Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   111916
Name   oriT_pIOMTU157 in_silico
Organism   Citrobacter portucalensis strain IOMTU157
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_AP023051 (47529..47679 [+], 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_pIOMTU157
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   7707 GenBank   WP_001326173
Name   mobH_IOMTU157_RS24220_pIOMTU157 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   8810 GenBank   WP_000178857
Name   traD_IOMTU157_RS24225_pIOMTU157 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   8811 GenBank   WP_000637384
Name   traC_IOMTU157_RS24330_pIOMTU157 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: 45613..54703

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
IOMTU157_RS24210 (IOMTU157_p067) 41644..41877 - 234 WP_001191890 hypothetical protein -
IOMTU157_RS24215 (IOMTU157_p068) 41859..42476 - 618 WP_001249395 hypothetical protein -
IOMTU157_RS24220 (IOMTU157_p069) 42644..45616 + 2973 WP_001326173 MobH family relaxase -
IOMTU157_RS24225 (IOMTU157_p070) 45613..47478 + 1866 WP_000178857 conjugative transfer system coupling protein TraD virb4
IOMTU157_RS24230 (IOMTU157_p071) 47528..48073 + 546 WP_000228720 hypothetical protein -
IOMTU157_RS24235 (IOMTU157_p072) 48030..48659 + 630 WP_000743449 DUF4400 domain-containing protein tfc7
IOMTU157_RS24240 48669..49115 + 447 WP_000122507 hypothetical protein -
IOMTU157_RS24245 (IOMTU157_p074) 49125..49502 + 378 WP_000869297 hypothetical protein -
IOMTU157_RS24250 (IOMTU157_p075) 49502..50164 + 663 WP_001231464 hypothetical protein -
IOMTU157_RS24255 (IOMTU157_p076) 50345..50488 + 144 WP_001275801 hypothetical protein -
IOMTU157_RS24260 (IOMTU157_p077) 50500..50865 + 366 WP_001052530 hypothetical protein -
IOMTU157_RS24265 (IOMTU157_p078) 51010..51291 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
IOMTU157_RS24270 (IOMTU157_p079) 51288..51914 + 627 WP_001049717 TraE/TraK family type IV conjugative transfer system protein traE
IOMTU157_RS24275 (IOMTU157_p080) 51898..52815 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
IOMTU157_RS24280 (IOMTU157_p081) 52815..54128 + 1314 WP_024131605 TraB/VirB10 family protein traB
IOMTU157_RS24285 (IOMTU157_p082) 54125..54703 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
IOMTU157_RS24290 (IOMTU157_p083) 54707..55099 + 393 WP_000479535 TraA family conjugative transfer protein -
IOMTU157_RS24295 (IOMTU157_p084) 55384..56556 + 1173 Protein_83 IS1380-like element ISEcp1 family transposase -
IOMTU157_RS24300 (IOMTU157_p085) 56662..57849 + 1188 WP_080399009 IS4 family transposase -
IOMTU157_RS24305 (IOMTU157_p086) 58304..59449 + 1146 WP_015056382 class C beta-lactamase CMY-4 -

Host bacterium

ID   12351 GenBank   NZ_AP023051
Plasmid name   pIOMTU157 Incompatibility group   IncA/C2
Plasmid size   174206 bp Coordinate of oriT [Strand]   47529..47679 [+]
Host baterium   Citrobacter portucalensis strain IOMTU157

Cargo genes

Drug resistance gene   blaCMY-4, dfrA12, aadA2, qacE, sul1, blaNDM-1, armA, msr(E), mph(E)
Virulence gene   -
Metal resistance gene   merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -