Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105377
Name   oriT_p28322-2 in_silico
Organism   Salmonella enterica subsp. enterica serovar Heidelberg strain CVM 28322
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP051360 (135392..135542 [+], 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_p28322-2
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3671 GenBank   WP_001326173
Name   mobH_HFS63_RS25515_p28322-2 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   3646 GenBank   WP_000178857
Name   traD_HFS63_RS25520_p28322-2 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   3647 GenBank   WP_000637384
Name   traC_HFS63_RS25620_p28322-2 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: 133476..142566

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HFS63_RS25505 (HFS63_25575) 129507..129740 - 234 WP_001191890 hypothetical protein -
HFS63_RS25510 (HFS63_25580) 129722..130339 - 618 WP_001249395 hypothetical protein -
HFS63_RS25515 (HFS63_25585) 130507..133479 + 2973 WP_001326173 MobH family relaxase -
HFS63_RS25520 (HFS63_25590) 133476..135341 + 1866 WP_000178857 conjugative transfer system coupling protein TraD virb4
HFS63_RS25525 (HFS63_25595) 135391..135936 + 546 WP_000228720 hypothetical protein -
HFS63_RS25530 (HFS63_25600) 135893..136522 + 630 WP_000743449 DUF4400 domain-containing protein tfc7
HFS63_RS25535 (HFS63_25605) 136532..136978 + 447 WP_000122507 hypothetical protein -
HFS63_RS25540 (HFS63_25610) 136988..137365 + 378 WP_000869297 hypothetical protein -
HFS63_RS25545 (HFS63_25615) 137365..138027 + 663 WP_001231464 hypothetical protein -
HFS63_RS25550 (HFS63_25620) 138208..138351 + 144 WP_001275801 hypothetical protein -
HFS63_RS25555 (HFS63_25625) 138363..138728 + 366 WP_001052530 hypothetical protein -
HFS63_RS25560 (HFS63_25630) 138873..139154 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
HFS63_RS25565 (HFS63_25635) 139151..139777 + 627 WP_001049717 TraE/TraK family type IV conjugative transfer system protein traE
HFS63_RS25570 (HFS63_25640) 139761..140678 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
HFS63_RS25575 (HFS63_25645) 140678..141991 + 1314 WP_024131605 TraB/VirB10 family protein traB
HFS63_RS25580 (HFS63_25650) 141988..142566 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
HFS63_RS25585 (HFS63_25655) 142570..142962 + 393 WP_000479535 TraA family conjugative transfer protein -
HFS63_RS25590 (HFS63_25660) 143247..144509 + 1263 WP_000608644 IS1380-like element ISEcp1 family transposase -
HFS63_RS25595 (HFS63_25665) 144833..145978 + 1146 WP_000976514 extended-spectrum class C beta-lactamase CMY-2 -
HFS63_RS25600 (HFS63_25670) 146072..146605 + 534 WP_001221666 lipocalin family protein -
HFS63_RS25605 (HFS63_25675) 146602..146919 - 318 WP_000118520 quaternary ammonium compound efflux SMR transporter SugE -
HFS63_RS26625 (HFS63_25680) 147176..147541 + 366 Protein_183 LuxR family transcriptional regulator -

Host bacterium

ID   5815 GenBank   NZ_CP051360
Plasmid name   p28322-2 Incompatibility group   IncA/C2
Plasmid size   167068 bp Coordinate of oriT [Strand]   135392..135542 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Heidelberg strain CVM 28322

Cargo genes

Drug resistance gene   dfrA1, qacE, blaTEM-1B, aph(3')-Ia, sul1, cmlA1, ant(2'')-Ia, tet(A), aph(6)-Id, aph(3'')-Ib, sul2, blaCMY-2
Virulence gene   -
Metal resistance gene   merD, merE, merB, merA, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -