Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103033
Name   oriT_pDGO100 in_silico
Organism   Escherichia coli strain VA292
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KU997026 (48667..48817 [+], 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_pDGO100
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2267 GenBank   WP_001326173
Name   TraI_2_HTI13_RS00350_pDGO100 insolico UniProt ID   F5BPR1
Length   990 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 990 a.a.        Molecular weight: 109356.90 Da        Isoelectric Point: 4.9395

>WP_001326173.1 MULTISPECIES: MobH family relaxase [Gammaproteobacteria]
MLKALNKLFGGRSGVIETAPSVRVLPLKDVEDEEIPRYPPFAKGLPVAPLDKILATQAELIEKVRNSLGF
TVDDFNRLVLPVIQRYAAFVHLLPASESHHHRGAGGLFRHGLEVAFWAAQASESVIFSIEGTPRERRDNE
PRWRLASCFSGLLHDVGKPLSDVSITDKDGSITWNPYSESLHDWAHRHEIDRYFIRWRDKRHKRHEQFSL
LAVDRIIPAETREFLSKSGPSIMEAMLEAISGTSVNQPVTKLMLRADQESVSRDLRQSRLDVDEFSYGVP
VERYVFDAIRRLVKTGKWKVNEPGAKVWHLNQGVFIAWKQLGDLYDLISHDKIPGIPRDPDTLADILIER
GFAVPNTVQEKGERAYYRYWEVLPEMLQEAAGSVKILMLRLESNDLVFTTEPPAAVAAEVVGDVEDAEIE
FVDPEEVDDDQEEDVSALNDDMLAAEQEAEKALAGLGFGDAMEMLKSTSDAVEEKPEQKDAGSTESSKPD
AGKKGKPQSKPGKAKPKSDTEKQPHKPEAKEDLSPQDIAKNAPPLANDNPLQALKDVGGGLGDIDFPFDA
FSASAETASTDATNSEIPDVAMPGKQEKQPKQDFVPQEQNSLQGDDFPMFGSSDEPPSWAIEPLPMLTDA
PEQTTPAPAMPPTDKPNLHEKDAKTLLVEMLAGYGEASALLEQAIMPVLEGKTTLGEVLCLMKGQAVILY
PDGARSLGAPSEVLSKLSHANAIVPDPIMPGRKVRDFSGVKAIVLAEQLSDAVVAAIKDAEASMGGYQDA
FELVSPPGLDASKNKSAPKQQSRKKAQQQKPEVNAGKPSPEQKAKGKDSQPQQKEKKVDVTSPVEEPQRQ
PVQEKQNVARLPKREVQPVAPEPKVEREKELGHVEVREREEPEVREFEPPKAKTNPKDINAEDFLPSGVT
PQKALQMLKDMIQKRSGRWLVTPVLEEDGCLVTSDKAFDMIAGENIGISKHILCGMLSRAQRRPLLKKRQ
GKLYLEVNET

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(51-357)


  Protein structure


Source ID Structure
AlphaFold DB F5BPR1


T4CP

ID   1962 GenBank   WP_000178857
Name   traD_HTI13_RS00355_pDGO100 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   1963 GenBank   WP_172688387
Name   traC_HTI13_RS00435_pDGO100 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: 92646.94 Da        Isoelectric Point: 5.9216

>WP_172688387.1 type IV secretion system protein TraC [Escherichia coli]
MIVTIKKKLEETLIPEHLRAAGIIPVLAYDEDDHVFLMDDHSAGFGFMCEPLCGADEKVQERMNGFLNQE
FPSKTTLQFVLFRSPDINQEMYRMMGLRDGFRHELLTSVIKERINFLQHHTTDRIFAKTNKGIYDNGLIQ
DLKLFVTCKVPIKNNNPTESELQQLAQLRTKVESSLQTVGLRPRTMTAVNYIRIMSTILNWGPDASWRHD
SVDWEMDKPICEQIFDYGTDVEVSKNGIRLGDYHAKVMSAKKLPDVFYFGDALTYAGDLSGGNSSIKENY
MVVTNVFFPEAESTKNTLERKRQFTVNQAYGPMLKFVPVLADKKESFDTLYESMKEGAKPVKITYSVVLF
APTKERVEAAAMAARNIWRESRFELMEDKFVALPMFLNCLPFCTDRDAVRDLFRYKTMTTEQAAVVLPVF
GEWKGTGTYHAALISRNGQLMSLSLHDSNTNKNLVIAAESGSGKSFLTNELIFSYLSEGAQVWVIDAGKS
YQKLSEMLNGDFVHFEEGTHVCLNPFELIQNYEDEEDAIVSLVCAMASAKGLLDEWQISALKQVLSRLWE
EKGKEMKVDDIAERCLEEENDQRLKDIGQQLYAFTSQGSYGKYFSRKNNVSFQNQFTVLELDELQGRKHL
RQVVLLQLIYQIQQEVFLGERNRKKVVIVDEAWDLLKEVEVSVFMEHAYRKFRKYGGSVVIATQSINDLY
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: 46751..71894

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTI13_RS00340 42782..43015 - 234 WP_001191890 hypothetical protein -
HTI13_RS00345 42997..43614 - 618 WP_001249395 hypothetical protein -
HTI13_RS00350 43782..46754 + 2973 WP_001326173 MobH family relaxase -
HTI13_RS00355 46751..48616 + 1866 WP_000178857 conjugative transfer system coupling protein TraD virb4
HTI13_RS00360 48627..49211 + 585 WP_000332868 hypothetical protein -
HTI13_RS00365 49168..49797 + 630 WP_000743449 DUF4400 domain-containing protein tfc7
HTI13_RS00370 49807..50253 + 447 WP_000122507 hypothetical protein -
HTI13_RS00375 50263..50640 + 378 WP_000869297 hypothetical protein -
HTI13_RS00380 50640..51302 + 663 WP_001231464 hypothetical protein -
HTI13_RS00385 51483..51626 + 144 WP_001275801 hypothetical protein -
HTI13_RS00390 51626..52003 + 378 WP_001326174 hypothetical protein -
HTI13_RS00395 52148..52429 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
HTI13_RS00400 52426..53052 + 627 WP_001049717 TraE/TraK family type IV conjugative transfer system protein traE
HTI13_RS00405 53036..53953 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
HTI13_RS00410 53953..55266 + 1314 WP_024131605 TraB/VirB10 family protein traB
HTI13_RS00415 55263..55841 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
HTI13_RS00420 55845..56237 + 393 WP_000479535 TraA family conjugative transfer protein -
HTI13_RS00425 56438..61924 + 5487 WP_000606835 Ig-like domain-containing protein -
HTI13_RS00430 62073..62780 + 708 WP_001259346 DsbC family protein -
HTI13_RS00435 62777..65224 + 2448 WP_172688387 type IV secretion system protein TraC virb4
HTI13_RS00440 65239..65556 + 318 WP_000351984 hypothetical protein -
HTI13_RS00445 65553..66083 + 531 WP_001010740 S26 family signal peptidase -
HTI13_RS00450 66046..67311 + 1266 WP_001447719 TrbC family F-type conjugative pilus assembly protein traW
HTI13_RS00455 67308..67979 + 672 WP_000575345 EAL domain-containing protein -
HTI13_RS00460 67979..68983 + 1005 WP_005507569 TraU family protein traU
HTI13_RS00465 69087..71894 + 2808 WP_001447718 conjugal transfer mating pair stabilization protein TraN traN
HTI13_RS00470 71933..72793 - 861 WP_172688388 hypothetical protein -
HTI13_RS00475 72916..73557 - 642 WP_000796664 hypothetical protein -
HTI13_RS00480 73852..74172 + 321 WP_000547566 hypothetical protein -
HTI13_RS00485 74476..74661 + 186 WP_001186917 hypothetical protein -
HTI13_RS00490 74881..75849 + 969 WP_000085160 AAA family ATPase -
HTI13_RS00495 75860..76768 + 909 WP_000739139 hypothetical protein -

Host bacterium

ID   3476 GenBank   NZ_KU997026
Plasmid name   pDGO100 Incompatibility group   IncA/C2
Plasmid size   217306 bp Coordinate of oriT [Strand]   48667..48817 [+]
Host baterium   Escherichia coli strain VA292

Cargo genes

Drug resistance gene   sul1, qacE, dfrB3, ant(2'')-Ia, dfrA10, blaTEM-1B, catA1, aph(3')-Ia
Virulence gene   -
Metal resistance gene   merR, merT, merP, merC, merA, merD, merE, fecE, fecD, merB
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -