Detailed information of oriT

oriT


The information of the oriT region


oriTDB ID   100098
Name   oriT_pVCR94deltaX experimental
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

>oriT_pVCR94deltaX
CCCAAAAGGGGCATATAGGTTGCTTTTCGGTGGCTTTTTGATCGTTGAGTAAGGGAACCTATGGGAACGCTGCACGGATAGGCTCAGATAAACAGACCTTACCCTCGCATCGAGAACCGCTTGCCCTCCAGCATCGAGAGACGGTGGTAAAGAGGCATTTGGAATCTTTGATGCCATATCCAATATATCTGGAATCTTTAAATATAGATTCATATGTAAAGAGGCTGTGAAAGAATAAGAGCATCAAGATTCCAGATAGATAGAGGGAAATTTGACAAATTCCAAAGATGGGTTAGCCTAGTGACAGAACTAGATTCCAGTATTGGAATAATCAGCTTTAAATTCCAGATAGATAGTTATGTGGATAGGAATTGGATAGGAATTGGGAGGGTATTGAG

Visualization of oriT structure (The oriT was characterized experimentally)

  oriT secondary structure

Predicted by RNAfold.

Download structure file

  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]


Relaxase


ID   93 GenBank   AHC56417
Name   TraI_pVCR94deltaX insolico 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

>AHC56417.1 TraI (plasmid) [Vibrio cholerae]
MLKALNKLFGGRSGVIETAPSARVLPLKDVEDEEIPRYPPFAKGLPVAPLDKILATQAELIEKVRNSLGF
TVDDFNRLVLPVIQRYAAFVHLLPASESHHHRGAGGLFRHGLEVAFWAAQASESVIFSIEGTPRERRDNE
PRWRLASCFSGLLHDVGKPLSDVSITDKDGSITWNPYSESLHDWAHRHEIDRYFIRWRDKRHKRHEQFSL
LAVDRIIPAETREFLSKSGPSIMEAMLEAISGTSVNQPVTKLMLRADQESVSRDLRQSRLDVDEFSYGVP
VERYVFDAIRRLVKTGKWKVNEPGAKVWHLNQGVFIAWKQLGDLYDLISHDKIPGIPRDPDTLADILIER
GFAVPNTVQEKGERAYYRYWEVLPEMLQEAAGSVKILMLRLESNDLVFTTEPPAAVAAEVVGDVEDAEIE
FVDPEEADDGDDQEEGEAALNDDMLAAEQEAEKALAGLGFGDAMEMLKSTSDAVEEKPEQKDAGPTESSK
PDAGKKGKPQSKPGKAKPKSDTEKQPHKPEAKEDLSPQDIAKNAPPLANDNPLQALKDVGGGLGDIDFPF
DAFNASAETTSTDATNSEIPDVAMPGKQEEQPKQDFVPQEQNSLQGDDFPMFGGSDEPPSWAIEPLPMLT
DAPEQPTHTPEMPHTDNVNQHEKDAKTLLVEMLSGYGEASALLEQAIMPVLEGKTTLGEVLCLMKGQAVI
LYPDGARSLGAPSEVLSKLSHANAIVPDPIMPGRKVRDFSGVKAIVLAEQLSDAVVAAIKDAEASMGGYQ
DAFELVSPPGLDASKNKSAPKQQSRKKAQQQKPEVNAGKASPEQKAKGKDSQPQPKEKKVDVTSPVEEQQ
RKPVQEKQNVARLPKREAQPVAPEPKVEREKELGHVEVREREEPEVREFEPPKAKTNPKDINAEDFLPSG
VTPQKALQMLKDMIQKRSGRWLVTPVLEEDGCLVTSDKAFDMIAGENIGISKHILCGMLSRAQRRPLLKK
RQGKLYLEVNET

  Protein domains


Predicted by InterproScan.

(51-357)


  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 insolico 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

>AHC56420.1 TraJ (plasmid) [Vibrio cholerae]
MKKPWLLVAWLLVIELLAILLLIPGDWTDRAIKRESVLVEQSLGVEARDWIQNKASTWFRSSVIDSGFYE
GMYQTLIPSEEERQKSKGMQDMGKGWFVWVKGRMEAFVNVIYQFYTRLALLAAWAPYMLILFVPAVYDGM
MTWRIKRTNFDYASPVLHRYSVRGTMYLMAGLFIAFFIPIALDPVVIPMTMMTCCVLVGLTFGNLQKRV

  Protein domains


Predicted by InterproScan.

(44-201)


  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 insolico 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

>AHC56418.1 TraD (plasmid) [Vibrio cholerae]
MTMSYDPLAYEMPWRPNYEKNAVAGWLAASGAALAVEQVSTMPPEPFYWMTGICGVMAMARLPKAIKLHL
LQKHLKGRDLEFISIAELQKYIKDTPDDMWLGSGFLWENRHAQRVFEILKRDWTSIVGRESTVKKVVRKI
QGKKKELPIGQPWIHGVEPKEEKLMQPLKHTEGHSLIVGTTGSGKTRMFDILISQAILRGEAVIIIDPKG
DKEMRDNARRACEAMGQPERFVSFHPAFPEESVRIDPLRNFTRVTEIASRLAALIPSEAGADPFKSFGWQ
ALNNIAQGLVITHDRPNLTKLRRFLEGGAAGLVIKAVQAYSERVMPDWEAEAAAYLEKVKNGSREKIAFA
LMKFYYDIIQPEHPNSDLEGLLSMFQHDQTHFSKMVANLLPIMNMLTSGELGPLLSPDSSDLSDERQITD
SAKIINNAQVAYLGLDSLTDNMVGSAMGSIFLSDLTAVAGDRYNYGVNNRPVNIFVDEAAEVINDPFIQL
LNKGRGAKLRLFVATQTFADFAARLGSKDKALQVLGNINNTFALRIVDGETQEYIADNLPKTRLKYVMRT
QGQNSDGKEPIMHGGNQGERLMEEEADLFPAQLLGMLPNLEYIAKISGGTIVKGRLPILTQ

  Protein domains


Predicted by InterproScan.

(170-299)

(471-598)

  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   -