Detailed information of oriT
oriT
The information of the oriT region
oriTDB ID | 100098 |
Name | oriT_pVCR94deltaX |
Organism | Vibrio cholerae strain BI144 |
Sequence Completeness | intact |
NCBI accession of oriT (coordinates [strand]) | KF551948 (_) |
oriT length | 398 nt |
IRs (inverted repeats) | IR1: 62..70, 71..79 (AACCCTTTC..GACAGGGTT) IR2: 143..150, 154..161 (TGGCCTGC..GGAGGCCA) |
Location of nic site | _ |
Conserved sequence flanking the nic site |
_ |
Note | _ |
oriT sequence
Download Length: 398 nt
CCCAAAAGGGGCATATAGGTTGCTTTTCGGTGGCTTTTTGATCGTTGAGTAAGGGAACCTATGGGAACGCTGCACGGATAGGCTCAGATAAACAGACCTTACCCTCGCATCGAGAACCGCTTGCCCTCCAGCATCGAGAGACGGTGGTAAAGAGGCATTTGGAATCTTTGATGCCATATCCAATATATCTGGAATCTTTAAATATAGATTCATATGTAAAGAGGCTGTGAAAGAATAAGAGCATCAAGATTCCAGATAGATAGAGGGAAATTTGACAAATTCCAAAGATGGGTTAGCCTAGTGACAGAACTAGATTCCAGTATTGGAATAATCAGCTTTAAATTCCAGATAGATAGTTATGTGGATAGGAATTGGATAGGAATTGGGAGGGTATTGAG
Visualization of oriT structure (The oriT was characterized experimentally)
oriT secondary structure
Predicted by RNAfold.
Download structure fileReference
[1] Carraro N et al. (2014) Development of pVCR94螖X from Vibrio cholerae, a prototype for studying multidrug resistant IncA/C conjugative plasmids. Front Microbiol. 0.238888889. [PMID:24567731]
Relaxase
ID | 93 | GenBank | AHC56417 |
Name | TraI_pVCR94deltaX | UniProt ID | V9SHT5 |
Length | 992 a.a. | PDB ID | |
Note | conjugative element relaxase |
Relaxase protein sequence
Download Length: 992 a.a. Molecular weight: 109595.88 Da Isoelectric Point: 4.8967
MLKALNKLFGGRSGVIETAPSARVLPLKDVEDEEIPRYPPFAKGLPVAPLDKILATQAELIEKVRNSLGF
TVDDFNRLVLPVIQRYAAFVHLLPASESHHHRGAGGLFRHGLEVAFWAAQASESVIFSIEGTPRERRDNE
PRWRLASCFSGLLHDVGKPLSDVSITDKDGSITWNPYSESLHDWAHRHEIDRYFIRWRDKRHKRHEQFSL
LAVDRIIPAETREFLSKSGPSIMEAMLEAISGTSVNQPVTKLMLRADQESVSRDLRQSRLDVDEFSYGVP
VERYVFDAIRRLVKTGKWKVNEPGAKVWHLNQGVFIAWKQLGDLYDLISHDKIPGIPRDPDTLADILIER
GFAVPNTVQEKGERAYYRYWEVLPEMLQEAAGSVKILMLRLESNDLVFTTEPPAAVAAEVVGDVEDAEIE
FVDPEEADDGDDQEEGEAALNDDMLAAEQEAEKALAGLGFGDAMEMLKSTSDAVEEKPEQKDAGPTESSK
PDAGKKGKPQSKPGKAKPKSDTEKQPHKPEAKEDLSPQDIAKNAPPLANDNPLQALKDVGGGLGDIDFPF
DAFNASAETTSTDATNSEIPDVAMPGKQEEQPKQDFVPQEQNSLQGDDFPMFGGSDEPPSWAIEPLPMLT
DAPEQPTHTPEMPHTDNVNQHEKDAKTLLVEMLSGYGEASALLEQAIMPVLEGKTTLGEVLCLMKGQAVI
LYPDGARSLGAPSEVLSKLSHANAIVPDPIMPGRKVRDFSGVKAIVLAEQLSDAVVAAIKDAEASMGGYQ
DAFELVSPPGLDASKNKSAPKQQSRKKAQQQKPEVNAGKASPEQKAKGKDSQPQPKEKKVDVTSPVEEQQ
RKPVQEKQNVARLPKREAQPVAPEPKVEREKELGHVEVREREEPEVREFEPPKAKTNPKDINAEDFLPSG
VTPQKALQMLKDMIQKRSGRWLVTPVLEEDGCLVTSDKAFDMIAGENIGISKHILCGMLSRAQRRPLLKK
RQGKLYLEVNET
Protein domains
Predicted by InterproScan.
Protein structure
Source | ID | Structure |
---|---|---|
AlphaFold DB | V9SHT5 |
Reference
[1] Carraro N et al. (2014) Development of pVCR94螖X from Vibrio cholerae, a prototype for studying multidrug resistant IncA/C conjugative plasmids. Front Microbiol. 0.238888889. [PMID:24567731]
Auxiliary protein
ID | 134 | GenBank | AHC56420 |
Name | TraJ_pVCR94deltaX | UniProt ID | V9SH95 |
Length | 209 a.a. | PDB ID | _ |
Note | _ |
Auxiliary protein sequence
Download Length: 209 a.a. Molecular weight: 24169.77 Da Isoelectric Point: 9.4782
MKKPWLLVAWLLVIELLAILLLIPGDWTDRAIKRESVLVEQSLGVEARDWIQNKASTWFRSSVIDSGFYE
GMYQTLIPSEEERQKSKGMQDMGKGWFVWVKGRMEAFVNVIYQFYTRLALLAAWAPYMLILFVPAVYDGM
MTWRIKRTNFDYASPVLHRYSVRGTMYLMAGLFIAFFIPIALDPVVIPMTMMTCCVLVGLTFGNLQKRV
Protein domains
Predicted by InterproScan.
Protein structure
Source | ID | Structure |
---|---|---|
AlphaFold DB | V9SH95 |
Reference
[1] Carraro N et al. (2014) Development of pVCR94螖X from Vibrio cholerae, a prototype for studying multidrug resistant IncA/C conjugative plasmids. Front Microbiol. 0.238888889. [PMID:24567731]
T4CP
ID | 93 | GenBank | AHC56418 |
Name | TraD_pVCR94deltaX | UniProt ID | V9SIV0 |
Length | 621 a.a. | PDB ID | _ |
Note | conjugative coupling factor TraD |
T4CP protein sequence
Download Length: 621 a.a. Molecular weight: 69225.71 Da Isoelectric Point: 6.9403
MTMSYDPLAYEMPWRPNYEKNAVAGWLAASGAALAVEQVSTMPPEPFYWMTGICGVMAMARLPKAIKLHL
LQKHLKGRDLEFISIAELQKYIKDTPDDMWLGSGFLWENRHAQRVFEILKRDWTSIVGRESTVKKVVRKI
QGKKKELPIGQPWIHGVEPKEEKLMQPLKHTEGHSLIVGTTGSGKTRMFDILISQAILRGEAVIIIDPKG
DKEMRDNARRACEAMGQPERFVSFHPAFPEESVRIDPLRNFTRVTEIASRLAALIPSEAGADPFKSFGWQ
ALNNIAQGLVITHDRPNLTKLRRFLEGGAAGLVIKAVQAYSERVMPDWEAEAAAYLEKVKNGSREKIAFA
LMKFYYDIIQPEHPNSDLEGLLSMFQHDQTHFSKMVANLLPIMNMLTSGELGPLLSPDSSDLSDERQITD
SAKIINNAQVAYLGLDSLTDNMVGSAMGSIFLSDLTAVAGDRYNYGVNNRPVNIFVDEAAEVINDPFIQL
LNKGRGAKLRLFVATQTFADFAARLGSKDKALQVLGNINNTFALRIVDGETQEYIADNLPKTRLKYVMRT
QGQNSDGKEPIMHGGNQGERLMEEEADLFPAQLLGMLPNLEYIAKISGGTIVKGRLPILTQ
Protein domains
Predicted by InterproScan.
Protein structure
Source | ID | Structure |
---|---|---|
AlphaFold DB | V9SIV0 |
T4SS
T4SS were predicted by using oriTfinder2.
Region 1: 38088..63279
Locus tag | Coordinates | Strand | Size (bp) | Protein ID | Product | Description |
---|---|---|---|---|---|---|
Vcrx058 | 34113..34346 | - | 234 | AHC56415 | hypothetical protein | - |
Vcrx059 | 34328..34945 | - | 618 | AHC56416 | hypothetical protein | - |
Vcrx060 | 35113..38091 | + | 2979 | AHC56417 | TraI | - |
Vcrx061 | 38088..39953 | + | 1866 | AHC56418 | TraD | virb4 |
Vcrx062 | 39964..40548 | + | 585 | AHC56419 | hypothetical protein | - |
Vcrx063 | 40505..41134 | + | 630 | AHC56420 | TraJ | tfc7 |
Vcrx064 | 41144..41590 | + | 447 | AHC56421 | hypothetical protein | - |
Vcrx065 | 41600..41977 | + | 378 | AHC56422 | hypothetical protein | - |
Vcrx066 | 41977..42639 | + | 663 | AHC56423 | hypothetical protein | - |
Vcrx067 | 42636..42776 | + | 141 | AHC56424 | hypothetical protein | - |
Vcrx068 | 42820..42963 | + | 144 | AHC56425 | hypothetical protein | - |
Vcrx069 | 42975..43340 | + | 366 | AHC56426 | hypothetical protein | - |
Vcrx070 | 43485..43766 | + | 282 | AHC56427 | TraL | traL |
Vcrx071 | 43763..44389 | + | 627 | AHC56428 | TraE | traE |
Vcrx072 | 44373..45290 | + | 918 | AHC56429 | TraK | traK |
Vcrx073 | 45287..46603 | + | 1317 | AHC56430 | TraB | traB |
Vcrx074 | 46600..47178 | + | 579 | AHC56431 | TraV | traV |
Vcrx075 | 47191..47574 | + | 384 | AHC56432 | TraA | - |
Vcrx076 | 47775..53306 | + | 5532 | AHC56433 | hypothetical protein | - |
Vcrx077 | 53455..54162 | + | 708 | AHC56434 | DsbC | - |
Vcrx078 | 54159..56606 | + | 2448 | AHC56435 | TraC | virb4 |
Vcrx079 | 56621..56938 | + | 318 | AHC56436 | hypothetical protein | - |
Vcrx080 | 56935..57465 | + | 531 | AHC56437 | TrhF | - |
Vcrx081 | 57476..58693 | + | 1218 | AHC56438 | TraW | traW |
Vcrx082 | 58690..59361 | + | 672 | AHC56439 | hypothetical protein | - |
Vcrx083 | 59358..60365 | + | 1008 | AHC56440 | TraU | traU |
Vcrx084 | 60481..63279 | + | 2799 | AHC56441 | TraN | traN |
Vcrx085 | 63318..64178 | - | 861 | AHC56442 | hypothetical protein | - |
Vcrx086 | 64301..64942 | - | 642 | AHC56443 | hypothetical protein | - |
Vcrx087 | 65235..65555 | + | 321 | AHC56444 | hypothetical protein | - |
Vcrx088 | 65859..66044 | + | 186 | AHC56445 | hypothetical protein | - |
Vcrx089 | 66263..67231 | + | 969 | AHC56446 | hypothetical protein | - |
Vcrx090 | 67242..68147 | + | 906 | AHC56447 | hypothetical protein | - |
Host bacterium
ID | 93 | GenBank | KF551948 |
Plasmid name | pVCR94deltaX | Incompatibility group | IncA/C2 |
Plasmid size | 120572 bp | Coordinate of oriT [Strand] | 39954..40504 [+] |
Host baterium | Vibrio cholerae strain BI144 |
Cargo genes
Drug resistance gene | resistance to sulfamethoxazole |
Virulence gene | - |
Metal resistance gene | - |
Degradation gene | - |
Symbiosis gene | - |
Anti-CRISPR | - |