Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   118839
Name   oriT_pFDL-VIM in_silico
Organism   Klebsiella oxytoca
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MN783744 (82312..82462 [+], 151 nt)
oriT length   151 nt
IRs (inverted repeats)      12..17, 24..29  (AACCCG..CGGGTT)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 151 nt

>oriT_pFDL-VIM
TGGTCGATGTGAACCCGTTTGACCGGGTTATGAATGAGTTGAAAAGTCGTGGCCGCAAGAACGCTCATATCCTGAGCATCCTTCAATTCGACTGGCCCGCATCGGAGGTCATCATCGAGAAGCTGAGCTGTTACATCACAGATGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   11943 GenBank   WP_058662807
Name   mobH_H5G46_RS00515_pFDL-VIM insolico UniProt ID   A0A221KLA3
Length   987 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 987 a.a.        Molecular weight: 109306.91 Da        Isoelectric Point: 4.9372

>WP_058662807.1 MULTISPECIES: MobH family relaxase [Gammaproteobacteria]
MLKALHKLFGGRSGAIETAPSARVLPLKDVEDEEIPRYPPFAKGLPVAPLDKILATQAELIEKVRNSLGF
TVDDFNRLVLPVIQRYAAFVHLLPASESHHHRGAGGLFRHGLEVAFWATQASESVIFSIEGTPRERRDNE
PRWRLASCFSGLLHDVGKPLSDVSITDKDGSITWNPYSESLHDWAYRHGIDRYFIRWRDKRHKRHEQFSL
LAWHRIIPAETQEFLSKSGPSIIEAMLEAISGTSVNQPVTKLMLRADQESVSRDLRQSRLDVNEFSYGVP
VERYVFDAIRRLVKTGKWKVNEPGAKVWHLNQGVFIAWKQLGDLYDLISQDKIPGIPRDPDTLADILIER
GFAVPNTVQEKGERAYYRYWEVLPEMLQEAAGPVKILMLRLESNDLVFTTEPPAAVTGEVVGDVEDAEIE
FVDPEEADEDQAEGDAGLNNDMLAAELEAEKALAGLGFGDAMAMLKSTSDIAEEKPEQEDTESTELPKPD
ASKKGKQQSKPGKARAEKQPQKPEVKEDLSPQDIAKNAPPLANDDPLQALKDVGGGLGDIDFPFDVFNAS
AETACTDATNLAIPDITEPVKQEEQPKPDFVPQEQNSLQNGDFPIFSDSDEPPSWAIEPLPMLTDTPEQT
IPAPDMQHAGKPKELEKDAKTLLSEMLAGYGEASTLLEQAIMPVLEGKTTLGEVLCLMKGQAVILYPEGA
RSLGAPSEVLSKLSHANAIVPDPIMPGRKVRDFSGVKAIVLVDQLSDAVVAAIKDAEASMGGYQEAFELV
SPPGSGVSKNKSAPKQQSRKKTQQQKPEVDAGAGSEQKTKDKSLQQQPKEKQGNVASLVEEQKRKPVQDQ
EKQNVARLPKREAQPVASKPKVEHERELGHVEVRERDEPEVREFEPPKAKTNPKDINEEDFLPSGVTPEK
ALLMLKDMIQKRSGRWLVTPVLEEDGCLVTSVKAFDMIAGENVGISKHILYGLLSRAQRRPLLKKRQGKL
YLEVDKA

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(51-357)


  Protein structure


Source ID Structure
AlphaFold DB A0A221KLA3


T4CP

ID   13979 GenBank   WP_000178858
Name   traD_H5G46_RS00520_pFDL-VIM 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: 69248.76 Da        Isoelectric Point: 7.1093

>WP_000178858.1 MULTISPECIES: conjugative transfer system coupling protein TraD [Gammaproteobacteria]
MTMSYDPLAYEMPWRPNYEKNAVAGWMAASCAALAVEQVSTMPSEPFYWMTGICGVMAMARLPKAIKLHL
LQKHLKGRDLEFISIAELQKYIKDTPEDMWLGSGFLWENRHAQRVFEILKRDWTSIVGKESTVKKVVRKI
QGKKKELPIGQPWIHGVEPKEEKLMQPLKHTEGHSLIVGTTGSGKTRMFDILISQAILRGEAVIIIDPKG
DKEMRDNARRACEAMGQPERFVSFHPAFPEESVRIDPLRNFTRVTEIASRLAALIPSEAGADPFKSFGWQ
ALNNIAQGLVLTHDRPNLTKLRRFLEGGAAGLVIKAVQAYSERVKPDWEAEAAAYLEKAKNGSREKIAFA
LMKFYYDIIQPEHPNSDLEGLLSMFQHDQTHFSKMVANLLPIMNMLTSGELGPLLSPDSSDLSDERQITD
SAKIINNAQVAYLGLDSLTDNMVGSAMGSIFLSDLTAVAGDRYNYGVNNRPVNIFVDEAAEVINDPFIQL
LNKGRGAKLRLFVATQTFADFAARLGSKDKALQVLGNINNTFALRIVDGETQEYIADNLPKTRLKYVMRT
QGQNTDGKEPIMHGGNQGERLMEEEADLFPAQLLGMLPNLEYIAKISGGTIVKGRLPILTQ

  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   13980 GenBank   WP_051479468
Name   traC_H5G46_RS00600_pFDL-VIM 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: 92523.78 Da        Isoelectric Point: 5.9204

>WP_051479468.1 MULTISPECIES: type IV secretion system protein TraC [Gammaproteobacteria]
MIITIKKKLEETLIPEHLRAAGIIPVLAYDEDDHVFLMDDQSVGFGFMCEPLCGADEKVQERMNGFLNQE
FPSKTSLQFVLFRSPDINQEMYRMMGLRDGFRHELLTSVIKERINFLQHHTTDRIFAKTSKGIYDNGLIQ
DLKLFVTCKVPIKNNNPTESELQHLAQIRTKVESSLQTVGLRPRTMTAVNYIRIMSTILNWGPDASWRHD
SVDWEMDKPICEQIFDYGTDVEVSKNGIRLGDYHAKVMSAKKLPDVFYFGDALTYAGDLSGGNSSIKENY
MVVTNVFFPEAESTKNTLERKRQFTVNQAYGPMLKFVPVLADKKESFDTLYESMKEGAKPVKITYSVVLF
APTKERVEAAAMAARNIWRESRFELMEDKFVALPMFLNCLPFCTDRDAVRDLFRYKTMTTEQAAVVLPVF
GEWKGTGTYHAALISRNGQLMSLSLHDSNTNKNLVIAAESGSGKSFLTNELIFSYLSEGAQVWVIDAGKS
YQKLSEMLNGDFVHFEEGTHVCLNPFELIQNYDDEEDAIVSLVCAMASAKGLLDEWQISALKQVLSRLWE
EKGKEMKVDDIAERCLEEENDQRLKDIGQQLYAFTSKGSYGKYFSQKNNVSFQNQFTVLELDELQGRKHL
RQVVLLQLIYQIQQEVFLGERNRKKVVIVDEAWDLLKEGEVSTFMEHAYRKFRKYGGSVVIATQSINDLY
ENAVGRAIAENSASMYLLGQTEETVESVKRSGRLTLSDGGFHTLKTVHTIQGVYSEIFIKSKSGMGVGRL
IVGDFQKLLYSTDPVDVNAIDQFVKQGMSIPEAIKAVMRSRKQAA

  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: 80396..105500

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
H5G46_RS00505 76436..76669 - 234 WP_039272424 hypothetical protein -
H5G46_RS00510 76651..77268 - 618 WP_012766323 hypothetical protein -
H5G46_RS00515 77436..80399 + 2964 WP_058662807 MobH family relaxase -
H5G46_RS00520 80396..82261 + 1866 WP_000178858 conjugative transfer system coupling protein TraD virb4
H5G46_RS00525 82272..82856 + 585 WP_000332867 hypothetical protein -
H5G46_RS00530 82813..83442 + 630 WP_000743448 DUF4400 domain-containing protein tfc7
H5G46_RS00535 83453..83899 + 447 WP_039272421 hypothetical protein -
H5G46_RS00540 83909..84286 + 378 WP_000869260 hypothetical protein -
H5G46_RS00545 84286..84948 + 663 WP_039272419 hypothetical protein -
H5G46_RS00550 85127..85270 + 144 WP_168199038 hypothetical protein -
H5G46_RS00555 85283..85630 + 348 WP_039272417 hypothetical protein -
H5G46_RS00560 85773..86054 + 282 WP_000805626 type IV conjugative transfer system protein TraL traL
H5G46_RS00565 86051..86677 + 627 WP_039272415 TraE/TraK family type IV conjugative transfer system protein traE
H5G46_RS00570 86661..87578 + 918 WP_012766326 type-F conjugative transfer system secretin TraK traK
H5G46_RS00575 87575..88891 + 1317 WP_039272412 TraB/VirB10 family protein traB
H5G46_RS00580 88888..89466 + 579 WP_039272410 type IV conjugative transfer system lipoprotein TraV traV
H5G46_RS00585 89470..89862 + 393 WP_012766327 TraA family conjugative transfer protein -
H5G46_RS00590 90063..95549 + 5487 WP_039272407 Ig-like domain-containing protein -
H5G46_RS00595 95698..96405 + 708 WP_001259344 DsbC family protein -
H5G46_RS00600 96402..98849 + 2448 WP_051479468 type IV secretion system protein TraC virb4
H5G46_RS00605 98864..99181 + 318 WP_000364398 hypothetical protein -
H5G46_RS00610 99178..99708 + 531 WP_000672456 S26 family signal peptidase -
H5G46_RS00615 99671..100939 + 1269 WP_039272404 TrbC family F-type conjugative pilus assembly protein traW
H5G46_RS00620 100936..101613 + 678 WP_039272402 EAL domain-containing protein -
H5G46_RS00625 101607..102611 + 1005 WP_000911304 TraU family protein traU
H5G46_RS00630 102762..105500 + 2739 WP_058662805 conjugal transfer mating pair stabilization protein TraN traN
H5G46_RS00635 105539..106399 - 861 WP_000679674 hypothetical protein -
H5G46_RS00640 106511..107161 - 651 WP_000796641 hypothetical protein -
H5G46_RS00645 107453..107773 + 321 WP_012766334 hypothetical protein -
H5G46_RS00650 108084..108269 + 186 WP_001186892 hypothetical protein -
H5G46_RS00655 108490..109458 + 969 WP_001553257 AAA family ATPase -
H5G46_RS00660 109470..110375 + 906 WP_058662804 hypothetical protein -

Host bacterium

ID   19271 GenBank   NZ_MN783744
Plasmid name   pFDL-VIM Incompatibility group   IncA/C
Plasmid size   164903 bp Coordinate of oriT [Strand]   82312..82462 [+]
Host baterium   Klebsiella oxytoca

Cargo genes

Drug resistance gene   sul2, aph(3'')-Ib, aph(6)-Id, qnrS1, blaVIM-1, aph(3')-XV, ant(3'')-Ia, catB2, qacE, sul1, dfrA14, mph(A), blaSHV-12
Virulence gene   -
Metal resistance gene   merR, merT, merP, merC, merA, merD
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -