Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103158
Name   oriT_pVVS1-per1 in_silico
Organism   Vibrio vulnificus
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KY014466 (136002..136152 [-], 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_pVVS1-per1
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2363 GenBank   WP_001337757
Name   TraI_2_HTL55_RS00845_pVVS1-per1 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   2102 GenBank   WP_000637386
Name   traC_HTL55_RS00760_pVVS1-per1 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   2103 GenBank   WP_000178856
Name   traD_HTL55_RS00840_pVVS1-per1 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: 112877..138068

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTL55_RS00700 108004..108912 - 909 WP_000739139 hypothetical protein -
HTL55_RS00705 108923..109891 - 969 WP_181728453 AAA family ATPase -
HTL55_RS00710 110111..110362 - 252 WP_001447717 hypothetical protein -
HTL55_RS00715 110600..110920 - 321 WP_000547566 hypothetical protein -
HTL55_RS00720 111214..111855 + 642 WP_000796664 hypothetical protein -
HTL55_RS00725 111978..112838 + 861 WP_000709517 hypothetical protein -
HTL55_RS00730 112877..115687 - 2811 WP_001909286 conjugal transfer mating pair stabilization protein TraN traN
HTL55_RS00735 115791..116795 - 1005 WP_043940352 TraU family protein traU
HTL55_RS00740 116795..117466 - 672 WP_001337754 EAL domain-containing protein -
HTL55_RS00745 117463..118728 - 1266 WP_000621288 TrbC family F-type conjugative pilus assembly protein traW
HTL55_RS00750 118691..119221 - 531 WP_001010738 S26 family signal peptidase -
HTL55_RS00755 119218..119535 - 318 WP_000351984 hypothetical protein -
HTL55_RS00760 119550..121997 - 2448 WP_000637386 type IV secretion system protein TraC virb4
HTL55_RS00765 121994..122701 - 708 WP_001259347 DsbC family protein -
HTL55_RS00770 122850..128381 - 5532 WP_181728454 Ig-like domain-containing protein -
HTL55_RS00775 128582..128974 - 393 WP_000479535 TraA family conjugative transfer protein -
HTL55_RS00780 128978..129556 - 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
HTL55_RS00785 129553..130866 - 1314 WP_024131605 TraB/VirB10 family protein traB
HTL55_RS00790 130866..131783 - 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
HTL55_RS00795 131767..132393 - 627 WP_001049716 TraE/TraK family type IV conjugative transfer system protein traE
HTL55_RS00800 132390..132671 - 282 WP_000805625 type IV conjugative transfer system protein TraL traL
HTL55_RS00805 132816..133181 - 366 WP_001052531 hypothetical protein -
HTL55_RS00810 133193..133336 - 144 WP_001275801 hypothetical protein -
HTL55_RS00815 133517..134179 - 663 WP_001231463 hypothetical protein -
HTL55_RS00820 134179..134556 - 378 WP_000869261 hypothetical protein -
HTL55_RS00825 134566..135012 - 447 WP_000122506 hypothetical protein -
HTL55_RS00830 135022..135651 - 630 WP_000743450 DUF4400 domain-containing protein tfc7
HTL55_RS00835 135608..136192 - 585 WP_000332866 hypothetical protein -
HTL55_RS00840 136203..138068 - 1866 WP_000178856 conjugative transfer system coupling protein TraD virb4
HTL55_RS00845 138065..141043 - 2979 WP_001337757 MobH family relaxase -
HTL55_RS00850 141211..141828 + 618 WP_001249396 hypothetical protein -
HTL55_RS00855 141810..142043 + 234 WP_001191892 hypothetical protein -

Host bacterium

ID   3601 GenBank   NZ_KY014466
Plasmid name   pVVS1-per1 Incompatibility group   IncA/C2
Plasmid size   156677 bp Coordinate of oriT [Strand]   136002..136152 [-]
Host baterium   Vibrio vulnificus

Cargo genes

Drug resistance gene   sul1, blaPER-1, qnrA1, qacE, aadA16, ARR-3, sul2
Virulence gene   -
Metal resistance gene   merR, merT, merP, merA, merB, merD, merE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -