Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   107846
Name   oriT_pZY-2 in_silico
Organism   Citrobacter freundii strain ZY198
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP055249 (42814..42964 [+], 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_pZY-2
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   5267 GenBank   WP_001337757
Name   mobH_GTH18_RS24770_pZY-2 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   5512 GenBank   WP_000178856
Name   traD_GTH18_RS24775_pZY-2 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   5513 GenBank   WP_000637386
Name   traC_GTH18_RS24855_pZY-2 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: 40898..66089

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
GTH18_RS24760 (GTH18_24760) 36923..37156 - 234 WP_001191892 hypothetical protein -
GTH18_RS24765 (GTH18_24765) 37138..37755 - 618 WP_001249396 hypothetical protein -
GTH18_RS24770 (GTH18_24770) 37923..40901 + 2979 WP_001337757 MobH family relaxase -
GTH18_RS24775 (GTH18_24775) 40898..42763 + 1866 WP_000178856 conjugative transfer system coupling protein TraD virb4
GTH18_RS24780 (GTH18_24780) 42813..43358 + 546 WP_000228720 hypothetical protein -
GTH18_RS24785 (GTH18_24785) 43315..43944 + 630 WP_000743450 DUF4400 domain-containing protein tfc7
GTH18_RS24790 (GTH18_24790) 43954..44400 + 447 WP_000122506 hypothetical protein -
GTH18_RS24795 (GTH18_24795) 44410..44787 + 378 WP_000869261 hypothetical protein -
GTH18_RS24800 (GTH18_24800) 44787..45449 + 663 WP_001231463 hypothetical protein -
GTH18_RS24805 (GTH18_24805) 45630..45773 + 144 WP_001275801 hypothetical protein -
GTH18_RS24810 (GTH18_24810) 45785..46150 + 366 WP_001052531 hypothetical protein -
GTH18_RS24815 (GTH18_24815) 46295..46576 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
GTH18_RS24820 (GTH18_24820) 46573..47199 + 627 WP_001049716 TraE/TraK family type IV conjugative transfer system protein traE
GTH18_RS24825 (GTH18_24825) 47183..48100 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
GTH18_RS24830 (GTH18_24830) 48100..49413 + 1314 WP_024131605 TraB/VirB10 family protein traB
GTH18_RS24835 (GTH18_24835) 49410..49988 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
GTH18_RS24840 (GTH18_24840) 49992..50384 + 393 WP_000479535 TraA family conjugative transfer protein -
GTH18_RS24845 (GTH18_24845) 50585..56116 + 5532 WP_000606833 Ig-like domain-containing protein -
GTH18_RS24850 (GTH18_24850) 56265..56972 + 708 WP_001259347 DsbC family protein -
GTH18_RS24855 (GTH18_24855) 56969..59416 + 2448 WP_000637386 type IV secretion system protein TraC virb4
GTH18_RS24860 (GTH18_24860) 59431..59748 + 318 WP_000351984 hypothetical protein -
GTH18_RS24865 (GTH18_24865) 59745..60275 + 531 WP_001010738 S26 family signal peptidase -
GTH18_RS24870 (GTH18_24870) 60238..61503 + 1266 WP_000621288 TrbC family F-type conjugative pilus assembly protein traW
GTH18_RS24875 (GTH18_24875) 61500..62171 + 672 WP_001337754 EAL domain-containing protein -
GTH18_RS24880 (GTH18_24880) 62171..63175 + 1005 WP_043940352 TraU family protein traU
GTH18_RS24885 (GTH18_24885) 63291..66089 + 2799 WP_001256487 conjugal transfer mating pair stabilization protein TraN traN
GTH18_RS24890 (GTH18_24890) 66128..66988 - 861 WP_000709517 hypothetical protein -
GTH18_RS24895 (GTH18_24895) 67111..67752 - 642 WP_000796664 hypothetical protein -
GTH18_RS24900 (GTH18_24900) 68046..68366 + 321 WP_000547566 hypothetical protein -
GTH18_RS24905 (GTH18_24905) 68670..68855 + 186 WP_001186917 hypothetical protein -
GTH18_RS24910 (GTH18_24910) 69075..70043 + 969 WP_000085162 AAA family ATPase -
GTH18_RS24915 (GTH18_24915) 70054..70962 + 909 WP_000739139 hypothetical protein -

Host bacterium

ID   8281 GenBank   NZ_CP055249
Plasmid name   pZY-2 Incompatibility group   IncA/C2
Plasmid size   143918 bp Coordinate of oriT [Strand]   42814..42964 [+]
Host baterium   Citrobacter freundii strain ZY198

Cargo genes

Drug resistance gene   aac(3)-IId, aph(6)-Id, aph(3'')-Ib, sul2
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -