Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   200147
Name   oriT2_ICEKpnQD23-1 in_silico
Organism   Klebsiella pneumoniae strain QD23
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   CP042858 ( 184382..184680 [-], 299 nt)
oriT length   299 nt
IRs (inverted repeats)      234..242, 254..262  (AAAGCCAAA..TTTGGCTTT)
 45..50, 52..57  (CAAACG..CGTTTG)
 7..12, 26..31  (TTTGGC..GCCAAA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 299 nt

>oriT2_ICEKpnQD23-1
GCTCTGTTTGGCGGCTGGTGACCTAGCCAAAAAAATTGAGACGCCAAACGTCGTTTGCATTCTGGCCTGAACTTGCCAAACGGTTTGTATCTTCATGGCGATACGTCTTTTTAGGTGTTTTTAAGTGAAATCAGCCTGTATCCCTTGTCGGGTATGGGATTGAGCGAGTCGATTTATATCGAGACGCCAAACAGTGATTGTGACGGCAGTTTTACGTTTGGCGTTTCGATCCAAAAGCCAAACGGATAGTGGTTTTGGCTTTAGGGGTTAATTGGATGGGGAAATTGGTTTGGTAGAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   14298 GenBank   QIF54881
Name   TraI_2_FU841_25385_ICEKpnQD23-1 insolico UniProt ID   _
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

>QIF54881.1 conjugal transfer protein TraI [Klebsiella pneumoniae]
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



No available structure.




T4CP

ID   16593 GenBank   QIF54865
Name   traC_FU841_25305_ICEKpnQD23-1 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

>QIF54865.1 type IV secretion system protein TraC [Klebsiella pneumoniae]
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.



ID   16594 GenBank   QIF54880
Name   traD_FU841_25380_ICEKpnQD23-1 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

>QIF54880.1 conjugative transfer system coupling protein TraD [Klebsiella pneumoniae]
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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 4959974..4985165

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
FU841_25245 4955101..4956009 - 909 QIF54853 hypothetical protein -
FU841_25250 4956020..4956988 - 969 QIF54854 CbbQ/NirQ/NorQ/GpvN family protein -
FU841_25255 4957208..4957393 - 186 QIF54855 hypothetical protein -
FU841_25260 4957697..4958017 - 321 QIF54856 hypothetical protein -
FU841_25265 4958311..4958952 + 642 QIF54857 hypothetical protein -
FU841_25270 4959075..4959935 + 861 QIF54858 hypothetical protein -
FU841_25275 4959974..4962784 - 2811 QIF54859 conjugal transfer mating pair stabilization protein TraN traN
FU841_25280 4962888..4963895 - 1008 QIF54860 conjugal transfer protein TraU traU
FU841_25285 4963892..4964563 - 672 QIF54861 EAL domain-containing protein -
FU841_25290 4964560..4965825 - 1266 QIF54862 conjugal transfer protein TraW traW
FU841_25295 4965788..4966318 - 531 QIF54863 S26 family signal peptidase -
FU841_25300 4966315..4966632 - 318 QIF54864 hypothetical protein -
FU841_25305 4966647..4969094 - 2448 QIF54865 type IV secretion system protein TraC virb4
FU841_25310 4969091..4969798 - 708 QIF54866 DsbC family protein -
FU841_25315 4969947..4975478 - 5532 QIF54867 DUF4165 domain-containing protein -
FU841_25320 4975679..4976071 - 393 QIF54868 conjugal transfer protein TraA -
FU841_25325 4976075..4976653 - 579 QIF54869 type IV conjugative transfer system lipoprotein TraV traV
FU841_25330 4976650..4977966 - 1317 QIF54870 conjugal transfer protein TraB traB
FU841_25335 4977963..4978880 - 918 QIF54871 conjugal transfer protein TraK traK
FU841_25340 4978864..4979490 - 627 QIF54872 pilus assembly protein traE
FU841_25345 4979487..4979768 - 282 QIF54873 type IV conjugative transfer system protein TraL traL
FU841_25350 4979913..4980290 - 378 QIF54874 hypothetical protein -
FU841_25355 4980614..4981276 - 663 QIF54875 hypothetical protein -
FU841_25360 4981276..4981653 - 378 QIF54876 hypothetical protein -
FU841_25365 4981663..4982109 - 447 QIF54877 hypothetical protein -
FU841_25370 4982119..4982748 - 630 QIF54878 DUF4400 domain-containing protein tfc7
FU841_25375 4982705..4983289 - 585 QIF54879 hypothetical protein -
FU841_25380 4983300..4985165 - 1866 QIF54880 conjugative transfer system coupling protein TraD virb4
FU841_25385 4985162..4988140 - 2979 QIF54881 conjugal transfer protein TraI -
FU841_25390 4988308..4988925 + 618 QIF54882 hypothetical protein -
FU841_25395 4988907..4989140 + 234 QIF54883 hypothetical protein -

Host bacterium

ID   148 Element type   ICE (Integrative and conjugative element)
Element name   ICEKpnQD23-1 GenBank   CP042858
Element size   5803733 bp Coordinate of oriT [Strand]   151575..151725 [-]; 184382..184680 [-]
Host bacterium   Klebsiella pneumoniae strain QD23 Coordinate of element   4831525..5022379

Cargo genes

Drug resistance gene   blaTEM-1B, aac(3)-IId, mph(A), sul1, qacE, ARR-3, blaNDM-3, aadA16, dfrA27, aac(6')-Ib-cr, sul2, aph(3'')-Ib, aph(6)-Id, floR
Virulence gene   -
Metal resistance gene   merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -