Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   105408
Name   oriT_p22437-1 in_silico
Organism   Salmonella enterica subsp. enterica serovar Uganda strain CVM 22437
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP051397 (140164..140314 [-], 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_p22437-1
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   3690 GenBank   WP_001326173
Name   mobH_HFQ89_RS24320_p22437-1 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   3672 GenBank   WP_000637384
Name   traC_HFQ89_RS23670_p22437-1 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   3673 GenBank   WP_000178857
Name   traD_HFQ89_RS24315_p22437-1 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: 133715..142230

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HFQ89_RS24235 (HFQ89_24250) 128824..129315 + 492 WP_000139717 hypothetical protein -
HFQ89_RS24240 (HFQ89_24260) 129642..130517 + 876 WP_001097010 DNA replication terminus site-binding protein -
HFQ89_RS24245 (HFQ89_24265) 130679..131719 + 1041 WP_000101568 DNA-binding protein -
HFQ89_RS24250 (HFQ89_24270) 132006..132479 + 474 Protein_143 DNA helicase -
HFQ89_RS24255 (HFQ89_24275) 132528..133232 - 705 WP_001067858 IS6-like element IS26 family transposase -
HFQ89_RS24260 (HFQ89_24280) 133296..133718 - 423 Protein_145 TraV family lipoprotein -
HFQ89_RS24265 (HFQ89_24285) 133715..135028 - 1314 WP_024131605 TraB/VirB10 family protein traB
HFQ89_RS24270 (HFQ89_24290) 135028..135945 - 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
HFQ89_RS24275 (HFQ89_24295) 135929..136555 - 627 WP_001049717 TraE/TraK family type IV conjugative transfer system protein traE
HFQ89_RS24280 (HFQ89_24300) 136552..136833 - 282 WP_000805625 type IV conjugative transfer system protein TraL traL
HFQ89_RS24285 (HFQ89_24305) 136978..137343 - 366 WP_001052530 hypothetical protein -
HFQ89_RS24290 (HFQ89_24310) 137679..138341 - 663 WP_001231464 hypothetical protein -
HFQ89_RS24295 (HFQ89_24315) 138341..138718 - 378 WP_000869297 hypothetical protein -
HFQ89_RS24300 (HFQ89_24320) 138728..139174 - 447 WP_000122507 hypothetical protein -
HFQ89_RS24305 (HFQ89_24325) 139184..139813 - 630 WP_000743449 DUF4400 domain-containing protein tfc7
HFQ89_RS24310 (HFQ89_24330) 139770..140315 - 546 WP_000228720 hypothetical protein -
HFQ89_RS24315 (HFQ89_24335) 140365..142230 - 1866 WP_000178857 conjugative transfer system coupling protein TraD virb4
HFQ89_RS24320 (HFQ89_24340) 142227..145199 - 2973 WP_001326173 MobH family relaxase -
HFQ89_RS24325 (HFQ89_24345) 145367..145984 + 618 WP_001249395 hypothetical protein -
HFQ89_RS24330 (HFQ89_24350) 145966..146199 + 234 WP_001191890 hypothetical protein -

Host bacterium

ID   5846 GenBank   NZ_CP051397
Plasmid name   p22437-1 Incompatibility group   IncA/C2
Plasmid size   191208 bp Coordinate of oriT [Strand]   140164..140314 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Uganda strain CVM 22437

Cargo genes

Drug resistance gene   blaCMY-2, tet(M), ant(2'')-Ia, aadA2, cmlA1, aadA15, qacE, sul2, aph(3'')-Ib, aph(6)-Id, tet(A), floR
Virulence gene   -
Metal resistance gene   merE, merD, merB, merA, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -