Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103161
Name   oriT_pB2-1 in_silico
Organism   Klebsiella pneumoniae strain B2
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KX458222 (48667..48817 [+], 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_pB2-1
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2364 GenBank   WP_001326173
Name   TraI_2_HTI84_RS00345_pB2-1 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   2105 GenBank   WP_000178857
Name   traD_HTI84_RS00350_pB2-1 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: 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   2106 GenBank   WP_000637384
Name   traC_HTI84_RS00435_pB2-1 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: 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: 46751..73146

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTI84_RS00335 42782..43015 - 234 WP_001191890 hypothetical protein -
HTI84_RS00340 42997..43614 - 618 WP_001249395 hypothetical protein -
HTI84_RS00345 43782..46754 + 2973 WP_001326173 MobH family relaxase -
HTI84_RS00350 46751..48616 + 1866 WP_000178857 conjugative transfer system coupling protein TraD virb4
HTI84_RS00355 48627..49211 + 585 WP_000332868 hypothetical protein -
HTI84_RS00360 49168..49797 + 630 WP_000743449 DUF4400 domain-containing protein tfc7
HTI84_RS00365 49807..50253 + 447 WP_000122507 hypothetical protein -
HTI84_RS00370 50263..50640 + 378 WP_000869297 hypothetical protein -
HTI84_RS00375 50640..51302 + 663 WP_001231464 hypothetical protein -
HTI84_RS00380 51483..51626 + 144 WP_001275801 hypothetical protein -
HTI84_RS00385 51638..52003 + 366 WP_001052530 hypothetical protein -
HTI84_RS00390 52148..52429 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
HTI84_RS00395 52426..53052 + 627 WP_001049717 TraE/TraK family type IV conjugative transfer system protein traE
HTI84_RS00400 53036..53953 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
HTI84_RS00405 53953..55266 + 1314 WP_024131605 TraB/VirB10 family protein traB
HTI84_RS00410 55263..55841 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
HTI84_RS00415 55845..56237 + 393 WP_000479535 TraA family conjugative transfer protein -
HTI84_RS00420 56438..61924 + 5487 WP_000606835 Ig-like domain-containing protein -
HTI84_RS00430 63346..64032 + 687 WP_228276452 DsbC family protein -
HTI84_RS00435 64029..66476 + 2448 WP_000637384 type IV secretion system protein TraC virb4
HTI84_RS00440 66491..66808 + 318 WP_000351984 hypothetical protein -
HTI84_RS00445 66805..67335 + 531 WP_001010740 S26 family signal peptidase -
HTI84_RS00450 67298..68563 + 1266 WP_001447719 TrbC family F-type conjugative pilus assembly protein traW
HTI84_RS00455 68560..69231 + 672 WP_000575345 EAL domain-containing protein -
HTI84_RS00460 69231..70235 + 1005 WP_005507569 TraU family protein traU
HTI84_RS00465 70351..73146 + 2796 WP_001256484 conjugal transfer mating pair stabilization protein TraN traN
HTI84_RS00470 73185..74045 - 861 WP_000709517 hypothetical protein -
HTI84_RS00475 74168..74809 - 642 WP_000796664 hypothetical protein -
HTI84_RS00480 75104..75424 + 321 WP_000547566 hypothetical protein -
HTI84_RS00485 75728..75913 + 186 WP_001186917 hypothetical protein -
HTI84_RS00490 76133..77101 + 969 WP_000085160 AAA family ATPase -
HTI84_RS00495 77112..78020 + 909 WP_000739139 hypothetical protein -

Host bacterium

ID   3604 GenBank   NZ_KX458222
Plasmid name   pB2-1 Incompatibility group   IncA/C2
Plasmid size   172152 bp Coordinate of oriT [Strand]   48667..48817 [+]
Host baterium   Klebsiella pneumoniae strain B2

Cargo genes

Drug resistance gene   ant(2'')-Ia, qacE, sul1, dfrA10, tet(B), aph(3')-Ia, blaTEM-1B
Virulence gene   -
Metal resistance gene   merE, merD, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -