Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105373
Name   oriT_p35009 in_silico
Organism   Salmonella enterica subsp. enterica serovar Uganda strain CVM 35009
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP051316 (54916..55066 [+], 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_p35009
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3667 GenBank   WP_001326173
Name   mobH_HFU03_RS23625_p35009 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   3641 GenBank   WP_077779971
Name   traD_HFU03_RS23630_p35009 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: 69253.76 Da        Isoelectric Point: 6.9403

>WP_077779971.1 MULTISPECIES: conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MTMSYDPLAYEMPWRPNYEKNAVAGWLAASGAALAVEQVSTMPPEPFYWMTGICGVMAMARLPKAIKLHL
LQKHLKGRDLEFISIAELQKYIKDTPDDMWLGSGFLWENRHAQRVFEILKRDWTSIVGRESTVKKVVRKI
QGKKKELPIGQPWIHGVEPKEEKLMQPLKHTEGHSLIVGTTGSGKTRMFDILISQAILRGEAVIIIDPKG
DKEMRDNARRACEAMGQPERFVSFHPVFPEESVRIDPLRNFTRVTEIASRLAALIPSEAGADPFKSFGWQ
ALNNIAQGLVITHDRPNLTKLRRFLEGGAAGLVIKAVQAYSERVMPDWEAEAAAYLEKVKNGSREKIAFA
LMKFYYDIIQPEHPNSDLEGLLSMFQHDQTHFSKMVANLLPIMNMLTSGELGPLLSPDSSDLSDERQITD
SAKIINNAQVAYLGLDSLTDNMVGSAMGSIFLSDLTAVAGDRYNYGVNNRPVNIFVDEAAEVINDPFIQL
LNKGRGAKLRLFVATQTFADFAARLGSKDKALQVLGNINNTFALRIVDGETQEYIADNLPKTRLKYVMRT
QGQNSDGKEPIMHGGNQGERLMEEEADLFPAQLLGMLPNLEYIAKISGGTIVKGRLPILTQ

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(170-302)

TraM recognition site of TraD and TraG (TraG-D_C)

(471-598)

  Protein structure



No available structure.



ID   3642 GenBank   WP_000637384
Name   traC_HFU03_RS23725_p35009 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: 53000..62090

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HFU03_RS23615 (HFU03_23645) 49031..49264 - 234 WP_001191890 hypothetical protein -
HFU03_RS23620 (HFU03_23650) 49246..49863 - 618 WP_001249395 hypothetical protein -
HFU03_RS23625 (HFU03_23655) 50031..53003 + 2973 WP_001326173 MobH family relaxase -
HFU03_RS23630 (HFU03_23660) 53000..54865 + 1866 WP_077779971 conjugative transfer system coupling protein TraD virb4
HFU03_RS23635 (HFU03_23665) 54915..55460 + 546 WP_000228720 hypothetical protein -
HFU03_RS23640 (HFU03_23670) 55417..56046 + 630 WP_000743449 DUF4400 domain-containing protein tfc7
HFU03_RS23645 (HFU03_23675) 56056..56502 + 447 WP_000122507 hypothetical protein -
HFU03_RS23650 (HFU03_23680) 56512..56889 + 378 WP_000869297 hypothetical protein -
HFU03_RS23655 (HFU03_23685) 56889..57551 + 663 WP_001231464 hypothetical protein -
HFU03_RS23660 (HFU03_23690) 57887..58252 + 366 WP_001052530 hypothetical protein -
HFU03_RS23665 (HFU03_23695) 58397..58678 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
HFU03_RS23670 (HFU03_23700) 58675..59301 + 627 WP_001049717 TraE/TraK family type IV conjugative transfer system protein traE
HFU03_RS23675 (HFU03_23705) 59285..60202 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
HFU03_RS23680 (HFU03_23710) 60202..61515 + 1314 WP_024131605 TraB/VirB10 family protein traB
HFU03_RS23685 (HFU03_23715) 61512..62090 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
HFU03_RS23690 (HFU03_23720) 62094..62486 + 393 WP_000479535 TraA family conjugative transfer protein -
HFU03_RS23695 (HFU03_23725) 62771..64033 + 1263 WP_000608644 IS1380-like element ISEcp1 family transposase -
HFU03_RS23700 (HFU03_23730) 64357..65502 + 1146 WP_000976514 extended-spectrum class C beta-lactamase CMY-2 -
HFU03_RS23705 (HFU03_23735) 65596..66129 + 534 WP_001221666 lipocalin family protein -
HFU03_RS23710 (HFU03_23740) 66126..66443 - 318 WP_000118520 quaternary ammonium compound efflux SMR transporter SugE -
HFU03_RS24650 (HFU03_23745) 66700..67065 + 366 Protein_95 LuxR family transcriptional regulator -

Host bacterium

ID   5811 GenBank   NZ_CP051316
Plasmid name   p35009 Incompatibility group   IncA/C2
Plasmid size   170832 bp Coordinate of oriT [Strand]   54916..55066 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Uganda strain CVM 35009

Cargo genes

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