Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120627
Name   oriT_pCFR-0b27 in_silico
Organism   Citrobacter freundii complex sp. CFNIH4
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP026233 (24675..24825 [-], 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_pCFR-0b27
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12995 GenBank   WP_001337757
Name   mobH_C2U41_RS26390_pCFR-0b27 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   15257 GenBank   WP_000637386
Name   traC_C2U41_RS26310_pCFR-0b27 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.



ID   15258 GenBank   WP_000178856
Name   traD_C2U41_RS26385_pCFR-0b27 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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 1550..26741

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
C2U41_RS26275 (C2U41_26245) 651..1511 + 861 WP_000709517 hypothetical protein -
C2U41_RS26280 (C2U41_26250) 1550..4348 - 2799 WP_001256487 conjugal transfer mating pair stabilization protein TraN traN
C2U41_RS26285 (C2U41_26255) 4464..5468 - 1005 WP_043940352 TraU family protein traU
C2U41_RS26290 (C2U41_26260) 5468..6139 - 672 WP_001337754 EAL domain-containing protein -
C2U41_RS26295 (C2U41_26265) 6136..7401 - 1266 WP_000621288 TrbC family F-type conjugative pilus assembly protein traW
C2U41_RS26300 (C2U41_26270) 7364..7894 - 531 WP_001010738 S26 family signal peptidase -
C2U41_RS26305 (C2U41_26275) 7891..8208 - 318 WP_000351984 hypothetical protein -
C2U41_RS26310 (C2U41_26280) 8223..10670 - 2448 WP_000637386 type IV secretion system protein TraC virb4
C2U41_RS26315 (C2U41_26285) 10667..11374 - 708 WP_001259347 DsbC family protein -
C2U41_RS26320 (C2U41_26290) 11523..17054 - 5532 WP_000606833 Ig-like domain-containing protein -
C2U41_RS26325 (C2U41_26295) 17255..17647 - 393 WP_000479535 TraA family conjugative transfer protein -
C2U41_RS26330 (C2U41_26300) 17651..18229 - 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
C2U41_RS26335 (C2U41_26305) 18226..19539 - 1314 WP_024131605 TraB/VirB10 family protein traB
C2U41_RS26340 (C2U41_26310) 19539..20456 - 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
C2U41_RS26345 (C2U41_26315) 20440..21066 - 627 WP_001049716 TraE/TraK family type IV conjugative transfer system protein traE
C2U41_RS26350 (C2U41_26320) 21063..21344 - 282 WP_000805625 type IV conjugative transfer system protein TraL traL
C2U41_RS26355 (C2U41_26325) 21489..21854 - 366 WP_001052531 hypothetical protein -
C2U41_RS29555 21866..22009 - 144 WP_001275801 hypothetical protein -
C2U41_RS26360 (C2U41_26330) 22190..22852 - 663 WP_001231463 hypothetical protein -
C2U41_RS26365 (C2U41_26335) 22852..23229 - 378 WP_000869261 hypothetical protein -
C2U41_RS26370 (C2U41_26340) 23239..23685 - 447 WP_000122506 hypothetical protein -
C2U41_RS26375 (C2U41_26345) 23695..24324 - 630 WP_000743450 DUF4400 domain-containing protein tfc7
C2U41_RS26380 (C2U41_26350) 24281..24826 - 546 WP_000228720 hypothetical protein -
C2U41_RS26385 (C2U41_26355) 24876..26741 - 1866 WP_000178856 conjugative transfer system coupling protein TraD virb4
C2U41_RS26390 (C2U41_26360) 26738..29716 - 2979 WP_001337757 MobH family relaxase -
C2U41_RS26395 (C2U41_26365) 29884..30501 + 618 WP_001249396 hypothetical protein -
C2U41_RS26400 (C2U41_26370) 30483..30716 + 234 WP_001191892 hypothetical protein -

Host bacterium

ID   21056 GenBank   NZ_CP026233
Plasmid name   pCFR-0b27 Incompatibility group   IncA/C2
Plasmid size   206795 bp Coordinate of oriT [Strand]   24675..24825 [-]
Host baterium   Citrobacter freundii complex sp. CFNIH4

Cargo genes

Drug resistance gene   blaFOX-5, sul1, mph(E), msr(E), qacE, catB3, ant(2'')-Ia, dfrA19, qnrA1, cmlA1, aadA2, blaCARB-2
Virulence gene   -
Metal resistance gene   merR, merT, merP, merC, merA, merD, merE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -