Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   120594
Name   oriT_p50935_IncC in_silico
Organism   Citrobacter freundii strain CF50935
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP070557 (58313..58463 [+], 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_p50935_IncC
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   12972 GenBank   WP_001337757
Name   mobH_JW298_RS02705_p50935_IncC 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   15233 GenBank   WP_000178856
Name   traD_JW298_RS02710_p50935_IncC 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   15234 GenBank   WP_000637386
Name   traC_JW298_RS02795_p50935_IncC 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: 56397..78932

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
JW298_RS02695 (JW298_02695) 52422..52655 - 234 WP_001191892 hypothetical protein -
JW298_RS02700 (JW298_02700) 52637..53254 - 618 WP_001249396 hypothetical protein -
JW298_RS02705 (JW298_02705) 53422..56400 + 2979 WP_001337757 MobH family relaxase -
JW298_RS02710 (JW298_02710) 56397..58262 + 1866 WP_000178856 conjugative transfer system coupling protein TraD virb4
JW298_RS02715 (JW298_02715) 58312..58857 + 546 WP_000228720 hypothetical protein -
JW298_RS02720 (JW298_02720) 58814..59443 + 630 WP_000743450 DUF4400 domain-containing protein tfc7
JW298_RS02725 (JW298_02725) 59453..59899 + 447 WP_000122506 hypothetical protein -
JW298_RS02730 (JW298_02730) 59909..60286 + 378 WP_000869261 hypothetical protein -
JW298_RS02735 (JW298_02735) 60286..60948 + 663 WP_001231463 hypothetical protein -
JW298_RS02740 (JW298_02740) 61129..61272 + 144 WP_001275801 hypothetical protein -
JW298_RS02745 (JW298_02745) 61284..61649 + 366 WP_001052531 hypothetical protein -
JW298_RS02750 (JW298_02750) 61794..62075 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
JW298_RS02755 (JW298_02755) 62072..62698 + 627 WP_001049716 TraE/TraK family type IV conjugative transfer system protein traE
JW298_RS02760 (JW298_02760) 62682..63599 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
JW298_RS02765 (JW298_02765) 63599..64912 + 1314 WP_024131605 TraB/VirB10 family protein traB
JW298_RS02770 (JW298_02770) 64909..65487 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
JW298_RS02775 (JW298_02775) 65491..65883 + 393 WP_000479535 TraA family conjugative transfer protein -
JW298_RS02780 (JW298_02780) 66084..71615 + 5532 WP_000606833 Ig-like domain-containing protein -
JW298_RS02785 (JW298_02785) 72114..73520 + 1407 WP_082261857 group II intron reverse transcriptase/maturase -
JW298_RS02790 (JW298_02790) 73694..74401 + 708 WP_001259347 DsbC family protein -
JW298_RS02795 (JW298_02795) 74398..76845 + 2448 WP_000637386 type IV secretion system protein TraC virb4
JW298_RS02800 (JW298_02800) 76860..77177 + 318 WP_000351984 hypothetical protein -
JW298_RS02805 (JW298_02805) 77174..77704 + 531 WP_001010738 S26 family signal peptidase -
JW298_RS02810 (JW298_02810) 77667..78932 + 1266 WP_000621288 TrbC family F-type conjugative pilus assembly protein traW
JW298_RS02815 (JW298_02815) 78929..79600 + 672 WP_001337754 EAL domain-containing protein -
JW298_RS02820 (JW298_02820) 79597..80019 + 423 Protein_98 TraU family protein -
JW298_RS02825 (JW298_02825) 80078..80782 + 705 WP_001067855 IS6-like element IS26 family transposase -
JW298_RS02830 (JW298_02830) 80836..81942 + 1107 Protein_100 IS21-like element ISAs29 family transposase -
JW298_RS02835 (JW298_02835) 81957..82712 + 756 WP_000194037 IS21-like element ISAs29 family helper ATPase IstB -
JW298_RS02840 (JW298_02840) 82793..82963 + 171 Protein_102 HU family DNA-binding protein -
JW298_RS02845 (JW298_02845) 83051..83344 + 294 WP_001239997 chromosome segregation protein ParM -
JW298_RS02850 (JW298_02850) 83371..83673 - 303 WP_000124640 XRE family transcriptional regulator -

Host bacterium

ID   21023 GenBank   NZ_CP070557
Plasmid name   p50935_IncC Incompatibility group   IncA/C2
Plasmid size   168105 bp Coordinate of oriT [Strand]   58313..58463 [+]
Host baterium   Citrobacter freundii strain CF50935

Cargo genes

Drug resistance gene   sul2, blaTEM-1A, blaTEM-1B, aac(3)-IIa, catA1
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -