Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   115104
Name   oriT_pVC1374 in_silico
Organism   Vibrio cholerae strain VC1374
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP040171 (110229..110379 [-], 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_pVC1374
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9660 GenBank   WP_001337757
Name   mobH_FDZ90_RS00680_pVC1374 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   11269 GenBank   WP_000637386
Name   traC_FDZ90_RS00595_pVC1374 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   11270 GenBank   WP_000178856
Name   traD_FDZ90_RS00675_pVC1374 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: 87104..112295

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
FDZ90_RS19740 82233..82766 - 534 WP_227543304 hypothetical protein -
FDZ90_RS19745 82709..83140 - 432 WP_228717829 hypothetical protein -
FDZ90_RS00540 (FDZ90_00575) 83144..84118 - 975 WP_180821247 AAA family ATPase -
FDZ90_RS00545 (FDZ90_00580) 84338..84523 - 186 WP_001186917 hypothetical protein -
FDZ90_RS00550 (FDZ90_00585) 84827..85147 - 321 WP_000547566 hypothetical protein -
FDZ90_RS00555 (FDZ90_00590) 85441..86082 + 642 WP_000796664 hypothetical protein -
FDZ90_RS00560 (FDZ90_00595) 86205..87065 + 861 WP_000709517 hypothetical protein -
FDZ90_RS00565 (FDZ90_00600) 87104..89902 - 2799 WP_001256487 conjugal transfer mating pair stabilization protein TraN traN
FDZ90_RS00570 (FDZ90_00605) 90018..91022 - 1005 WP_043940352 TraU family protein traU
FDZ90_RS00575 (FDZ90_00610) 91022..91693 - 672 WP_001337754 EAL domain-containing protein -
FDZ90_RS00580 (FDZ90_00615) 91690..92955 - 1266 WP_000621288 TrbC family F-type conjugative pilus assembly protein traW
FDZ90_RS00585 (FDZ90_00620) 92918..93448 - 531 WP_001010738 S26 family signal peptidase -
FDZ90_RS00590 (FDZ90_00625) 93445..93762 - 318 WP_000351984 hypothetical protein -
FDZ90_RS00595 (FDZ90_00630) 93777..96224 - 2448 WP_000637386 type IV secretion system protein TraC virb4
FDZ90_RS00600 (FDZ90_00635) 96221..96928 - 708 WP_001259347 DsbC family protein -
FDZ90_RS00605 (FDZ90_00640) 97077..102608 - 5532 WP_000606833 Ig-like domain-containing protein -
FDZ90_RS00610 (FDZ90_00645) 102809..103201 - 393 WP_000479535 TraA family conjugative transfer protein -
FDZ90_RS00615 (FDZ90_00650) 103205..103783 - 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
FDZ90_RS00620 (FDZ90_00655) 103780..105093 - 1314 WP_024131605 TraB/VirB10 family protein traB
FDZ90_RS00625 (FDZ90_00660) 105093..106010 - 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
FDZ90_RS00630 (FDZ90_00665) 105994..106620 - 627 WP_001049716 TraE/TraK family type IV conjugative transfer system protein traE
FDZ90_RS00635 (FDZ90_00670) 106617..106898 - 282 WP_000805625 type IV conjugative transfer system protein TraL traL
FDZ90_RS00640 (FDZ90_00675) 107043..107408 - 366 WP_001052531 hypothetical protein -
FDZ90_RS00645 107420..107563 - 144 WP_001275801 hypothetical protein -
FDZ90_RS00650 (FDZ90_00680) 107744..108406 - 663 WP_001231463 hypothetical protein -
FDZ90_RS00655 (FDZ90_00685) 108406..108783 - 378 WP_000869261 hypothetical protein -
FDZ90_RS00660 (FDZ90_00690) 108793..109239 - 447 WP_000122506 hypothetical protein -
FDZ90_RS00665 (FDZ90_00695) 109249..109878 - 630 WP_000743450 DUF4400 domain-containing protein tfc7
FDZ90_RS00670 (FDZ90_00700) 109835..110380 - 546 WP_000228720 hypothetical protein -
FDZ90_RS00675 (FDZ90_00705) 110430..112295 - 1866 WP_000178856 conjugative transfer system coupling protein TraD virb4
FDZ90_RS00680 (FDZ90_00710) 112292..115270 - 2979 WP_001337757 MobH family relaxase -
FDZ90_RS00685 (FDZ90_00715) 115438..116055 + 618 WP_001249396 hypothetical protein -
FDZ90_RS00690 (FDZ90_00720) 116037..116270 + 234 WP_001191892 hypothetical protein -

Host bacterium

ID   15539 GenBank   NZ_CP040171
Plasmid name   pVC1374 Incompatibility group   IncA/C2
Plasmid size   140291 bp Coordinate of oriT [Strand]   110229..110379 [-]
Host baterium   Vibrio cholerae strain VC1374

Cargo genes

Drug resistance gene   blaTEM-1C, sul2
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -