Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107866
Name   oriT_pVB32-18 in_silico
Organism   Vibrio parahaemolyticus strain 18-VB00032
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MN380474 (118334..118484 [-], 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_pVB32-18
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5281 GenBank   WP_211119999
Name   mobH_KFE11_RS00740_pVB32-18 insolico UniProt ID   _
Length   992 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 992 a.a.        Molecular weight: 109568.87 Da        Isoelectric Point: 4.8714

>WP_211119999.1 MULTISPECIES: MobH family relaxase [Gammaproteobacteria]
MLKALNKLFGGRSGVIETAPSARVLPLKDVEDEEIPRYPPFAKGLPVAPLDKILATQAELIEKVRNSLGF
TVDDFNRLVLPVIQRYAAFVHLLPASESHHHRGAGGLFRHGLEVAFWAAQASESVIFSIEGTPRERRDNE
PRWRLASCFSGLLHDVGKPLSDVSITDKDGSITWNPYSESLHDWAHRHEIDRYFIRWRDKRHKRHEQFSL
LAVDRIIPAETREFLSKSGPSIMEAMLEAISGTSVNQPVTKLMLRADQESVSRDLRQSRLDVDEFSYGVP
VERYVFDAIRRLVKTGKWKVNEPGAKVWHLNQGVFIAWKQLGDLYDLISHDKIPGIPRDPDTLADILIER
GFAVPNTVQEMGERAFYRYWEVLPEMLQEAAGSVKILMLRLESNDLVFTTEPPAAVAAEVVGDVEDAEIE
FVDPEEADDGDDQEEGEAALNDDMLAAEQEAEKALAGLGFGDAMEMLKSTSDAVEEKPEQKDAGPTESSK
PDAGKKGKPQSKPGKAKPKSDTEKQPHKPEAKEDLSPQDIAKNAPPLANDNPLQALKDVGGGLGDIDFPF
DAFNASAETTSTDATNSEIPDVAMPGKQEEQPKQDFVPQEQNSLQGDDFPMFGGSDEPPSWAIEPLPMLT
DAPEQPTHTPEMPHTDNVNQHEKDAKTLLVEMLSGYGEASALLEQAIMPVLEGKTTLGEVLCLMKGQAVI
LYPDGARSLGAPSEVLSKLSHANAIVPDPIMPGRKVRDFSGVKAIVLAEQLSDAVVAAIKDAEASMGGYQ
DAFELVSPPGLDASKNKSAPKQQSRKKAQQQKPEVNAGKASPEQKAKGKDSQPQPKEKKVDVTSPVEEQQ
RKPVQEKQNVARLPKREAQPVAPEPKVEREKELGHVEVREREDPEVREFEPPKAKTNPKDINAEDFLPSG
VTPQKALQMLKDMIQKRSGRWLVTPVLEEDGCLVTSDKAFDMIAGENIGISKHILCGMLSRAQRRPLLKK
RQGKLYLEVNET

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(51-357)


  Protein structure



No available structure.




T4CP

ID   5531 GenBank   WP_000637386
Name   traC_KFE11_RS00655_pVB32-18 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.



ID   5532 GenBank   WP_000178856
Name   traD_KFE11_RS00735_pVB32-18 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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 95209..120400

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
KFE11_RS00595 90336..91244 - 909 WP_000739139 hypothetical protein -
KFE11_RS00600 91255..92223 - 969 WP_000085162 AAA family ATPase -
KFE11_RS00605 92443..92628 - 186 WP_001186917 hypothetical protein -
KFE11_RS00610 92932..93252 - 321 WP_000547566 hypothetical protein -
KFE11_RS00615 93546..94187 + 642 WP_000796664 hypothetical protein -
KFE11_RS00620 94310..95170 + 861 WP_000709517 hypothetical protein -
KFE11_RS00625 95209..98007 - 2799 WP_001256487 conjugal transfer mating pair stabilization protein TraN traN
KFE11_RS00630 98123..99127 - 1005 WP_043940352 TraU family protein traU
KFE11_RS00635 99127..99798 - 672 WP_001337754 EAL domain-containing protein -
KFE11_RS00640 99795..101060 - 1266 WP_000621288 TrbC family F-type conjugative pilus assembly protein traW
KFE11_RS00645 101023..101553 - 531 WP_001010738 S26 family signal peptidase -
KFE11_RS00650 101550..101867 - 318 WP_000351984 hypothetical protein -
KFE11_RS00655 101882..104329 - 2448 WP_000637386 type IV secretion system protein TraC virb4
KFE11_RS00660 104326..105033 - 708 WP_001259347 DsbC family protein -
KFE11_RS00665 105182..110713 - 5532 WP_000606833 Ig-like domain-containing protein -
KFE11_RS00670 110914..111306 - 393 WP_000479535 TraA family conjugative transfer protein -
KFE11_RS00675 111310..111888 - 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
KFE11_RS00680 111885..113198 - 1314 WP_024131605 TraB/VirB10 family protein traB
KFE11_RS00685 113198..114115 - 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
KFE11_RS00690 114099..114725 - 627 WP_001049716 TraE/TraK family type IV conjugative transfer system protein traE
KFE11_RS00695 114722..115003 - 282 WP_000805625 type IV conjugative transfer system protein TraL traL
KFE11_RS00700 115148..115513 - 366 WP_001052531 hypothetical protein -
KFE11_RS00705 115525..115668 - 144 WP_001275801 hypothetical protein -
KFE11_RS00710 115849..116511 - 663 WP_001231463 hypothetical protein -
KFE11_RS00715 116511..116888 - 378 WP_000869261 hypothetical protein -
KFE11_RS00720 116898..117344 - 447 WP_000122506 hypothetical protein -
KFE11_RS00725 117354..117983 - 630 WP_000743450 DUF4400 domain-containing protein tfc7
KFE11_RS00730 117940..118524 - 585 WP_000332866 hypothetical protein -
KFE11_RS00735 118535..120400 - 1866 WP_000178856 conjugative transfer system coupling protein TraD virb4
KFE11_RS00740 120397..123375 - 2979 WP_211119999 MobH family relaxase -
KFE11_RS00745 123543..124160 + 618 WP_001249396 hypothetical protein -
KFE11_RS00750 124142..124375 + 234 WP_001191892 hypothetical protein -

Host bacterium

ID   8301 GenBank   NZ_MN380474
Plasmid name   pVB32-18 Incompatibility group   IncA/C2
Plasmid size   137081 bp Coordinate of oriT [Strand]   118334..118484 [-]
Host baterium   Vibrio parahaemolyticus strain 18-VB00032

Cargo genes

Drug resistance gene   blaNDM-1, aph(3')-VI, sul1
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -