Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   101587
Name   oriT_pEW758-NDM-1 in_silico
Organism   Klebsiella pneumoniae strain EW758
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_JBAFZR010000001 (54056..54206 [+], 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_pEW758-NDM-1
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1408 GenBank   WP_001337757
Name   mobH_V5H62_RS00375_pEW758-NDM-1 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   1062 GenBank   WP_000178856
Name   traD_V5H62_RS00380_pEW758-NDM-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

>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   1063 GenBank   WP_000637386
Name   traC_V5H62_RS00460_pEW758-NDM-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

>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: 52140..77331

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
V5H62_RS00365 (V5H62_00365) 48165..48398 - 234 WP_001191892 hypothetical protein -
V5H62_RS00370 (V5H62_00370) 48380..48997 - 618 WP_001249396 hypothetical protein -
V5H62_RS00375 (V5H62_00375) 49165..52143 + 2979 WP_001337757 MobH family relaxase -
V5H62_RS00380 (V5H62_00380) 52140..54005 + 1866 WP_000178856 conjugative transfer system coupling protein TraD virb4
V5H62_RS00385 (V5H62_00385) 54055..54600 + 546 WP_000228720 hypothetical protein -
V5H62_RS00390 (V5H62_00390) 54557..55186 + 630 WP_000743450 DUF4400 domain-containing protein tfc7
V5H62_RS00395 (V5H62_00395) 55196..55642 + 447 WP_000122506 hypothetical protein -
V5H62_RS00400 (V5H62_00400) 55652..56029 + 378 WP_000869261 hypothetical protein -
V5H62_RS00405 (V5H62_00405) 56029..56691 + 663 WP_001231463 hypothetical protein -
V5H62_RS00410 (V5H62_00410) 56872..57015 + 144 WP_001275801 hypothetical protein -
V5H62_RS00415 (V5H62_00415) 57027..57392 + 366 WP_001052531 hypothetical protein -
V5H62_RS00420 (V5H62_00420) 57537..57818 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
V5H62_RS00425 (V5H62_00425) 57815..58441 + 627 WP_001049716 TraE/TraK family type IV conjugative transfer system protein traE
V5H62_RS00430 (V5H62_00430) 58425..59342 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
V5H62_RS00435 (V5H62_00435) 59342..60655 + 1314 WP_024131605 TraB/VirB10 family protein traB
V5H62_RS00440 (V5H62_00440) 60652..61230 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
V5H62_RS00445 (V5H62_00445) 61234..61626 + 393 WP_106731457 TraA family conjugative transfer protein -
V5H62_RS00450 (V5H62_00450) 61827..67358 + 5532 WP_000606833 Ig-like domain-containing protein -
V5H62_RS00455 (V5H62_00455) 67507..68214 + 708 WP_001259347 DsbC family protein -
V5H62_RS00460 (V5H62_00460) 68211..70658 + 2448 WP_000637386 type IV secretion system protein TraC virb4
V5H62_RS00465 (V5H62_00465) 70673..70990 + 318 WP_000351984 hypothetical protein -
V5H62_RS00470 (V5H62_00470) 70987..71517 + 531 WP_001010738 S26 family signal peptidase -
V5H62_RS00475 (V5H62_00475) 71480..72745 + 1266 WP_000621288 TrbC family F-type conjugative pilus assembly protein traW
V5H62_RS00480 (V5H62_00480) 72742..73413 + 672 WP_001337754 EAL domain-containing protein -
V5H62_RS00485 (V5H62_00485) 73413..74417 + 1005 WP_227511115 TraU family protein traU
V5H62_RS00490 (V5H62_00490) 74533..77331 + 2799 WP_001256487 conjugal transfer mating pair stabilization protein TraN traN
V5H62_RS00495 (V5H62_00495) 77370..78230 - 861 WP_000709517 hypothetical protein -
V5H62_RS00500 (V5H62_00500) 78353..78994 - 642 WP_000796664 hypothetical protein -
V5H62_RS00505 (V5H62_00505) 79288..79608 + 321 WP_000547566 hypothetical protein -
V5H62_RS00510 (V5H62_00510) 79912..80097 + 186 WP_001186917 hypothetical protein -
V5H62_RS00515 (V5H62_00515) 80317..81285 + 969 WP_000085162 AAA family ATPase -
V5H62_RS00520 (V5H62_00520) 81296..82204 + 909 WP_000739139 hypothetical protein -

Host bacterium

ID   2031 GenBank   NZ_JBAFZR010000001
Plasmid name   pEW758-NDM-1 Incompatibility group   IncA/C2
Plasmid size   136103 bp Coordinate of oriT [Strand]   54056..54206 [+]
Host baterium   Klebsiella pneumoniae strain EW758

Cargo genes

Drug resistance gene   sul1, aph(3')-VI, blaNDM-1
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -