Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105416
Name   oriT_p20723-1 in_silico
Organism   Salmonella enterica subsp. enterica serovar Uganda strain CVM 20723
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP051426 (106143..106293 [-], 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_p20723-1
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3694 GenBank   WP_001326173
Name   mobH_HFQ25_RS24225_p20723-1 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   3678 GenBank   WP_000637384
Name   traC_HFQ25_RS24125_p20723-1 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   3679 GenBank   WP_000178857
Name   traD_HFQ25_RS24220_p20723-1 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: 99119..108209

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HFQ25_RS25175 (HFQ25_24150) 94144..94509 - 366 Protein_101 LuxR family transcriptional regulator -
HFQ25_RS24140 (HFQ25_24155) 94766..95083 + 318 WP_000118520 quaternary ammonium compound efflux SMR transporter SugE -
HFQ25_RS24145 (HFQ25_24160) 95080..95613 - 534 WP_001221666 lipocalin family protein -
HFQ25_RS24150 (HFQ25_24165) 95707..96852 - 1146 WP_000976514 extended-spectrum class C beta-lactamase CMY-2 -
HFQ25_RS24155 (HFQ25_24170) 97176..98438 - 1263 WP_000608644 IS1380-like element ISEcp1 family transposase -
HFQ25_RS24160 (HFQ25_24175) 98723..99115 - 393 WP_000479535 TraA family conjugative transfer protein -
HFQ25_RS24165 (HFQ25_24180) 99119..99697 - 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
HFQ25_RS24170 (HFQ25_24185) 99694..101007 - 1314 WP_024131605 TraB/VirB10 family protein traB
HFQ25_RS24175 (HFQ25_24190) 101007..101924 - 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
HFQ25_RS24180 (HFQ25_24195) 101908..102534 - 627 WP_001049717 TraE/TraK family type IV conjugative transfer system protein traE
HFQ25_RS24185 (HFQ25_24200) 102531..102812 - 282 WP_000805625 type IV conjugative transfer system protein TraL traL
HFQ25_RS24190 (HFQ25_24205) 102957..103322 - 366 WP_001052530 hypothetical protein -
HFQ25_RS24195 (HFQ25_24210) 103658..104320 - 663 WP_001231464 hypothetical protein -
HFQ25_RS24200 (HFQ25_24215) 104320..104697 - 378 WP_000869297 hypothetical protein -
HFQ25_RS24205 (HFQ25_24220) 104707..105153 - 447 WP_000122507 hypothetical protein -
HFQ25_RS24210 (HFQ25_24225) 105163..105792 - 630 WP_000743449 DUF4400 domain-containing protein tfc7
HFQ25_RS24215 (HFQ25_24230) 105749..106294 - 546 WP_000228720 hypothetical protein -
HFQ25_RS24220 (HFQ25_24235) 106344..108209 - 1866 WP_000178857 conjugative transfer system coupling protein TraD virb4
HFQ25_RS24225 (HFQ25_24240) 108206..111178 - 2973 WP_001326173 MobH family relaxase -
HFQ25_RS24230 (HFQ25_24245) 111346..111963 + 618 WP_001249395 hypothetical protein -
HFQ25_RS24235 (HFQ25_24250) 111945..112178 + 234 WP_001191890 hypothetical protein -

Host bacterium

ID   5854 GenBank   NZ_CP051426
Plasmid name   p20723-1 Incompatibility group   IncA/C2
Plasmid size   188725 bp Coordinate of oriT [Strand]   106143..106293 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Uganda strain CVM 20723

Cargo genes

Drug resistance gene   sul1, qacE, aadA15, cmlA1, aadA2, ant(2'')-Ia, tet(M), blaCMY-2, sul2, aph(3'')-Ib, aph(6)-Id, tet(A), floR
Virulence gene   -
Metal resistance gene   merB, merD, merE, merR, merT, merP, merA
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -