Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   121114
Name   oriT_pF2613-NDM in_silico
Organism   Citrobacter freundii strain F2613
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP137204 (52778..52928 [+], 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_pF2613-NDM
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   13331 GenBank   WP_001326173
Name   mobH_R4T23_RS24145_pF2613-NDM insolico UniProt ID   F5BPR1
Length   990 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 990 a.a.        Molecular weight: 109356.90 Da        Isoelectric Point: 4.9395

>WP_001326173.1 MULTISPECIES: MobH family relaxase [Gammaproteobacteria]
MLKALNKLFGGRSGVIETAPSVRVLPLKDVEDEEIPRYPPFAKGLPVAPLDKILATQAELIEKVRNSLGF
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 F5BPR1


T4CP

ID   15619 GenBank   WP_000178857
Name   traD_R4T23_RS24150_pF2613-NDM 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.



ID   15620 GenBank   WP_000637384
Name   traC_R4T23_RS24255_pF2613-NDM 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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 50862..59952

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
R4T23_RS24135 (R4T23_24130) 46893..47126 - 234 WP_001191890 hypothetical protein -
R4T23_RS24140 (R4T23_24135) 47108..47725 - 618 WP_001249395 hypothetical protein -
R4T23_RS24145 (R4T23_24140) 47893..50865 + 2973 WP_001326173 MobH family relaxase -
R4T23_RS24150 (R4T23_24145) 50862..52727 + 1866 WP_000178857 conjugative transfer system coupling protein TraD virb4
R4T23_RS24155 (R4T23_24150) 52777..53322 + 546 WP_000228720 hypothetical protein -
R4T23_RS24160 (R4T23_24155) 53279..53908 + 630 WP_000743449 DUF4400 domain-containing protein tfc7
R4T23_RS24165 (R4T23_24160) 53918..54364 + 447 WP_000122507 hypothetical protein -
R4T23_RS24170 (R4T23_24165) 54374..54751 + 378 WP_000869297 hypothetical protein -
R4T23_RS24175 (R4T23_24170) 54751..55413 + 663 WP_001231464 hypothetical protein -
R4T23_RS24180 (R4T23_24175) 55594..55737 + 144 WP_001275801 hypothetical protein -
R4T23_RS24185 (R4T23_24180) 55749..56114 + 366 WP_001052530 hypothetical protein -
R4T23_RS24190 (R4T23_24185) 56259..56540 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
R4T23_RS24195 (R4T23_24190) 56537..57163 + 627 WP_001049717 TraE/TraK family type IV conjugative transfer system protein traE
R4T23_RS24200 (R4T23_24195) 57147..58064 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
R4T23_RS24205 (R4T23_24200) 58064..59377 + 1314 WP_024131605 TraB/VirB10 family protein traB
R4T23_RS24210 (R4T23_24205) 59374..59952 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
R4T23_RS24215 (R4T23_24210) 59956..60348 + 393 WP_000479535 TraA family conjugative transfer protein -
R4T23_RS24220 (R4T23_24215) 60633..61895 + 1263 WP_000608644 IS1380-like element ISEcp1 family transposase -
R4T23_RS24225 (R4T23_24220) 62219..63364 + 1146 WP_015058212 class C beta-lactamase CMY-6 -
R4T23_RS24230 (R4T23_24225) 63458..63991 + 534 WP_001221666 lipocalin family protein -
R4T23_RS24235 (R4T23_24230) 63988..64305 - 318 WP_000118520 quaternary ammonium compound efflux SMR transporter SugE -
R4T23_RS24240 (R4T23_24235) 64562..64927 + 366 Protein_91 LuxR family transcriptional regulator -

Host bacterium

ID   21542 GenBank   NZ_CP137204
Plasmid name   pF2613-NDM Incompatibility group   IncA/C2
Plasmid size   142801 bp Coordinate of oriT [Strand]   52778..52928 [+]
Host baterium   Citrobacter freundii strain F2613

Cargo genes

Drug resistance gene   blaCMY-6, aac(6')-Ib, qacE, sul1, rmtC, blaNDM-1
Virulence gene   htpB
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -