Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   111824
Name   oriT_p24A19005_B_KPC in_silico
Organism   Citrobacter freundii strain 24A19CPO005
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_OQ821155 (58028..58178 [+], 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_p24A19005_B_KPC
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   7664 GenBank   WP_001337757
Name   mobH_SLH58_RS00415_p24A19005_B_KPC 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   8754 GenBank   WP_000178856
Name   traD_SLH58_RS00420_p24A19005_B_KPC 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   8755 GenBank   WP_000637386
Name   traC_SLH58_RS00500_p24A19005_B_KPC 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: 56112..81303

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
SLH58_RS00405 (MIBNNLFC_00086) 52137..52370 - 234 WP_001191892 hypothetical protein -
SLH58_RS00410 (MIBNNLFC_00087) 52352..52969 - 618 WP_001249396 hypothetical protein -
SLH58_RS00415 (MIBNNLFC_00088) 53137..56115 + 2979 WP_001337757 MobH family relaxase -
SLH58_RS00420 (MIBNNLFC_00089) 56112..57977 + 1866 WP_000178856 conjugative transfer system coupling protein TraD virb4
SLH58_RS00425 (MIBNNLFC_00090) 57988..58572 + 585 WP_000332866 hypothetical protein -
SLH58_RS00430 (MIBNNLFC_00091) 58529..59158 + 630 WP_000743450 DUF4400 domain-containing protein tfc7
SLH58_RS00435 (MIBNNLFC_00092) 59168..59614 + 447 WP_000122506 hypothetical protein -
SLH58_RS00440 (MIBNNLFC_00093) 59624..60001 + 378 WP_000869261 hypothetical protein -
SLH58_RS00445 (MIBNNLFC_00094) 60001..60663 + 663 WP_001231463 hypothetical protein -
SLH58_RS00450 (MIBNNLFC_00095) 60844..60987 + 144 WP_001275801 hypothetical protein -
SLH58_RS00455 (MIBNNLFC_00096) 60999..61364 + 366 WP_001052531 hypothetical protein -
SLH58_RS00460 (MIBNNLFC_00097) 61509..61790 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
SLH58_RS00465 (MIBNNLFC_00098) 61787..62413 + 627 WP_001049716 TraE/TraK family type IV conjugative transfer system protein traE
SLH58_RS00470 (MIBNNLFC_00099) 62397..63314 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
SLH58_RS00475 (MIBNNLFC_00100) 63314..64627 + 1314 WP_024131605 TraB/VirB10 family protein traB
SLH58_RS00480 (MIBNNLFC_00101) 64624..65202 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
SLH58_RS00485 (MIBNNLFC_00102) 65206..65598 + 393 WP_000479535 TraA family conjugative transfer protein -
SLH58_RS00490 (MIBNNLFC_00103) 65799..71330 + 5532 WP_000606833 Ig-like domain-containing protein -
SLH58_RS00495 (MIBNNLFC_00104) 71479..72186 + 708 WP_001259347 DsbC family protein -
SLH58_RS00500 (MIBNNLFC_00105) 72183..74630 + 2448 WP_000637386 type IV secretion system protein TraC virb4
SLH58_RS00505 (MIBNNLFC_00106) 74645..74962 + 318 WP_000351984 hypothetical protein -
SLH58_RS00510 (MIBNNLFC_00107) 74959..75489 + 531 WP_001010738 S26 family signal peptidase -
SLH58_RS00515 (MIBNNLFC_00108) 75452..76717 + 1266 WP_000621288 TrbC family F-type conjugative pilus assembly protein traW
SLH58_RS00520 (MIBNNLFC_00109) 76714..77385 + 672 WP_001337754 EAL domain-containing protein -
SLH58_RS00525 (MIBNNLFC_00110) 77385..78389 + 1005 WP_043940352 TraU family protein traU
SLH58_RS00530 (MIBNNLFC_00111) 78493..81303 + 2811 WP_001909286 conjugal transfer mating pair stabilization protein TraN traN
SLH58_RS00535 (MIBNNLFC_00112) 81342..82202 - 861 WP_000709517 hypothetical protein -
SLH58_RS00540 (MIBNNLFC_00113) 82325..82966 - 642 WP_000796664 hypothetical protein -
SLH58_RS00545 (MIBNNLFC_00114) 83260..83580 + 321 WP_000547566 hypothetical protein -
SLH58_RS00550 (MIBNNLFC_00116) 83884..84069 + 186 WP_001186917 hypothetical protein -
SLH58_RS00555 (MIBNNLFC_00117) 84289..85257 + 969 WP_000085162 AAA family ATPase -
SLH58_RS00560 (MIBNNLFC_00118) 85268..86176 + 909 WP_000739139 hypothetical protein -

Host bacterium

ID   12259 GenBank   NZ_OQ821155
Plasmid name   p24A19005_B_KPC Incompatibility group   IncA/C2
Plasmid size   195919 bp Coordinate of oriT [Strand]   58028..58178 [+]
Host baterium   Citrobacter freundii strain 24A19CPO005

Cargo genes

Drug resistance gene   blaCARB-2, aadA2, cmlA1, qacE, sul1, dfrA19, ant(2'')-Ia, catB3, msr(E), mph(E), blaKPC-3
Virulence gene   -
Metal resistance gene   merE, merD, merA, merC, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -