Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103181
Name   oriT_pVC211 in_silico
Organism   Vibrio cholerae O139 strain ICDC-211
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KY399978 (66415..66565 [+], 151 nt)
oriT length   151 nt
IRs (inverted repeats)      93..98, 106..111  (TGGCCT..AGGCCA)
 12..17, 24..29  (AACCCT..AGGGTT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 151 nt

>oriT_pVC211
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2382 GenBank   WP_001337757
Name   TraI_2_HTM30_RS00455_pVC211 insolico UniProt ID   A0A709FRI2
Length   992 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 992 a.a.        Molecular weight: 109581.85 Da        Isoelectric Point: 4.8956

>WP_001337757.1 MULTISPECIES: MobH family relaxase [Gammaproteobacteria]
MLKALNKLFGGRSGVIETAPSARVLPLKDVEDEEIPRYPPFAKGLPVAPLDKILATQAELIEKVRNSLGF
TVDDFNRLVLPVIQRYAAFVHLLPASESHHHRGAGGLFRHGLEVAFWAAQASESVIFSIEGTPRERRDNE
PRWRLASCFSGLLHDVGKPLSDVSITDKDGSITWNPYSESLHDWAHRHEIDRYFIRWRDKRHKRHEQFSL
LAVDRIIPAETREFLSKSGPSIMEAMLEAISGTSVNQPVTKLMLRADQESVSRDLRQSRLDVDEFSYGVP
VERYVFDAIRRLVKTGKWKVNEPGAKVWHLNQGVFIAWKQLGDLYDLISHDKIPGIPRDPDTLADILIER
GFAVPNTVQEKGERAYYRYWEVLPEMLQEAAGSVKILMLRLESNDLVFTTEPPAAVAAEVVGDVEDAEIE
FVDPEEADDGDDQEEGEAALNDDMLAAEQEAEKALAGLGFGDAMEMLKSTSDAVEEKPEQKDAGPTESSK
PDAGKKGKPQSKPGKAKPKSDTEKQPHKPEAKEDLSPQDIAKNAPPLANDNPLQALKDVGGGLGDIDFPF
DAFNASAETTSTDATNSEIPDVAMPGKQEEQPKQDFVPQEQNSLQGDDFPMFGGSDEPPSWAIEPLPMLT
DAPEQPTHTPEMPHTDNVNQHEKDAKTLLVEMLSGYGEASALLEQAIMPVLEGKTTLGEVLCLMKGQAVI
LYPDGARSLGAPSEVLSKLSHANAIVPDPIMPGRKVRDFSGVKAIVLAEQLSDAVVAAIKDAEASMGGYQ
DAFELVSPPGLDASKNKSAPKQQSRKKAQQQKPEVNAGKASPEQKAKGKDSQPQPKEKKVDVTSPVEEQQ
RKPVQEKQNVARLPKREAQPVAPEPKVEREKELGHVEVREREDPEVREFEPPKAKTNPKDINAEDFLPSG
VTPQKALQMLKDMIQKRSGRWLVTPVLEEDGCLVTSDKAFDMIAGENIGISKHILCGMLSRAQRRPLLKK
RQGKLYLEVNET

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(51-357)


  Protein structure


Source ID Structure
AlphaFold DB A0A709FRI2


T4CP

ID   2130 GenBank   WP_000178856
Name   traD_HTM30_RS00460_pVC211 insolico UniProt ID   _
Length   621 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 621 a.a.        Molecular weight: 69197.66 Da        Isoelectric Point: 6.9403

>WP_000178856.1 MULTISPECIES: conjugative transfer system coupling protein TraD [Gammaproteobacteria]
MTMSYDPLAYEMPWRPNYEKNAVAGWLAASGAALAVEQVSTMPPEPFYWMTGICGVMAMARLPKAIKLHL
LQKHLKGRDLEFISIAELQKYIKDTPDDMWLGSGFLWENRHAQRVFEILKRDWTSIVGRESTVKKVVRKI
QGKKKELPIGQPWIHGVEPKEEKLMQPLKHTEGHSLIVGTTGSGKTRMFDILISQAILRGEAVIIIDPKG
DKEMRDNARRACEAMGQPERFVSFHPAFPEESVRIDPLRNFTRVTEIASRLAALIPSEAGADPFKSFGWQ
ALNNIAQGLVITHDRPNLTKLRRFLEGGAAGLVIKAVQAYSERVMPDWEAEAAAYLEKAKNGSREKIAFA
LMKFYYDIIQPEHPNSDLEGLLSMFQHDQTHFSKMVANLLPIMNMLTSGELGPLLSPDSSDLSDERQITD
SAKIINNAQVAYLGLDSLTDNMVGSAMGSIFLSDLTAVAGDRYNYGVNNRPVNIFVDEAAEVINDPFIQL
LNKGRGAKLRLFVATQTFADFAARLGSKDKALQVLGNINNTFALRIVDGETQEYIADNLPKTRLKYVMRT
QGQNSDGKEPIMHGGNQGERLMEEEADLFPAQLLGMLPNLEYIAKISGGTIVKGRLPILTQ

  Protein domains


Predicted by InterproScan.

TraM recognition site of TraD and TraG (TraG-D_C)

(471-598)

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(170-297)

  Protein structure



No available structure.



ID   2131 GenBank   WP_000637386
Name   traC_HTM30_RS00540_pVC211 insolico UniProt ID   _
Length   815 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 815 a.a.        Molecular weight: 92590.87 Da        Isoelectric Point: 5.9222

>WP_000637386.1 MULTISPECIES: type IV secretion system protein TraC [Gammaproteobacteria]
MIVTIKKKLEETLIPEHLRAAGIIPVLAYDEDDHVFLMDDHSAGFGFMCEPLCGADEKVQERMNGFLNQE
FPSKTTLQFVLFRSPDINQEMYRMMGLRDGFRHELLTSVIKERINFLQHHTTERIFAKTNKGIYDNGLIQ
DLKLFVTCKVPIKNNNPTESELQQLAQLRTKVESSLQTVGLRPRTMTAVNYIRIMSTILNWGPDASWRHD
SVDWEMDKPICEQIFDYGTDVEVSKNGIRLGDYHAKVMSAKKLPDVFYFGDALTYAGDLSGGNSSIKENY
MVVTNVFFPEAESTKNTLERKRQFTVNQAYGPMLKFVPVLADKKESFDTLYESMKEGAKPVKITYSVVLF
APTKERVEAAAMAARNIWRESRFELMEDKFVALPMFLNCLPFCTDRDAVRDLFRYKTMTTEQAAVVLPVF
GEWKGTGTYHAALISRNGQLMSLSLHDSNTNKNLVIAAESGSGKSFLTNELIFSYLSEGAQVWVIDAGKS
YQKLSEMLNGDFVHFEEGTHVCLNPFELIQNYEDEEDAIVSLVCAMASAKGLLDEWQISALKQVLSRLWE
EKGKEMKVDDIAERCLEEENDQRLKDIGQQLYAFTSKGSYGKYFSRKNNVSFQNQFTVLELDELQGRKHL
RQVVLLQLIYQIQQEVFLGERNRKKVVIVDEAWDLLKEGEVSVFMEHAYRKFRKYGGSVVIATQSINDLY
ENAVGRAIAENSASMYLLGQTEETVESVKRSGRLTLSEGGFHTLKTVHTIQGVYSEIFIKSKSGMGVGRL
IVGDFQKLLYSTDPVDVNAIDQFVKQGMSIPEAIKAVMRSRQQAA

  Protein domains


Predicted by InterproScan.

TraG P-loop domain (P-loop_TraG)

(449-809)

Family of unknown function (DUF5934) (DUF5934)

(284-434)

TraC protein (TraC_F_IV)

(21-255)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 64499..89690

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTM30_RS00445 60524..60757 - 234 WP_001191892 hypothetical protein -
HTM30_RS00450 60739..61356 - 618 WP_001249396 hypothetical protein -
HTM30_RS00455 61524..64502 + 2979 WP_001337757 MobH family relaxase -
HTM30_RS00460 64499..66364 + 1866 WP_000178856 conjugative transfer system coupling protein TraD virb4
HTM30_RS00465 66375..66959 + 585 WP_000332866 hypothetical protein -
HTM30_RS00470 66916..67545 + 630 WP_000743450 DUF4400 domain-containing protein tfc7
HTM30_RS00475 67555..68001 + 447 WP_000122506 hypothetical protein -
HTM30_RS00480 68011..68388 + 378 WP_000869261 hypothetical protein -
HTM30_RS00485 68388..69050 + 663 WP_001231463 hypothetical protein -
HTM30_RS00490 69231..69374 + 144 WP_001275801 hypothetical protein -
HTM30_RS00495 69386..69751 + 366 WP_001052531 hypothetical protein -
HTM30_RS00500 69896..70177 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
HTM30_RS00505 70174..70800 + 627 WP_001049716 TraE/TraK family type IV conjugative transfer system protein traE
HTM30_RS00510 70784..71701 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
HTM30_RS00515 71701..73014 + 1314 WP_024131605 TraB/VirB10 family protein traB
HTM30_RS00520 73011..73589 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
HTM30_RS00525 73593..73985 + 393 WP_000479535 TraA family conjugative transfer protein -
HTM30_RS00530 74186..79717 + 5532 WP_000606833 Ig-like domain-containing protein -
HTM30_RS00535 79866..80573 + 708 WP_001259347 DsbC family protein -
HTM30_RS00540 80570..83017 + 2448 WP_000637386 type IV secretion system protein TraC virb4
HTM30_RS00545 83032..83349 + 318 WP_000351984 hypothetical protein -
HTM30_RS00550 83346..83876 + 531 WP_001010738 S26 family signal peptidase -
HTM30_RS00555 83839..85104 + 1266 WP_000621288 TrbC family F-type conjugative pilus assembly protein traW
HTM30_RS00560 85101..85772 + 672 WP_001337754 EAL domain-containing protein -
HTM30_RS00565 85772..86776 + 1005 WP_043940352 TraU family protein traU
HTM30_RS00570 86880..89690 + 2811 WP_001909286 conjugal transfer mating pair stabilization protein TraN traN
HTM30_RS00575 89729..90589 - 861 WP_000709517 hypothetical protein -
HTM30_RS00580 90712..91353 - 642 WP_000796664 hypothetical protein -
HTM30_RS00585 91647..91967 + 321 WP_000547566 hypothetical protein -
HTM30_RS00590 92271..92456 + 186 WP_001186917 hypothetical protein -
HTM30_RS00595 92676..93644 + 969 WP_000085162 AAA family ATPase -
HTM30_RS00600 93655..94563 + 909 WP_000739139 hypothetical protein -

Host bacterium

ID   3624 GenBank   NZ_KY399978
Plasmid name   pVC211 Incompatibility group   IncA/C2
Plasmid size   148456 bp Coordinate of oriT [Strand]   66415..66565 [+]
Host baterium   Vibrio cholerae O139 strain ICDC-211

Cargo genes

Drug resistance gene   dfrA14, ARR-3, aadA3, qacE, sul1, mph(A), msr(E), mph(E), floR, tet(A), aph(6)-Id, aph(3'')-Ib, sul2
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -