Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   114650
Name   oriT_pVb1282-tet in_silico
Organism   Vibrio parahaemolyticus strain Vb1282
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_OQ622010 (50161..50311 [+], 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_pVb1282-tet
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9396 GenBank   WP_001326173
Name   mobH_RA150_RS00350_pVb1282-tet insolico UniProt ID   F5BPR1
Length   990 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 990 a.a.        Molecular weight: 109356.90 Da        Isoelectric Point: 4.9395

>WP_001326173.1 MULTISPECIES: MobH family relaxase [Gammaproteobacteria]
MLKALNKLFGGRSGVIETAPSVRVLPLKDVEDEEIPRYPPFAKGLPVAPLDKILATQAELIEKVRNSLGF
TVDDFNRLVLPVIQRYAAFVHLLPASESHHHRGAGGLFRHGLEVAFWAAQASESVIFSIEGTPRERRDNE
PRWRLASCFSGLLHDVGKPLSDVSITDKDGSITWNPYSESLHDWAHRHEIDRYFIRWRDKRHKRHEQFSL
LAVDRIIPAETREFLSKSGPSIMEAMLEAISGTSVNQPVTKLMLRADQESVSRDLRQSRLDVDEFSYGVP
VERYVFDAIRRLVKTGKWKVNEPGAKVWHLNQGVFIAWKQLGDLYDLISHDKIPGIPRDPDTLADILIER
GFAVPNTVQEKGERAYYRYWEVLPEMLQEAAGSVKILMLRLESNDLVFTTEPPAAVAAEVVGDVEDAEIE
FVDPEEVDDDQEEDVSALNDDMLAAEQEAEKALAGLGFGDAMEMLKSTSDAVEEKPEQKDAGSTESSKPD
AGKKGKPQSKPGKAKPKSDTEKQPHKPEAKEDLSPQDIAKNAPPLANDNPLQALKDVGGGLGDIDFPFDA
FSASAETASTDATNSEIPDVAMPGKQEKQPKQDFVPQEQNSLQGDDFPMFGSSDEPPSWAIEPLPMLTDA
PEQTTPAPAMPPTDKPNLHEKDAKTLLVEMLAGYGEASALLEQAIMPVLEGKTTLGEVLCLMKGQAVILY
PDGARSLGAPSEVLSKLSHANAIVPDPIMPGRKVRDFSGVKAIVLAEQLSDAVVAAIKDAEASMGGYQDA
FELVSPPGLDASKNKSAPKQQSRKKAQQQKPEVNAGKPSPEQKAKGKDSQPQQKEKKVDVTSPVEEPQRQ
PVQEKQNVARLPKREVQPVAPEPKVEREKELGHVEVREREEPEVREFEPPKAKTNPKDINAEDFLPSGVT
PQKALQMLKDMIQKRSGRWLVTPVLEEDGCLVTSDKAFDMIAGENIGISKHILCGMLSRAQRRPLLKKRQ
GKLYLEVNET

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(51-357)


  Protein structure


Source ID Structure
AlphaFold DB F5BPR1


T4CP

ID   10910 GenBank   WP_000178857
Name   traD_RA150_RS00355_pVb1282-tet 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: 69225.71 Da        Isoelectric Point: 6.9403

>WP_000178857.1 MULTISPECIES: conjugative transfer system coupling protein TraD [Gammaproteobacteria]
MTMSYDPLAYEMPWRPNYEKNAVAGWLAASGAALAVEQVSTMPPEPFYWMTGICGVMAMARLPKAIKLHL
LQKHLKGRDLEFISIAELQKYIKDTPDDMWLGSGFLWENRHAQRVFEILKRDWTSIVGRESTVKKVVRKI
QGKKKELPIGQPWIHGVEPKEEKLMQPLKHTEGHSLIVGTTGSGKTRMFDILISQAILRGEAVIIIDPKG
DKEMRDNARRACEAMGQPERFVSFHPAFPEESVRIDPLRNFTRVTEIASRLAALIPSEAGADPFKSFGWQ
ALNNIAQGLVITHDRPNLTKLRRFLEGGAAGLVIKAVQAYSERVMPDWEAEAAAYLEKVKNGSREKIAFA
LMKFYYDIIQPEHPNSDLEGLLSMFQHDQTHFSKMVANLLPIMNMLTSGELGPLLSPDSSDLSDERQITD
SAKIINNAQVAYLGLDSLTDNMVGSAMGSIFLSDLTAVAGDRYNYGVNNRPVNIFVDEAAEVINDPFIQL
LNKGRGAKLRLFVATQTFADFAARLGSKDKALQVLGNINNTFALRIVDGETQEYIADNLPKTRLKYVMRT
QGQNSDGKEPIMHGGNQGERLMEEEADLFPAQLLGMLPNLEYIAKISGGTIVKGRLPILTQ

  Protein domains


Predicted by InterproScan.

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

(170-299)

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

(471-598)

  Protein structure



No available structure.



ID   10911 GenBank   WP_000637386
Name   traC_RA150_RS00435_pVb1282-tet 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: 48245..73436

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
RA150_RS00340 44276..44509 - 234 WP_001191890 hypothetical protein -
RA150_RS00345 44491..45108 - 618 WP_001249395 hypothetical protein -
RA150_RS00350 45276..48248 + 2973 WP_001326173 MobH family relaxase -
RA150_RS00355 48245..50110 + 1866 WP_000178857 conjugative transfer system coupling protein TraD virb4
RA150_RS00360 50121..50705 + 585 WP_000332868 hypothetical protein -
RA150_RS00365 50662..51291 + 630 WP_000743449 DUF4400 domain-containing protein tfc7
RA150_RS00370 51301..51747 + 447 WP_172692927 hypothetical protein -
RA150_RS00375 51757..52134 + 378 WP_000869261 hypothetical protein -
RA150_RS00380 52134..52796 + 663 WP_001231463 hypothetical protein -
RA150_RS00385 52977..53120 + 144 WP_001275801 hypothetical protein -
RA150_RS00390 53120..53497 + 378 WP_000509509 hypothetical protein -
RA150_RS00395 53642..53923 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
RA150_RS00400 53920..54546 + 627 WP_001049716 TraE/TraK family type IV conjugative transfer system protein traE
RA150_RS00405 54530..55447 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
RA150_RS00410 55447..56760 + 1314 WP_024131605 TraB/VirB10 family protein traB
RA150_RS00415 56757..57335 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
RA150_RS00420 57339..57731 + 393 WP_000479535 TraA family conjugative transfer protein -
RA150_RS00425 57932..63463 + 5532 WP_000606833 Ig-like domain-containing protein -
RA150_RS00430 63612..64319 + 708 WP_172692928 DsbC family protein -
RA150_RS00435 64316..66763 + 2448 WP_000637386 type IV secretion system protein TraC virb4
RA150_RS00440 66778..67095 + 318 WP_000351984 hypothetical protein -
RA150_RS00445 67092..67622 + 531 WP_001010738 S26 family signal peptidase -
RA150_RS00450 67585..68850 + 1266 WP_000621288 TrbC family F-type conjugative pilus assembly protein traW
RA150_RS00455 68847..69518 + 672 WP_001337754 EAL domain-containing protein -
RA150_RS00460 69518..70522 + 1005 WP_043940352 TraU family protein traU
RA150_RS00465 70626..73436 + 2811 WP_001909286 conjugal transfer mating pair stabilization protein TraN traN
RA150_RS00470 73475..74335 - 861 WP_000709517 hypothetical protein -
RA150_RS00475 74458..75099 - 642 WP_000796664 hypothetical protein -
RA150_RS00480 75393..75713 + 321 WP_000547566 hypothetical protein -
RA150_RS00485 76017..76202 + 186 WP_001186917 hypothetical protein -
RA150_RS00490 76422..77390 + 969 WP_000085162 AAA family ATPase -
RA150_RS00495 77401..78309 + 909 WP_000739139 hypothetical protein -

Host bacterium

ID   15085 GenBank   NZ_OQ622010
Plasmid name   pVb1282-tet Incompatibility group   IncA/C2
Plasmid size   167705 bp Coordinate of oriT [Strand]   50161..50311 [+]
Host baterium   Vibrio parahaemolyticus strain Vb1282

Cargo genes

Drug resistance gene   floR, tet(A), aph(6)-Id, aph(3'')-Ib, sul2, blaVMB-1, dfrA1, blaCARB-4, ARR-3, dfrA27, aadA16, qacE, sul1, mph(A)
Virulence gene   -
Metal resistance gene   merE, merD, merB, merA, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -