Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   104634
Name   oriT_p6_B in_silico
Organism   Citrobacter freundii strain 62
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP048384 (48428..48578 [+], 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_p6_B
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3330 GenBank   WP_001337757
Name   mobH_GZS04_RS24340_p6_B 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   3270 GenBank   WP_000178856
Name   traD_GZS04_RS24345_p6_B 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   3271 GenBank   WP_000637386
Name   traC_GZS04_RS24420_p6_B 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: 46512..71703

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
GZS04_RS24330 (GZS04_24330) 42537..42770 - 234 WP_001191892 hypothetical protein -
GZS04_RS24335 (GZS04_24335) 42752..43369 - 618 WP_001249396 hypothetical protein -
GZS04_RS24340 (GZS04_24340) 43537..46515 + 2979 WP_001337757 MobH family relaxase -
GZS04_RS24345 (GZS04_24345) 46512..48377 + 1866 WP_000178856 conjugative transfer system coupling protein TraD virb4
GZS04_RS24350 (GZS04_24350) 48427..48972 + 546 WP_000228720 hypothetical protein -
GZS04_RS24355 (GZS04_24355) 48929..49558 + 630 WP_000743450 DUF4400 domain-containing protein tfc7
GZS04_RS24360 (GZS04_24360) 49568..50014 + 447 WP_000122506 hypothetical protein -
GZS04_RS24365 (GZS04_24365) 50024..50401 + 378 WP_000869261 hypothetical protein -
GZS04_RS24370 (GZS04_24370) 50401..51063 + 663 WP_001231463 hypothetical protein -
GZS04_RS25850 51244..51387 + 144 WP_001275801 hypothetical protein -
GZS04_RS24375 (GZS04_24375) 51399..51764 + 366 WP_001052531 hypothetical protein -
GZS04_RS24380 (GZS04_24380) 51909..52190 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
GZS04_RS24385 (GZS04_24385) 52187..52813 + 627 WP_001049716 TraE/TraK family type IV conjugative transfer system protein traE
GZS04_RS24390 (GZS04_24390) 52797..53714 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
GZS04_RS24395 (GZS04_24395) 53714..55027 + 1314 WP_024131605 TraB/VirB10 family protein traB
GZS04_RS24400 (GZS04_24400) 55024..55602 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
GZS04_RS24405 (GZS04_24405) 55606..55998 + 393 WP_000479535 TraA family conjugative transfer protein -
GZS04_RS24410 (GZS04_24410) 56199..61730 + 5532 WP_000606833 Ig-like domain-containing protein -
GZS04_RS24415 (GZS04_24415) 61879..62586 + 708 WP_001259347 DsbC family protein -
GZS04_RS24420 (GZS04_24420) 62583..65030 + 2448 WP_000637386 type IV secretion system protein TraC virb4
GZS04_RS24425 (GZS04_24425) 65045..65362 + 318 WP_000351984 hypothetical protein -
GZS04_RS24430 (GZS04_24430) 65359..65889 + 531 WP_001010738 S26 family signal peptidase -
GZS04_RS24435 (GZS04_24435) 65852..67117 + 1266 WP_000621288 TrbC family F-type conjugative pilus assembly protein traW
GZS04_RS24440 (GZS04_24440) 67114..67785 + 672 WP_001337754 EAL domain-containing protein -
GZS04_RS24445 (GZS04_24445) 67785..68789 + 1005 WP_043940352 TraU family protein traU
GZS04_RS24450 (GZS04_24450) 68905..71703 + 2799 WP_001256487 conjugal transfer mating pair stabilization protein TraN traN
GZS04_RS24455 (GZS04_24455) 71742..72602 - 861 WP_000709517 hypothetical protein -
GZS04_RS24460 (GZS04_24460) 72725..73366 - 642 WP_000796664 hypothetical protein -
GZS04_RS24465 (GZS04_24465) 73660..73980 + 321 WP_000547566 hypothetical protein -
GZS04_RS24470 (GZS04_24470) 74284..74469 + 186 WP_001186917 hypothetical protein -
GZS04_RS24475 (GZS04_24475) 74689..75657 + 969 WP_000085162 AAA family ATPase -
GZS04_RS24480 (GZS04_24480) 75668..76576 + 909 WP_162648851 hypothetical protein -

Host bacterium

ID   5073 GenBank   NZ_CP048384
Plasmid name   p6_B Incompatibility group   IncA/C2
Plasmid size   190655 bp Coordinate of oriT [Strand]   48428..48578 [+]
Host baterium   Citrobacter freundii strain 62

Cargo genes

Drug resistance gene   aph(3')-Ia, aph(6)-Id, aph(3'')-Ib, sul2, ant(2'')-Ia, dfrA12, aadA2, qacE, sul1, blaKPC-2, blaOXA-9, blaTEM-1A, blaCTX-M-25
Virulence gene   -
Metal resistance gene   merE, merD, merA, merC, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -