDSPALFTGNHGER
LMEEEGDMFPPQLLGQLPNLEYIAKLSGGRVIKGRIPILTSSTQAA
MKENAYEMPWRTNYEAMAAAGWLVGATGAIAAEMLTELPPEPFWWMTGISSGMALYRLPEAYRLYKLQMG
LKGKPLAFMELSHLQKVMAKHPDELWLGYGFEWDQRHAQRAYEILKRDKKTLLNQGHGKQMGSTWIHGVE
PKEEDVYQPVGHTEGHTLIVGTTGAGKTRCFDAMITQAILRNEAVIIIDPKGDKELKDNAQRACIAAGSP
ERFVYFHPGFPEHSVRLNPLRNFNRGTEIASRIAALIPSETGADPFKAFGQMALNNIVQGLLLTSQRPDL
KTLRRFLEGGPEGLVVKAVTAWGEQVYPNFSVEIKRFTEKANTLAKQAMAMLLFYYERIQPVAANTDLEG
LLSMFEHDRTHYSKMVASLMPVLNMLTSSELGPLLSPIANDVDDSRLITDSGRIINNAQVAYIGLDSLTD
AMVGSAIGSLLLSDLTAVAGDRYNYGVENRPVNIFIDEAAEVVNDPFIQLLNKGRGAKMRCVIATQTFAD
FAARTGSEAKARQVLGNINNLIALRVMDAETQQYITDNLPKTRLQYIMQTQGMSSNSDSPALFTGNHGER
LMEEEGDMFPPQLLGQLPNLEYIAKLSGGRVIKGRIPILTSSTQAA
Protein domains
Predicted by InterproScan.
Protein structure
No available structure.
| ID | 16568 | GenBank | AHM25076 |
| Name | t4cp2_-_ICEVchNep1 |
UniProt ID | _ |
| Length | 606 a.a. | PDB ID | _ |
| Note | Predicted by oriTfinder 2.0 | ||
T4CP protein sequence
Download Length: 606 a.a. Molecular weight: 67115.98 Da Isoelectric Point: 6.5130
>AHM25076.1 IncF plasmid conjugative transfer protein TraD [Vibrio cholerae]
MKENAYEMPWRTNYEAMAAAGWLVGATGAIAAEMLTELPPEPFWWMTGISSGMALYRLPEAYRLYKLQMG
LKGKPLAFMELSHLQKVMAKHPDELWLGYGFEWDQRHAQRAYEILKRDKKTLLNQGHGKQMGSTWIHGVE
PKEEDVYQPVGHTEGHTLIVGTTGAGKTRCFDAMITQAILRNEAVIIIDPKGDKELKDNAQRACIAAGSP
ERFVYFHPGFPEHSVRLNPLRNFNRGTEIASRIAALIPSETGADPFKAFGQMALNNIVQGLLLTSQRPDL
KTLRRFLEGGPEGLVVKAVTAWGEQVYPNFSVEIKRFTEKANTLAKQAMAMLLFYYERIQPVAANTDLEG
LLSMFEHDRTHYSKMVASLMPVLNMLTSSELGPLLSPIANDVDDSRLITDSGRIINNAQVAYIGLDSLTD
AMVGSAIGSLLLSDLTAVAGDRYNYGVENRPVNIFIDEAAEVVNDPFIQLLNKGRGAKMRCVIATQTFAD
FAARTGSEAKARQVLGNINNLIALRVMDAETQQYITDNLPKTRLQYIMQTQGMSSNSDSPALFTGNHGER
LMEEEGDMFPPQLLGQLPNLEYIAKLSGGRVIKGRIPILTSSTQAA
MKENAYEMPWRTNYEAMAAAGWLVGATGAIAAEMLTELPPEPFWWMTGISSGMALYRLPEAYRLYKLQMG
LKGKPLAFMELSHLQKVMAKHPDELWLGYGFEWDQRHAQRAYEILKRDKKTLLNQGHGKQMGSTWIHGVE
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: 44095..64266
| Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
|---|---|---|---|---|---|---|
| Locus_34 | 40154..40924 | + | 771 | AHM25073 | hypothetical protein | - |
| Locus_35 | 40959..41774 | + | 816 | AHM25074 | hypothetical protein | - |
| Locus_36 | 41896..44046 | + | 2151 | AHM25075 | Conjugative transfer protein TraI, relaxase | - |
| Locus_37 | 44095..45915 | + | 1821 | AHM25076 | IncF plasmid conjugative transfer protein TraD | virb4 |
| Locus_38 | 45949..46485 | + | 537 | AHM25077 | Conjugative transfer protein 234 | - |
| Locus_39 | 46472..47107 | + | 636 | AHM25078 | Conjugative transfer protein s043 | tfc7 |
| Locus_40 | 47134..47721 | - | 588 | AHM25079 | hypothetical protein | - |
| Locus_41 | 48010..48291 | + | 282 | AHM25080 | IncF plasmid conjugative transfer pilus assembly protein TraL | traL |
| Locus_42 | 48288..48914 | + | 627 | AHM25081 | IncF plasmid conjugative transfer pilus assembly protein TraE | traE |
| Locus_43 | 48898..49536 | + | 639 | AHM25082 | IncF plasmid conjugative transfer pilus assembly protein TraK | traK |
| Locus_44 | 49597..49872 | + | 276 | AHM25083 | IncF plasmid conjugative transfer pilus assembly protein TraK | traK |
| Locus_45 | 49875..51164 | + | 1290 | AHM25084 | IncF plasmid conjugative transfer pilus assembly protein TraB | traB |
| Locus_46 | 51161..51811 | + | 651 | AHM25085 | Conjugative transfer protein TraV | traV |
| Locus_47 | 51808..52194 | + | 387 | AHM25086 | Conjugative transfer protein TraA | - |
| Locus_48 | 52415..53206 | + | 792 | AHM25087 | Ynd | - |
| Locus_49 | 53199..54137 | + | 939 | AHM25088 | Ync | - |
| Locus_50 | 54269..54961 | + | 693 | AHM25089 | Thiol:disulfide involved in conjugative transfer | trbB |
| Locus_51 | 54961..57360 | + | 2400 | AHM25090 | IncF plasmid conjugative transfer pilus assembly protein TraC | virb4 |
| Locus_52 | 57353..57700 | + | 348 | AHM25091 | Conjugative transfer protein 345 | - |
| Locus_53 | 57684..58196 | + | 513 | AHM25092 | Conjugative signal peptidase TrhF | - |
| Locus_54 | 58207..58659 | + | 453 | AHM25093 | IncF plasmid conjugative transfer pilus assembly protein TraW | trbC |
| Locus_55 | 58782..59441 | + | 660 | AHM25094 | IncF plasmid conjugative transfer pilus assembly protein TraW | traW |
| Locus_56 | 59425..60453 | + | 1029 | AHM25095 | IncF plasmid conjugative transfer pilus assembly protein TraU | traU |
| Locus_57 | 60456..61364 | + | 909 | AHM25096 | IncF plasmid conjugative transfer protein TraN | traN |
| Locus_58 | 61498..62187 | + | 690 | AHM25097 | IncF plasmid conjugative transfer protein TraN | traN |
| Locus_59 | 62521..64266 | + | 1746 | AHM25098 | IncF plasmid conjugative transfer protein TraN | traN |
| Locus_60 | 64357..65973 | - | 1617 | AHM25099 | ATPase involved in DNA repair | - |
| Locus_61 | 66053..66808 | - | 756 | AHM25100 | Mobile element protein | - |
| Locus_62 | 66798..68306 | - | 1509 | AHM25101 | Mobile element protein | - |
Host bacterium
| ID | 140 | Element type | ICE (Integrative and conjugative element) |
| Element name | ICEVchNep1 | GenBank | KC886257 |
| Element size | 98222 bp | Coordinate of oriT [Strand] | 5166..5464 [+] |
| Host bacterium | Vibrio cholerae strain VC504 ICE element | Coordinate of element | 528..97877 |
Cargo genes
| Drug resistance gene | floR, aph(6)-Id, aph(3'')-Ib, sul2, dfrA1 |
| Virulence gene | - |
| Metal resistance gene | - |
| Degradation gene | - |
| Symbiosis gene | - |
| Anti-CRISPR | - |