Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103933
Name   oriT_pCFSAN007427_01 in_silico
Organism   Salmonella enterica subsp. enterica serovar Infantis strain CFSAN007427 isolate N20272
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP009413 (102062..102212 [-], 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_pCFSAN007427_01
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2925 GenBank   WP_001326173
Name   mobH_JV44_RS00640_pCFSAN007427_01 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   2775 GenBank   WP_000637384
Name   traC_JV44_RS00530_pCFSAN007427_01 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   2776 GenBank   WP_000178857
Name   traD_JV44_RS00635_pCFSAN007427_01 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: 95038..104128

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
JV44_RS00545 (JV44_00565) 90063..90428 - 366 Protein_104 LuxR family transcriptional regulator -
JV44_RS00550 (JV44_00570) 90685..91002 + 318 WP_000118520 quaternary ammonium compound efflux SMR transporter SugE -
JV44_RS00555 (JV44_00575) 90999..91532 - 534 WP_001221666 lipocalin family protein -
JV44_RS00560 (JV44_00580) 91626..92771 - 1146 WP_000976514 extended-spectrum class C beta-lactamase CMY-2 -
JV44_RS00565 (JV44_00585) 93095..94357 - 1263 WP_000608644 IS1380-like element ISEcp1 family transposase -
JV44_RS00570 (JV44_00590) 94642..95034 - 393 WP_000479535 TraA family conjugative transfer protein -
JV44_RS00575 (JV44_00595) 95038..95616 - 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
JV44_RS00580 (JV44_00600) 95613..96926 - 1314 WP_024131605 TraB/VirB10 family protein traB
JV44_RS00585 (JV44_00605) 96926..97843 - 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
JV44_RS00590 (JV44_00610) 97827..98453 - 627 WP_001049717 TraE/TraK family type IV conjugative transfer system protein traE
JV44_RS00595 (JV44_00615) 98450..98731 - 282 WP_000805625 type IV conjugative transfer system protein TraL traL
JV44_RS00600 (JV44_00620) 98876..99241 - 366 WP_001052530 hypothetical protein -
JV44_RS00605 99253..99396 - 144 WP_001275801 hypothetical protein -
JV44_RS00610 (JV44_00625) 99577..100239 - 663 WP_001231464 hypothetical protein -
JV44_RS00615 (JV44_00630) 100239..100616 - 378 WP_000869297 hypothetical protein -
JV44_RS00620 (JV44_00635) 100626..101072 - 447 WP_000122507 hypothetical protein -
JV44_RS00625 (JV44_00640) 101082..101711 - 630 WP_000743449 DUF4400 domain-containing protein tfc7
JV44_RS00630 (JV44_00645) 101668..102252 - 585 WP_000332868 hypothetical protein -
JV44_RS00635 (JV44_00650) 102263..104128 - 1866 WP_000178857 conjugative transfer system coupling protein TraD virb4
JV44_RS00640 (JV44_00655) 104125..107097 - 2973 WP_001326173 MobH family relaxase -
JV44_RS00645 (JV44_00660) 107265..107882 + 618 WP_001249395 hypothetical protein -
JV44_RS00650 (JV44_00665) 107864..108097 + 234 WP_001191890 hypothetical protein -

Host bacterium

ID   4373 GenBank   NZ_CP009413
Plasmid name   pCFSAN007427_01 Incompatibility group   IncA/C2
Plasmid size   175517 bp Coordinate of oriT [Strand]   102062..102212 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Infantis strain CFSAN007427 isolate N20272

Cargo genes

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