Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103739
Name   oriT_pCVM21550 in_silico
Organism   Salmonella enterica subsp. enterica serovar Newport str. CVM 21550
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP009564 (108261..108411 [+], 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_pCVM21550
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2769 GenBank   WP_001326173
Name   mobH_SEEN550_RS00660_pCVM21550 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   2598 GenBank   WP_000637384
Name   traC_SEEN550_RS00070_pCVM21550 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   2599 GenBank   WP_000178857
Name   traD_SEEN550_RS00665_pCVM21550 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: 106345..117665

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
SEEN550_RS00650 (SEEN550_00620) 102376..102609 - 234 WP_001191890 hypothetical protein -
SEEN550_RS00655 (SEEN550_00625) 102591..103208 - 618 WP_001249395 hypothetical protein -
SEEN550_RS00660 (SEEN550_00630) 103376..106348 + 2973 WP_001326173 MobH family relaxase -
SEEN550_RS00665 (SEEN550_00635) 106345..108210 + 1866 WP_000178857 conjugative transfer system coupling protein TraD virb4
SEEN550_RS00670 (SEEN550_00640) 108260..108805 + 546 WP_000228720 hypothetical protein -
SEEN550_RS00675 (SEEN550_00645) 108762..109391 + 630 WP_000743449 DUF4400 domain-containing protein tfc7
SEEN550_RS00680 (SEEN550_00650) 109401..109847 + 447 WP_000122507 hypothetical protein -
SEEN550_RS00685 (SEEN550_00655) 109857..110234 + 378 WP_000869297 hypothetical protein -
SEEN550_RS00690 (SEEN550_00660) 110234..110896 + 663 WP_001231464 hypothetical protein -
SEEN550_RS00695 (SEEN550_00670) 111232..111597 + 366 WP_001052530 hypothetical protein -
SEEN550_RS00700 (SEEN550_00675) 111742..112023 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
SEEN550_RS00705 (SEEN550_00680) 112020..112646 + 627 WP_001049717 TraE/TraK family type IV conjugative transfer system protein traE
SEEN550_RS00710 (SEEN550_00685) 112630..113547 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
SEEN550_RS00715 (SEEN550_00690) 113547..114860 + 1314 WP_024131605 TraB/VirB10 family protein traB
SEEN550_RS00720 (SEEN550_00695) 114857..115435 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
SEEN550_RS00725 (SEEN550_00700) 115439..115831 + 393 WP_000479535 TraA family conjugative transfer protein -
SEEN550_RS00730 116116..117075 + 960 Protein_138 IS1380-like element ISEcp1 family transposase -
SEEN550_RS00735 (SEEN550_00710) 117069..117776 - 708 WP_000637385 conjugal transfer protein TraC -
SEEN550_RS00740 (SEEN550_00715) 117773..118480 - 708 WP_001259346 DsbC family protein -

Host bacterium

ID   4179 GenBank   NZ_CP009564
Plasmid name   pCVM21550 Incompatibility group   IncA/C2
Plasmid size   120340 bp Coordinate of oriT [Strand]   108261..108411 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Newport str. CVM 21550

Cargo genes

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