Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113328
Name   oriT_S12_VPH_Chula|unnamed1 in_silico
Organism   Salmonella enterica strain S12_VPH_Chula
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP121381 (63163..63313 [+], 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_S12_VPH_Chula|unnamed1
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8548 GenBank   WP_001326173
Name   mobH_QAT96_RS24010_S12_VPH_Chula|unnamed1 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   9862 GenBank   WP_000178857
Name   traD_QAT96_RS24015_S12_VPH_Chula|unnamed1 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   9863 GenBank   WP_000637384
Name   traC_QAT96_RS24115_S12_VPH_Chula|unnamed1 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: 61247..70967

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
QAT96_RS24000 (QAT96_24000) 57278..57511 - 234 WP_001191890 hypothetical protein -
QAT96_RS24005 (QAT96_24005) 57493..58110 - 618 WP_001249395 hypothetical protein -
QAT96_RS24010 (QAT96_24010) 58278..61250 + 2973 WP_001326173 MobH family relaxase -
QAT96_RS24015 (QAT96_24015) 61247..63112 + 1866 WP_000178857 conjugative transfer system coupling protein TraD virb4
QAT96_RS24020 (QAT96_24020) 63162..63707 + 546 WP_000228720 hypothetical protein -
QAT96_RS24025 (QAT96_24025) 63664..64293 + 630 WP_000743449 DUF4400 domain-containing protein tfc7
QAT96_RS24030 (QAT96_24030) 64303..64749 + 447 WP_000122507 hypothetical protein -
QAT96_RS24035 (QAT96_24035) 64759..65136 + 378 WP_000869297 hypothetical protein -
QAT96_RS24040 (QAT96_24040) 65136..65798 + 663 WP_001231464 hypothetical protein -
QAT96_RS24045 (QAT96_24045) 66134..66499 + 366 WP_001052530 hypothetical protein -
QAT96_RS24050 (QAT96_24050) 66667..67101 + 435 WP_038989254 IS200/IS605 family transposase -
QAT96_RS24055 (QAT96_24055) 67274..67555 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
QAT96_RS24060 (QAT96_24060) 67552..68178 + 627 WP_001049717 TraE/TraK family type IV conjugative transfer system protein traE
QAT96_RS24065 (QAT96_24065) 68162..69079 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
QAT96_RS24070 (QAT96_24070) 69079..70392 + 1314 WP_024131605 TraB/VirB10 family protein traB
QAT96_RS24075 (QAT96_24075) 70389..70967 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
QAT96_RS24080 (QAT96_24080) 70971..71363 + 393 WP_000479535 TraA family conjugative transfer protein -
QAT96_RS24085 (QAT96_24085) 71648..72910 + 1263 WP_000608644 IS1380-like element ISEcp1 family transposase -
QAT96_RS24090 (QAT96_24090) 73234..74379 + 1146 WP_000976514 extended-spectrum class C beta-lactamase CMY-2 -
QAT96_RS24095 (QAT96_24095) 74473..75006 + 534 WP_001221666 lipocalin family protein -
QAT96_RS24100 (QAT96_24100) 75003..75320 - 318 WP_000118520 quaternary ammonium compound efflux SMR transporter SugE -
QAT96_RS25055 75577..75942 + 366 Protein_101 LuxR family transcriptional regulator -

Host bacterium

ID   13763 GenBank   NZ_CP121381
Plasmid name   S12_VPH_Chula|unnamed1 Incompatibility group   IncA/C2
Plasmid size   182559 bp Coordinate of oriT [Strand]   63163..63313 [+]
Host baterium   Salmonella enterica strain S12_VPH_Chula

Cargo genes

Drug resistance gene   aph(3')-Ia, floR, tet(A), aph(6)-Id, aph(3'')-Ib, sul2, blaCMY-2, lnu(G), ant(3'')-Ia, aac(3)-VIa, qacE, sul1, blaTEM-1B
Virulence gene   htpB
Metal resistance gene   merE, merD
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -