Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105404
Name   oriT_p20723-2 in_silico
Organism   Salmonella enterica subsp. enterica serovar Newport strain CVM 24374
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP051373 (22242..22392 [-], 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_p20723-2
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3687 GenBank   WP_001326173
Name   mobH_HFS12_RS22600_p20723-2 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   3667 GenBank   WP_000178857
Name   traD_HFS12_RS22595_p20723-2 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: 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   3668 GenBank   WP_000637384
Name   traC_HFS12_RS23150_p20723-2 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: 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: 12988..24308

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HFS12_RS22520 (HFS12_22540) 12173..12880 + 708 WP_001259346 DsbC family protein -
HFS12_RS22525 (HFS12_22545) 12988..13584 + 597 WP_232166453 conjugal transfer protein TraC virb4
HFS12_RS22530 (HFS12_22550) 13578..14537 - 960 Protein_11 IS1380-like element ISEcp1 family transposase -
HFS12_RS22535 (HFS12_22555) 14822..15214 - 393 WP_000479535 TraA family conjugative transfer protein -
HFS12_RS22540 (HFS12_22560) 15218..15796 - 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
HFS12_RS22545 (HFS12_22565) 15793..17106 - 1314 WP_024131605 TraB/VirB10 family protein traB
HFS12_RS22550 (HFS12_22570) 17106..18023 - 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
HFS12_RS22555 (HFS12_22575) 18007..18633 - 627 WP_001049717 TraE/TraK family type IV conjugative transfer system protein traE
HFS12_RS22560 (HFS12_22580) 18630..18911 - 282 WP_000805625 type IV conjugative transfer system protein TraL traL
HFS12_RS22565 (HFS12_22585) 19056..19421 - 366 WP_001052530 hypothetical protein -
HFS12_RS22570 (HFS12_22590) 19757..20419 - 663 WP_001231464 hypothetical protein -
HFS12_RS22575 (HFS12_22595) 20419..20796 - 378 WP_000869297 hypothetical protein -
HFS12_RS22580 (HFS12_22600) 20806..21252 - 447 WP_000122507 hypothetical protein -
HFS12_RS22585 (HFS12_22605) 21262..21891 - 630 WP_000743449 DUF4400 domain-containing protein tfc7
HFS12_RS22590 (HFS12_22610) 21848..22393 - 546 WP_000228720 hypothetical protein -
HFS12_RS22595 (HFS12_22615) 22443..24308 - 1866 WP_000178857 conjugative transfer system coupling protein TraD virb4
HFS12_RS22600 (HFS12_22620) 24305..27277 - 2973 WP_001326173 MobH family relaxase -
HFS12_RS22605 (HFS12_22625) 27445..28062 + 618 WP_001249395 hypothetical protein -
HFS12_RS22610 (HFS12_22630) 28044..28277 + 234 WP_001191890 hypothetical protein -

Host bacterium

ID   5842 GenBank   NZ_CP051373
Plasmid name   p20723-2 Incompatibility group   IncA/C2
Plasmid size   122954 bp Coordinate of oriT [Strand]   22242..22392 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Newport strain CVM 24374

Cargo genes

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