Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   115437
Name   oriT_pYA00120881 in_silico
Organism   Vibrio cholerae strain YA00120881
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MT151380 (79083..79233 [+], 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_pYA00120881
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9883 GenBank   WP_001337757
Name   mobH_H5I17_RS00515_pYA00120881 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   11521 GenBank   WP_000178856
Name   traD_H5I17_RS00520_pYA00120881 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.



ID   11522 GenBank   WP_000637386
Name   traC_H5I17_RS00600_pYA00120881 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: 77167..102358

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
H5I17_RS00505 73192..73425 - 234 WP_001191892 hypothetical protein -
H5I17_RS00510 73407..74024 - 618 WP_001249396 hypothetical protein -
H5I17_RS00515 74192..77170 + 2979 WP_001337757 MobH family relaxase -
H5I17_RS00520 77167..79032 + 1866 WP_000178856 conjugative transfer system coupling protein TraD virb4
H5I17_RS00525 79043..79627 + 585 WP_000332866 hypothetical protein -
H5I17_RS00530 79584..80213 + 630 WP_000743450 DUF4400 domain-containing protein tfc7
H5I17_RS00535 80223..80669 + 447 WP_000122506 hypothetical protein -
H5I17_RS00540 80679..81056 + 378 WP_000869261 hypothetical protein -
H5I17_RS00545 81056..81718 + 663 WP_001231463 hypothetical protein -
H5I17_RS00550 81899..82042 + 144 WP_001275801 hypothetical protein -
H5I17_RS00555 82054..82419 + 366 WP_001052531 hypothetical protein -
H5I17_RS00560 82564..82845 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
H5I17_RS00565 82842..83468 + 627 WP_001049716 TraE/TraK family type IV conjugative transfer system protein traE
H5I17_RS00570 83452..84369 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
H5I17_RS00575 84369..85682 + 1314 WP_181726432 TraB/VirB10 family protein traB
H5I17_RS00580 85679..86257 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
H5I17_RS00585 86261..86653 + 393 WP_000479535 TraA family conjugative transfer protein -
H5I17_RS00590 86854..92385 + 5532 WP_000606833 Ig-like domain-containing protein -
H5I17_RS00595 92534..93241 + 708 WP_001259347 DsbC family protein -
H5I17_RS00600 93238..95685 + 2448 WP_000637386 type IV secretion system protein TraC virb4
H5I17_RS00605 95700..96017 + 318 WP_000351984 hypothetical protein -
H5I17_RS00610 96014..96544 + 531 WP_001010738 S26 family signal peptidase -
H5I17_RS00615 96507..97772 + 1266 WP_000621288 TrbC family F-type conjugative pilus assembly protein traW
H5I17_RS00620 97769..98440 + 672 WP_001337754 EAL domain-containing protein -
H5I17_RS00625 98440..99444 + 1005 WP_097518477 TraU family protein traU
H5I17_RS00630 99548..102358 + 2811 WP_001909286 conjugal transfer mating pair stabilization protein TraN traN
H5I17_RS00635 102397..103257 - 861 WP_000709517 hypothetical protein -
H5I17_RS00640 103380..104021 - 642 WP_000796664 hypothetical protein -
H5I17_RS00645 104315..104635 + 321 WP_000547566 hypothetical protein -
H5I17_RS00650 104939..105124 + 186 WP_001186917 hypothetical protein -
H5I17_RS00655 105344..106312 + 969 WP_000085162 AAA family ATPase -
H5I17_RS00660 106323..107231 + 909 WP_000739139 hypothetical protein -

Host bacterium

ID   15870 GenBank   NZ_MT151380
Plasmid name   pYA00120881 Incompatibility group   IncA/C2
Plasmid size   159889 bp Coordinate of oriT [Strand]   79083..79233 [+]
Host baterium   Vibrio cholerae strain YA00120881

Cargo genes

Drug resistance gene   aac(3)-IIa, blaOXA-1, aac(6')-Ib-cr, blaCTX-M-15, ARR-3, cmlA1, blaOXA-10, ant(3'')-Ia, qacE, sul1, dfrA23, floR, tet(A), aph(6)-Id, aph(3'')-Ib, sul2
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -