Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113786
Name   oriT_pNDM-116-17 in_silico
Organism   Vibrio cholerae isolate V. cholerae 116-17a
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_LN831185 (4887..5037 [+], 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_pNDM-116-17
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8827 GenBank   WP_052686861
Name   mobH_GWA90_RS00005_pNDM-116-17 insolico UniProt ID   A0A722GY04
Length   990 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 990 a.a.        Molecular weight: 109417.00 Da        Isoelectric Point: 4.9395

>WP_052686861.1 MULTISPECIES: MobH family relaxase [Gammaproteobacteria]
MLKALNKLFGGRSGVIETAPSVRVLPLKDVEDEEIPRYPPFAKGLPVAPLDKILATQAELIEKVRNSLGF
TVDDFNRLVLPVIQRYAAFVHLLPASESHHHRGAGGLFRHGLEVAFWAAQASESVIFSIEGTPRERRDNE
PRWRLASCFSGLLHDVGKPLSDVSITDKDGSITWNPYSESLHDWAHRHEIDRYFIRWRDKRHKRHEQFSL
LAVDRIIPAETREFLSKSGPSIMEAMLEAISGTSVNQPVTKLMLRADQESVSRDLRQSRLDVDEFSYGVP
VERYVFDAIRRLVKTGKWKVNEPGAKVWHLNQGVFIAWKQLGDLYDLISHDKIPGIPRDPDTLADILIER
GFAVPNTVQEKGERAYYRYWEVLPEMLQEAAGSVKILMLRLESNDLVFTTEPPAAVAAEVVGDVEDAEIE
FVDPEEVDDDQEEDVSALNDDMLAAEQEAEKALAGLGFGDAMEMLKSTSDAVEEKPEQKDAGSTESSKPD
AGKKGKPQSKPGKAKPKSDTEKQPHKPEAKEDLSPQDIAKNAPPLANDNPLQALKDVGGGLGDIDFPFDA
FSASAETASTDATNSEIPDVAMPGKQEKQPKQDFVPQEQNSLQGDDFPMFGSFDEPPSWAIEPLPMLTDA
PEQTTPAPAMPPTDKPNLHEKDAKTLLVEMLAGYGEASALLEQAIMPVLEGKTTLGEVLCLMKGQAVILY
PDGARSLGAPSEVLSKLSHANAIVPDPIMPGRKVRDFSGVKAIVLAEQLSDAVVAAIKDAEASMGGYQDA
FELVSPPGLDASKNKSAPKQQSRKKAQQQKPEVNAGKPSPEQKAKGKDSQPQQKEKKVDVTSPVEEPQRQ
PVQEKQNVARLPKREVQPVAPEPKVEREKELGHVEVREREEPEVREFEPPKAKTNPKDINAEDFLPSGVT
PQKALQMLKDMIQKRSGRWLVTPVLEEDGCLVTSDKAFDMIAGENIGISKHILCGMLSRAQRRPLLKKRQ
GKLYLEVNET

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(51-357)


  Protein structure


Source ID Structure
AlphaFold DB A0A722GY04


T4CP

ID   10239 GenBank   WP_000178857
Name   traD_GWA90_RS00010_pNDM-116-17 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   10240 GenBank   WP_000637384
Name   traC_GWA90_RS00085_pNDM-116-17 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: 92604.86 Da        Isoelectric Point: 5.9216

>WP_000637384.1 MULTISPECIES: type IV secretion system protein TraC [Gammaproteobacteria]
MIVTIKKKLEETLIPEHLRAAGIIPVLAYDEDDHVFLMDDHSAGFGFMCEPLCGADEKVQERMNGFLNQE
FPSKTTLQFVLFRSPDINQEMYRMMGLRDGFRHELLTSVIKERINFLQHHTTDRIFAKTNKGIYDNGLIQ
DLKLFVTCKVPIKNNNPTESELQQLAQLRTKVESSLQTVGLRPRTMTAVNYIRIMSTILNWGPDASWRHD
SVDWEMDKPICEQIFDYGTDVEVSKNGIRLGDYHAKVMSAKKLPDVFYFGDALTYAGDLSGGNSSIKENY
MVVTNVFFPEAESTKNTLERKRQFTVNQAYGPMLKFVPVLADKKESFDTLYESMKEGAKPVKITYSVVLF
APTKERVEAAAMAARNIWRESRFELMEDKFVALPMFLNCLPFCTDRDAVRDLFRYKTMTTEQAAVVLPVF
GEWKGTGTYHAALISRNGQLMSLSLHDSNTNKNLVIAAESGSGKSFLTNELIFSYLSEGAQVWVIDAGKS
YQKLSEMLNGDFVHFEEGTHVCLNPFELIQNYEDEEDAIVSLVCAMASAKGLLDEWQISALKQVLSRLWE
EKGKEMKVDDIAERCLEEENDQRLKDIGQQLYAFTSQGSYGKYFSRKNNVSFQNQFTVLELDELQGRKHL
RQVVLLQLIYQIQQEVFLGERNRKKVVIVDEAWDLLKEGEVSVFMEHAYRKFRKYGGSVVIATQSINDLY
ENAVGRAIAENSASMYLLGQTEETVESVKRSGRLTLSEGGFHTLKTVHTIQGVYSEIFIKSKSGMGVGRL
IVGDFQKLLYSTDPVDVNAIDQFVKQGMSIPEAIKAVMRSRRQAA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(284-434)

TraC protein (TraC_F_IV)

(21-255)

TraG P-loop domain (P-loop_TraG)

(449-809)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 2971..28114

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
GWA90_RS00005 2..2974 + 2973 WP_052686861 MobH family relaxase -
GWA90_RS00010 2971..4836 + 1866 WP_000178857 conjugative transfer system coupling protein TraD virb4
GWA90_RS00015 4847..5431 + 585 WP_000332868 hypothetical protein -
GWA90_RS00020 5388..6017 + 630 WP_000743449 DUF4400 domain-containing protein tfc7
GWA90_RS00025 6027..6473 + 447 WP_000122507 hypothetical protein -
GWA90_RS00030 6483..6860 + 378 WP_000869297 hypothetical protein -
GWA90_RS00035 6860..7522 + 663 WP_001231464 hypothetical protein -
GWA90_RS00980 7703..7846 + 144 WP_001275801 hypothetical protein -
GWA90_RS00040 7858..8223 + 366 WP_001052530 hypothetical protein -
GWA90_RS00045 8368..8649 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
GWA90_RS00050 8646..9272 + 627 WP_001049717 TraE/TraK family type IV conjugative transfer system protein traE
GWA90_RS00055 9256..10173 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
GWA90_RS00060 10173..11486 + 1314 WP_024131605 TraB/VirB10 family protein traB
GWA90_RS00065 11483..12061 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
GWA90_RS00070 12065..12457 + 393 WP_000479535 TraA family conjugative transfer protein -
GWA90_RS00075 12658..18144 + 5487 WP_000606835 Ig-like domain-containing protein -
GWA90_RS00080 18293..19000 + 708 WP_001259346 DsbC family protein -
GWA90_RS00085 18997..21444 + 2448 WP_000637384 type IV secretion system protein TraC virb4
GWA90_RS00090 21459..21776 + 318 WP_000351984 hypothetical protein -
GWA90_RS00095 21773..22303 + 531 WP_001010740 S26 family signal peptidase -
GWA90_RS00100 22266..23531 + 1266 WP_001447719 TrbC family F-type conjugative pilus assembly protein traW
GWA90_RS00105 23528..24199 + 672 WP_000575345 EAL domain-containing protein -
GWA90_RS00110 24199..25203 + 1005 WP_005507569 TraU family protein traU
GWA90_RS00115 25307..28114 + 2808 WP_001447718 conjugal transfer mating pair stabilization protein TraN traN
GWA90_RS00120 28153..29013 - 861 WP_000709517 hypothetical protein -
GWA90_RS00125 29136..29777 - 642 WP_000796664 hypothetical protein -
GWA90_RS00130 30072..30392 + 321 WP_000547566 hypothetical protein -
GWA90_RS00135 30696..30881 + 186 WP_001186917 hypothetical protein -
GWA90_RS00140 31101..32069 + 969 WP_000085160 AAA family ATPase -
GWA90_RS00145 32080..32988 + 909 WP_000739139 hypothetical protein -

Host bacterium

ID   14221 GenBank   NZ_LN831185
Plasmid name   pNDM-116-17 Incompatibility group   IncA/C2
Plasmid size   167382 bp Coordinate of oriT [Strand]   4887..5037 [+]
Host baterium   Vibrio cholerae isolate V. cholerae 116-17a

Cargo genes

Drug resistance gene   ARR-3, cmlA1, blaOXA-10, ant(3'')-Ia, qacE, mph(E), msr(E), sul1, blaNDM-1
Virulence gene   -
Metal resistance gene   merE, merD, merA, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -