Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105388
Name   oriT_p21978-1 in_silico
Organism   Salmonella enterica subsp. enterica serovar Reading strain CVM 21978
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP051451 (155840..155990 [-], 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_p21978-1
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3677 GenBank   WP_001326173
Name   mobH_HFQ72_RS25160_p21978-1 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   3655 GenBank   WP_000637384
Name   traC_HFQ72_RS25060_p21978-1 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   3656 GenBank   WP_000178857
Name   traD_HFQ72_RS25155_p21978-1 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: 148816..157906

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HFQ72_RS25625 (HFQ72_25130) 143841..144206 - 366 Protein_165 LuxR family transcriptional regulator -
HFQ72_RS25075 (HFQ72_25135) 144463..144780 + 318 WP_000118520 quaternary ammonium compound efflux SMR transporter SugE -
HFQ72_RS25080 (HFQ72_25140) 144777..145310 - 534 WP_001221666 lipocalin family protein -
HFQ72_RS25085 (HFQ72_25145) 145404..146549 - 1146 WP_000976514 extended-spectrum class C beta-lactamase CMY-2 -
HFQ72_RS25090 (HFQ72_25150) 146873..148135 - 1263 WP_000608644 IS1380-like element ISEcp1 family transposase -
HFQ72_RS25095 (HFQ72_25155) 148420..148812 - 393 WP_000479535 TraA family conjugative transfer protein -
HFQ72_RS25100 (HFQ72_25160) 148816..149394 - 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
HFQ72_RS25105 (HFQ72_25165) 149391..150704 - 1314 WP_024131605 TraB/VirB10 family protein traB
HFQ72_RS25110 (HFQ72_25170) 150704..151621 - 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
HFQ72_RS25115 (HFQ72_25175) 151605..152231 - 627 WP_001049717 TraE/TraK family type IV conjugative transfer system protein traE
HFQ72_RS25120 (HFQ72_25180) 152228..152509 - 282 WP_000805625 type IV conjugative transfer system protein TraL traL
HFQ72_RS25125 (HFQ72_25185) 152654..153019 - 366 WP_001052530 hypothetical protein -
HFQ72_RS25130 (HFQ72_25190) 153355..154017 - 663 WP_001231464 hypothetical protein -
HFQ72_RS25135 (HFQ72_25195) 154017..154394 - 378 WP_000869297 hypothetical protein -
HFQ72_RS25140 (HFQ72_25200) 154404..154850 - 447 WP_000122507 hypothetical protein -
HFQ72_RS25145 (HFQ72_25205) 154860..155489 - 630 WP_000743449 DUF4400 domain-containing protein tfc7
HFQ72_RS25150 (HFQ72_25210) 155446..155991 - 546 WP_000228720 hypothetical protein -
HFQ72_RS25155 (HFQ72_25215) 156041..157906 - 1866 WP_000178857 conjugative transfer system coupling protein TraD virb4
HFQ72_RS25160 (HFQ72_25220) 157903..160875 - 2973 WP_001326173 MobH family relaxase -
HFQ72_RS25165 (HFQ72_25225) 161043..161660 + 618 WP_001249395 hypothetical protein -
HFQ72_RS25170 (HFQ72_25230) 161642..161875 + 234 WP_001191890 hypothetical protein -

Host bacterium

ID   5826 GenBank   NZ_CP051451
Plasmid name   p21978-1 Incompatibility group   IncA/C2
Plasmid size   168106 bp Coordinate of oriT [Strand]   155840..155990 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Reading strain CVM 21978

Cargo genes

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