Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   115418
Name   oriT_pCC23 in_silico
Organism   Enterobacter cloacae strain CC23
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_LC556210 (88500..88650 [+], 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_pCC23
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   9868 GenBank   WP_001337757
Name   mobH_H5B75_RS00600_pCC23 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   11505 GenBank   WP_000178856
Name   traD_H5B75_RS00605_pCC23 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   11506 GenBank   WP_000637386
Name   traC_H5B75_RS00685_pCC23 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: 86584..111775

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
H5B75_RS00590 82609..82842 - 234 WP_001191892 hypothetical protein -
H5B75_RS00595 82824..83441 - 618 WP_181708637 hypothetical protein -
H5B75_RS00600 83609..86587 + 2979 WP_001337757 MobH family relaxase -
H5B75_RS00605 86584..88449 + 1866 WP_000178856 conjugative transfer system coupling protein TraD virb4
H5B75_RS00610 88460..89044 + 585 WP_000332866 hypothetical protein -
H5B75_RS00615 89001..89630 + 630 WP_000743450 DUF4400 domain-containing protein tfc7
H5B75_RS00620 89640..90086 + 447 WP_000122506 hypothetical protein -
H5B75_RS00625 90096..90473 + 378 WP_000869261 hypothetical protein -
H5B75_RS00630 90473..91135 + 663 WP_001231463 hypothetical protein -
H5B75_RS00635 91316..91459 + 144 WP_001275801 hypothetical protein -
H5B75_RS00640 91471..91836 + 366 WP_001052531 hypothetical protein -
H5B75_RS00645 91981..92262 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
H5B75_RS00650 92259..92885 + 627 WP_001049716 TraE/TraK family type IV conjugative transfer system protein traE
H5B75_RS00655 92869..93786 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
H5B75_RS00660 93786..95099 + 1314 WP_024131605 TraB/VirB10 family protein traB
H5B75_RS00665 95096..95674 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
H5B75_RS00670 95678..96070 + 393 WP_000479535 TraA family conjugative transfer protein -
H5B75_RS00675 96271..101802 + 5532 WP_000606833 Ig-like domain-containing protein -
H5B75_RS00680 101951..102658 + 708 WP_001259347 DsbC family protein -
H5B75_RS00685 102655..105102 + 2448 WP_000637386 type IV secretion system protein TraC virb4
H5B75_RS00690 105117..105434 + 318 WP_000351984 hypothetical protein -
H5B75_RS00695 105431..105961 + 531 WP_001010738 S26 family signal peptidase -
H5B75_RS00700 105924..107189 + 1266 WP_000621288 TrbC family F-type conjugative pilus assembly protein traW
H5B75_RS00705 107186..107857 + 672 WP_001337754 EAL domain-containing protein -
H5B75_RS00710 107857..108861 + 1005 WP_043940352 TraU family protein traU
H5B75_RS00715 108965..111775 + 2811 WP_001909286 conjugal transfer mating pair stabilization protein TraN traN
H5B75_RS00720 111814..112674 - 861 WP_000709517 hypothetical protein -
H5B75_RS00725 112797..113438 - 642 WP_000796664 hypothetical protein -
H5B75_RS00730 113732..114052 + 321 WP_000547566 hypothetical protein -
H5B75_RS00735 114356..114541 + 186 WP_001186917 hypothetical protein -
H5B75_RS00740 114761..115729 + 969 WP_000085162 AAA family ATPase -
H5B75_RS00745 115740..116648 + 909 WP_000739139 hypothetical protein -

Host bacterium

ID   15851 GenBank   NZ_LC556210
Plasmid name   pCC23 Incompatibility group   IncA/C2
Plasmid size   218194 bp Coordinate of oriT [Strand]   88500..88650 [+]
Host baterium   Enterobacter cloacae strain CC23

Cargo genes

Drug resistance gene   aac(3)-Ia, blaOXA-21, qacE, sul1, blaCTX-M-25, sul2, aph(3'')-Ib, aph(6)-Id, ant(2'')-Ia, aph(3')-Ia
Virulence gene   -
Metal resistance gene   merE, merD, merA, merC, merP, merT, merR, fecE, fecD, arsH, arsR, arsB, arsC
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -