Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103322
Name   oriT_pVb0506 in_silico
Organism   Vibrio alginolyticus strain Vb0506
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MF497432 (52939..53089 [+], 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_pVb0506
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2480 GenBank   WP_001337757
Name   TraI_2_HTP67_RS00375_pVb0506 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   2266 GenBank   WP_000178856
Name   traD_HTP67_RS00380_pVb0506 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   2267 GenBank   WP_000637386
Name   traC_HTP67_RS00460_pVb0506 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: 51023..76214

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTP67_RS00365 47048..47281 - 234 WP_001191892 hypothetical protein -
HTP67_RS00370 47263..47880 - 618 WP_001249396 hypothetical protein -
HTP67_RS00375 48048..51026 + 2979 WP_001337757 MobH family relaxase -
HTP67_RS00380 51023..52888 + 1866 WP_000178856 conjugative transfer system coupling protein TraD virb4
HTP67_RS00385 52899..53483 + 585 WP_000332866 hypothetical protein -
HTP67_RS00390 53440..54069 + 630 WP_000743450 DUF4400 domain-containing protein tfc7
HTP67_RS00395 54079..54525 + 447 WP_000122506 hypothetical protein -
HTP67_RS00400 54535..54912 + 378 WP_000869261 hypothetical protein -
HTP67_RS00405 54912..55574 + 663 WP_001231463 hypothetical protein -
HTP67_RS00410 55755..55898 + 144 WP_001275801 hypothetical protein -
HTP67_RS00415 55910..56275 + 366 WP_001052531 hypothetical protein -
HTP67_RS00420 56420..56701 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
HTP67_RS00425 56698..57324 + 627 WP_001049716 TraE/TraK family type IV conjugative transfer system protein traE
HTP67_RS00430 57308..58225 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
HTP67_RS00435 58225..59538 + 1314 WP_024131605 TraB/VirB10 family protein traB
HTP67_RS00440 59535..60113 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
HTP67_RS00445 60117..60509 + 393 WP_000479535 TraA family conjugative transfer protein -
HTP67_RS00450 60710..66241 + 5532 WP_000606833 Ig-like domain-containing protein -
HTP67_RS00455 66390..67097 + 708 WP_001259347 DsbC family protein -
HTP67_RS00460 67094..69541 + 2448 WP_000637386 type IV secretion system protein TraC virb4
HTP67_RS00465 69556..69873 + 318 WP_000351984 hypothetical protein -
HTP67_RS00470 69870..70400 + 531 WP_001010738 S26 family signal peptidase -
HTP67_RS00475 70363..71628 + 1266 WP_000621288 TrbC family F-type conjugative pilus assembly protein traW
HTP67_RS00480 71625..72296 + 672 WP_001337754 EAL domain-containing protein -
HTP67_RS00485 72296..73300 + 1005 WP_043940352 TraU family protein traU
HTP67_RS00490 73416..76214 + 2799 WP_001256487 conjugal transfer mating pair stabilization protein TraN traN
HTP67_RS00495 76253..77113 - 861 WP_000709517 hypothetical protein -
HTP67_RS00500 77236..77877 - 642 WP_000796664 hypothetical protein -
HTP67_RS00505 78171..78491 + 321 WP_000547566 hypothetical protein -
HTP67_RS00510 78729..78980 + 252 WP_001447717 hypothetical protein -
HTP67_RS00515 79200..80168 + 969 WP_000085162 AAA family ATPase -
HTP67_RS00520 80179..81087 + 909 WP_000739139 hypothetical protein -

Host bacterium

ID   3765 GenBank   NZ_MF497432
Plasmid name   pVb0506 Incompatibility group   IncA/C2
Plasmid size   133742 bp Coordinate of oriT [Strand]   52939..53089 [+]
Host baterium   Vibrio alginolyticus strain Vb0506

Cargo genes

Drug resistance gene   dfrA23, blaCTX-M-15, tet(A), aph(6)-Id, aph(3'')-Ib, sul2
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -