Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104614
Name   oriT_pVCR94 in_silico
Organism   Vibrio cholerae strain E4
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP033514 (16873..17023 [+], 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_pVCR94
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3316 GenBank   WP_011872892
Name   mobH_EEL44_RS05400_pVCR94 insolico UniProt ID   A0A1W6AQM7
Length   992 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 992 a.a.        Molecular weight: 109595.88 Da        Isoelectric Point: 4.8967

>WP_011872892.1 MULTISPECIES: MobH family relaxase [Gammaproteobacteria]
MLKALNKLFGGRSGVIETAPSARVLPLKDVEDEEIPRYPPFAKGLPVAPLDKILATQAELIEKVRNSLGF
TVDDFNRLVLPVIQRYAAFVHLLPASESHHHRGAGGLFRHGLEVAFWAAQASESVIFSIEGTPRERRDNE
PRWRLASCFSGLLHDVGKPLSDVSITDKDGSITWNPYSESLHDWAHRHEIDRYFIRWRDKRHKRHEQFSL
LAVDRIIPAETREFLSKSGPSIMEAMLEAISGTSVNQPVTKLMLRADQESVSRDLRQSRLDVDEFSYGVP
VERYVFDAIRRLVKTGKWKVNEPGAKVWHLNQGVFIAWKQLGDLYDLISHDKIPGIPRDPDTLADILIER
GFAVPNTVQEKGERAYYRYWEVLPEMLQEAAGSVKILMLRLESNDLVFTTEPPAAVAAEVVGDVEDAEIE
FVDPEEADDGDDQEEGEAALNDDMLAAEQEAEKALAGLGFGDAMEMLKSTSDAVEEKPEQKDAGPTESSK
PDAGKKGKPQSKPGKAKPKSDTEKQPHKPEAKEDLSPQDIAKNAPPLANDNPLQALKDVGGGLGDIDFPF
DAFNASAETTSTDATNSEIPDVAMPGKQEEQPKQDFVPQEQNSLQGDDFPMFGGSDEPPSWAIEPLPMLT
DAPEQPTHTPEMPHTDNVNQHEKDAKTLLVEMLSGYGEASALLEQAIMPVLEGKTTLGEVLCLMKGQAVI
LYPDGARSLGAPSEVLSKLSHANAIVPDPIMPGRKVRDFSGVKAIVLAEQLSDAVVAAIKDAEASMGGYQ
DAFELVSPPGLDASKNKSAPKQQSRKKAQQQKPEVNAGKASPEQKAKGKDSQPQPKEKKVDVTSPVEEQQ
RKPVQEKQNVARLPKREAQPVAPEPKVEREKELGHVEVREREEPEVREFEPPKAKTNPKDINAEDFLPSG
VTPQKALQMLKDMIQKRSGRWLVTPVLEEDGCLVTSDKAFDMIAGENIGISKHILCGMLSRAQRRPLLKK
RQGKLYLEVNET

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(51-357)


  Protein structure


Source ID Structure
AlphaFold DB A0A1W6AQM7


T4CP

ID   3256 GenBank   WP_000178857
Name   traD_EEL44_RS05405_pVCR94 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   3257 GenBank   WP_011872839
Name   traC_EEL44_RS05480_pVCR94 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: 92576.85 Da        Isoelectric Point: 5.9216

>WP_011872839.1 MULTISPECIES: type IV secretion system protein TraC [Gammaproteobacteria]
MIVTIKKKLEETLIPEHLRAAGIIPVLAYDEDDHVFLMDDHSAGFGFMCEPLCGADEKVQERMNGFLNQE
FPSKTTLQFVLFRSPDINQEMYRMMGLRDGFRHELLTSVIKERINFLQHHTTDRIFAKTNKGIYDNGLIQ
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: 14957..40147

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
EEL44_RS05390 (EEL44_05390) 10983..11216 - 234 WP_001191892 hypothetical protein -
EEL44_RS05395 (EEL44_05395) 11198..11815 - 618 WP_001249396 hypothetical protein -
EEL44_RS05400 (EEL44_05400) 11982..14960 + 2979 WP_011872892 MobH family relaxase -
EEL44_RS05405 (EEL44_05405) 14957..16822 + 1866 WP_000178857 conjugative transfer system coupling protein TraD virb4
EEL44_RS05410 (EEL44_05410) 16872..17417 + 546 WP_000228720 hypothetical protein -
EEL44_RS05415 (EEL44_05415) 17374..18003 + 630 WP_000743450 DUF4400 domain-containing protein tfc7
EEL44_RS05420 (EEL44_05420) 18013..18459 + 447 WP_000122506 hypothetical protein -
EEL44_RS05425 (EEL44_05425) 18469..18846 + 378 WP_000869261 hypothetical protein -
EEL44_RS05430 (EEL44_05430) 18846..19508 + 663 WP_021293632 hypothetical protein -
EEL44_RS20995 19689..19832 + 144 WP_001275801 hypothetical protein -
EEL44_RS05435 (EEL44_05435) 19844..20209 + 366 WP_001052531 hypothetical protein -
EEL44_RS05440 (EEL44_05440) 20354..20634 + 281 Protein_25 type IV conjugative transfer system protein TraL -
EEL44_RS05445 (EEL44_05445) 20631..21257 + 627 WP_001049716 TraE/TraK family type IV conjugative transfer system protein traE
EEL44_RS05450 (EEL44_05450) 21241..22158 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
EEL44_RS05455 (EEL44_05455) 22158..23471 + 1314 WP_164491403 TraB/VirB10 family protein traB
EEL44_RS05460 (EEL44_05460) 23468..24046 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
EEL44_RS05465 (EEL44_05465) 24050..24442 + 393 WP_069369997 TraA family conjugative transfer protein -
EEL44_RS05470 (EEL44_05470) 24643..30174 + 5532 WP_024126918 Ig-like domain-containing protein -
EEL44_RS05475 (EEL44_05475) 30323..31030 + 708 WP_001259347 DsbC family protein -
EEL44_RS05480 (EEL44_05480) 31027..33474 + 2448 WP_011872839 type IV secretion system protein TraC virb4
EEL44_RS05485 (EEL44_05485) 33489..33806 + 318 WP_011872858 hypothetical protein -
EEL44_RS05490 (EEL44_05490) 33803..34333 + 531 WP_021293639 S26 family signal peptidase -
EEL44_RS05495 (EEL44_05495) 34296..35561 + 1266 WP_121926692 TrbC family F-type conjugative pilus assembly protein traW
EEL44_RS05500 (EEL44_05500) 35558..36229 + 672 WP_024126920 EAL domain-containing protein -
EEL44_RS05505 (EEL44_05505) 36250..37233 + 984 WP_241154238 TraU family protein traU
EEL44_RS05510 (EEL44_05510) 37349..40147 + 2799 WP_024126922 conjugal transfer mating pair stabilization protein TraN traN
EEL44_RS05515 (EEL44_05515) 40186..41046 - 861 WP_000709517 hypothetical protein -
EEL44_RS05520 (EEL44_05520) 41169..41810 - 642 WP_024126923 hypothetical protein -
EEL44_RS05525 (EEL44_05525) 42103..42423 + 321 WP_024126924 hypothetical protein -
EEL44_RS05530 (EEL44_05530) 42727..42912 + 186 WP_001186916 hypothetical protein -
EEL44_RS05535 (EEL44_05535) 43131..44099 + 969 WP_024126925 AAA family ATPase -
EEL44_RS05540 (EEL44_05540) 44110..45015 + 906 WP_021293644 hypothetical protein -

Host bacterium

ID   5053 GenBank   NZ_CP033514
Plasmid name   pVCR94 Incompatibility group   IncA/C2
Plasmid size   171829 bp Coordinate of oriT [Strand]   16873..17023 [+]
Host baterium   Vibrio cholerae strain E4

Cargo genes

Drug resistance gene   tet(C), tet(B), catA1, aph(3'')-Ib, aph(6)-Id, blaCARB-4, dfrA15, qacE, sul1, sul2
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -