Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103303
Name   oriT_p112298-tetA in_silico
Organism   Citrobacter freundii strain 112298
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KY986974 (138262..138412 [+], 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_p112298-tetA
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2467 GenBank   WP_064986968
Name   TraI_2_HTN34_RS00840_p112298-tetA insolico UniProt ID   A0A6D1JL47
Length   990 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 990 a.a.        Molecular weight: 109328.85 Da        Isoelectric Point: 4.9395

>WP_064986968.1 MULTISPECIES: MobH family relaxase [Enterobacterales]
MLKALNKLFGGRSGVIETAPSARVLPLKDVEDEEIPRYPPFAKGLPVAPLDKILATQAELIEKVRNSLGF
TVDDFNRLVLPVIQRYAAFVHLLPASESHHHRGAGGLFRHGLEVAFWAAQASESVIFSIEGTPRERRDNE
PRWRLASCFSGLLHDVGKPLSDVSITDKDGSITWNPYSESLHDWAHRHEIDRYFIRWRDKRHKRHEQFSL
LAVDRIIPAETREFLSKSGPSIMEAMLEAISGTSVNQPVTKLMLRADQESVSRDLRQSRLDVDEFSYGVP
VERYVFDAIRRLVKTGKWKVNEPGAKVWHLNQGVFIAWKQLGDLYDLISHDKIPGIPRDPDTLADILIER
GFAVPNTVQEKGERAYYRYWEVLPEMLQEAAGSVKILMLRLESNDLVFTTEPPAAVAAEVVGDVEDAEIE
FVDPEEVDDDQEEDVSALNDDMLAAEQEAEKALAGLGFGDAMEMLKSTSDAVEEKPEQKDAGSTESSKPD
AGKKGKPQSKPGKAKPKSDTEKQPHKPEAKEDLSPQDIAKNAPPLANDNPLQALKDVGGGLGDIDFPFDA
FSASAETASTDATNSEIPDVAMPGKQEKQPKQDFVPQEQNSLQGDDFPMFGSSDEPPSWAIEPLPMLTDA
PEQTTPAPAMPPTDKPNLHEKDAKTLLVEMLAGYGEASALLEQAIMPVLEGKTTLGEVLCLMKGQAVILY
PDGARSLGAPSEVLSKLSHANAIVPDPIMPGRKVRDFSGVKAIVLAEQLSDAVVAAIKDAEASMGGYQDA
FELVSPPGLDASKNKSAPKQQSRKKAQQQKPEVNAGKPSPEQKAKGKDSQPQQKEKKVDVTSPVEEPQRQ
PVQEKQNVARLPKREVQPVAPEPKVEREKELGHVEVREREEPEVREFEPPKAKTNPKDINAEDFLPSGVT
PQKALQMLKDMIQKRSGRWLVTPVLEEDGCLVTSDKAFDMIAGENIGISKHILCGMLSRAQRRPLLKKRQ
GKLYLEVNET

  Protein domains


Predicted by InterproScan.

Putative helicase (TraI_2)

(51-357)


  Protein structure


Source ID Structure
AlphaFold DB A0A6D1JL47


T4CP

ID   2242 GenBank   WP_000637384
Name   traC_HTN34_RS00315_p112298-tetA 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: 92604.86 Da        Isoelectric Point: 5.9216

>WP_000637384.1 MULTISPECIES: type IV secretion system protein TraC [Gammaproteobacteria]
MIVTIKKKLEETLIPEHLRAAGIIPVLAYDEDDHVFLMDDHSAGFGFMCEPLCGADEKVQERMNGFLNQE
FPSKTTLQFVLFRSPDINQEMYRMMGLRDGFRHELLTSVIKERINFLQHHTTDRIFAKTNKGIYDNGLIQ
DLKLFVTCKVPIKNNNPTESELQQLAQLRTKVESSLQTVGLRPRTMTAVNYIRIMSTILNWGPDASWRHD
SVDWEMDKPICEQIFDYGTDVEVSKNGIRLGDYHAKVMSAKKLPDVFYFGDALTYAGDLSGGNSSIKENY
MVVTNVFFPEAESTKNTLERKRQFTVNQAYGPMLKFVPVLADKKESFDTLYESMKEGAKPVKITYSVVLF
APTKERVEAAAMAARNIWRESRFELMEDKFVALPMFLNCLPFCTDRDAVRDLFRYKTMTTEQAAVVLPVF
GEWKGTGTYHAALISRNGQLMSLSLHDSNTNKNLVIAAESGSGKSFLTNELIFSYLSEGAQVWVIDAGKS
YQKLSEMLNGDFVHFEEGTHVCLNPFELIQNYEDEEDAIVSLVCAMASAKGLLDEWQISALKQVLSRLWE
EKGKEMKVDDIAERCLEEENDQRLKDIGQQLYAFTSQGSYGKYFSRKNNVSFQNQFTVLELDELQGRKHL
RQVVLLQLIYQIQQEVFLGERNRKKVVIVDEAWDLLKEGEVSVFMEHAYRKFRKYGGSVVIATQSINDLY
ENAVGRAIAENSASMYLLGQTEETVESVKRSGRLTLSEGGFHTLKTVHTIQGVYSEIFIKSKSGMGVGRL
IVGDFQKLLYSTDPVDVNAIDQFVKQGMSIPEAIKAVMRSRRQAA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(284-434)

TraC protein (TraC_F_IV)

(21-255)

TraG P-loop domain (P-loop_TraG)

(449-809)

  Protein structure



No available structure.



ID   2243 GenBank   WP_000178857
Name   traD_HTN34_RS00845_p112298-tetA 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: 69225.71 Da        Isoelectric Point: 6.9403

>WP_000178857.1 MULTISPECIES: conjugative transfer system coupling protein TraD [Gammaproteobacteria]
MTMSYDPLAYEMPWRPNYEKNAVAGWLAASGAALAVEQVSTMPPEPFYWMTGICGVMAMARLPKAIKLHL
LQKHLKGRDLEFISIAELQKYIKDTPDDMWLGSGFLWENRHAQRVFEILKRDWTSIVGRESTVKKVVRKI
QGKKKELPIGQPWIHGVEPKEEKLMQPLKHTEGHSLIVGTTGSGKTRMFDILISQAILRGEAVIIIDPKG
DKEMRDNARRACEAMGQPERFVSFHPAFPEESVRIDPLRNFTRVTEIASRLAALIPSEAGADPFKSFGWQ
ALNNIAQGLVITHDRPNLTKLRRFLEGGAAGLVIKAVQAYSERVMPDWEAEAAAYLEKVKNGSREKIAFA
LMKFYYDIIQPEHPNSDLEGLLSMFQHDQTHFSKMVANLLPIMNMLTSGELGPLLSPDSSDLSDERQITD
SAKIINNAQVAYLGLDSLTDNMVGSAMGSIFLSDLTAVAGDRYNYGVNNRPVNIFVDEAAEVINDPFIQL
LNKGRGAKLRLFVATQTFADFAARLGSKDKALQVLGNINNTFALRIVDGETQEYIADNLPKTRLKYVMRT
QGQNSDGKEPIMHGGNQGERLMEEEADLFPAQLLGMLPNLEYIAKISGGTIVKGRLPILTQ

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(170-299)

TraM recognition site of TraD and TraG (TraG-D_C)

(471-598)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 136346..145436

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTN34_RS00830 132377..132610 - 234 WP_001191892 hypothetical protein -
HTN34_RS00835 132592..133209 - 618 WP_001249396 hypothetical protein -
HTN34_RS00840 133377..136349 + 2973 WP_064986968 MobH family relaxase -
HTN34_RS00845 136346..138211 + 1866 WP_000178857 conjugative transfer system coupling protein TraD virb4
HTN34_RS00850 138222..138806 + 585 WP_000332868 hypothetical protein -
HTN34_RS00855 138763..139392 + 630 WP_000743449 DUF4400 domain-containing protein tfc7
HTN34_RS00860 139402..139848 + 447 WP_000122507 hypothetical protein -
HTN34_RS00865 139858..140235 + 378 WP_000869297 hypothetical protein -
HTN34_RS00870 140235..140897 + 663 WP_001231464 hypothetical protein -
HTN34_RS00875 141078..141221 + 144 WP_001275801 hypothetical protein -
HTN34_RS00880 141281..141598 + 318 WP_223847817 hypothetical protein -
HTN34_RS00885 141743..142024 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
HTN34_RS00890 142021..142647 + 627 WP_001049717 TraE/TraK family type IV conjugative transfer system protein traE
HTN34_RS00895 142631..143548 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
HTN34_RS00900 143548..144861 + 1314 WP_024131605 TraB/VirB10 family protein traB
HTN34_RS00905 144858..145436 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
HTN34_RS00910 145440..145832 + 393 WP_000479535 TraA family conjugative transfer protein -
HTN34_RS00915 146116..147141 + 1026 Protein_186 IS1380-like element ISEcp1 family transposase -
HTN34_RS00920 147198..148166 - 969 WP_000654804 IS5-like element IS903B family transposase -
HTN34_RS00925 148200..148934 + 735 WP_236849182 shufflon system plasmid conjugative transfer pilus tip adhesin PilV -
HTN34_RS00930 149191..150399 + 1209 WP_001339197 IS4-like element ISVsa5 family transposase -

Host bacterium

ID   3746 GenBank   NZ_KY986974
Plasmid name   p112298-tetA Incompatibility group   IncA/C2
Plasmid size   190310 bp Coordinate of oriT [Strand]   138262..138412 [+]
Host baterium   Citrobacter freundii strain 112298

Cargo genes

Drug resistance gene   floR, tet(A), aph(6)-Id, aph(3'')-Ib, sul2, blaCMY-2, aac(6')-Il, sul1, blaKPC-2
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -