Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   106012
Name   oriT_pKpn14-3 in_silico
Organism   Klebsiella pneumoniae strain Kpn-14
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP047703 (47529..47679 [+], 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_pKpn14-3
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4044 GenBank   WP_001326173
Name   mobH_GVI79_RS29275_pKpn14-3 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   4056 GenBank   WP_000178857
Name   traD_GVI79_RS29280_pKpn14-3 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   4057 GenBank   WP_000637384
Name   traC_GVI79_RS29380_pKpn14-3 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: 45613..54703

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
GVI79_RS29265 (GVI79_28885) 41644..41877 - 234 WP_001191890 hypothetical protein -
GVI79_RS29270 (GVI79_28890) 41859..42476 - 618 WP_001249395 hypothetical protein -
GVI79_RS29275 (GVI79_28895) 42644..45616 + 2973 WP_001326173 MobH family relaxase -
GVI79_RS29280 (GVI79_28900) 45613..47478 + 1866 WP_000178857 conjugative transfer system coupling protein TraD virb4
GVI79_RS29285 (GVI79_28905) 47528..48073 + 546 WP_000228720 hypothetical protein -
GVI79_RS29290 (GVI79_28910) 48030..48659 + 630 WP_000743449 DUF4400 domain-containing protein tfc7
GVI79_RS29295 (GVI79_28915) 48669..49115 + 447 WP_000122507 hypothetical protein -
GVI79_RS29300 (GVI79_28920) 49125..49502 + 378 WP_000869297 hypothetical protein -
GVI79_RS29305 (GVI79_28925) 49502..50164 + 663 WP_001231464 hypothetical protein -
GVI79_RS29310 50345..50488 + 144 WP_001275801 hypothetical protein -
GVI79_RS29315 (GVI79_28930) 50500..50865 + 366 WP_001052530 hypothetical protein -
GVI79_RS29320 (GVI79_28935) 51010..51291 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
GVI79_RS29325 (GVI79_28940) 51288..51914 + 627 WP_001049717 TraE/TraK family type IV conjugative transfer system protein traE
GVI79_RS29330 (GVI79_28945) 51898..52815 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
GVI79_RS29335 (GVI79_28950) 52815..54128 + 1314 WP_024131605 TraB/VirB10 family protein traB
GVI79_RS29340 (GVI79_28955) 54125..54703 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
GVI79_RS29345 (GVI79_28960) 54707..55099 + 393 WP_000479535 TraA family conjugative transfer protein -
GVI79_RS29350 (GVI79_28965) 55384..56646 + 1263 WP_000608644 IS1380-like element ISEcp1 family transposase -
GVI79_RS29355 (GVI79_28970) 56970..58115 + 1146 WP_000976514 extended-spectrum class C beta-lactamase CMY-2 -
GVI79_RS29360 (GVI79_28975) 58209..58742 + 534 WP_001221666 lipocalin family protein -
GVI79_RS29365 (GVI79_28980) 58739..59056 - 318 WP_000118520 quaternary ammonium compound efflux SMR transporter SugE -
GVI79_RS30845 (GVI79_28985) 59313..59678 + 366 Protein_86 LuxR family transcriptional regulator -

Host bacterium

ID   6449 GenBank   NZ_CP047703
Plasmid name   pKpn14-3 Incompatibility group   IncA/C2
Plasmid size   150505 bp Coordinate of oriT [Strand]   47529..47679 [+]
Host baterium   Klebsiella pneumoniae strain Kpn-14

Cargo genes

Drug resistance gene   blaCMY-2, sul1, qacE, aadA15, dfrA1, aac(6')-Il, blaVIM-1
Virulence gene   -
Metal resistance gene   merR, merT, merP, merA, merB, merD, merE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -