Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   116228
Name   oriT_pJZ30-tet(X4) in_silico
Organism   Proteus vulgaris strain JZ30
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_ON390809 (58654..58804 [+], 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_pJZ30-tet(X4)
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   10381 GenBank   WP_001326173
Name   mobH_ODR51_RS00375_pJZ30-tet(X4) 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   12118 GenBank   WP_000178857
Name   traD_ODR51_RS00380_pJZ30-tet(X4) 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   12119 GenBank   WP_000637384
Name   traC_ODR51_RS00485_pJZ30-tet(X4) 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: 56738..65828

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
ODR51_RS00365 52769..53002 - 234 WP_001191890 hypothetical protein -
ODR51_RS00370 52984..53601 - 618 WP_001249395 hypothetical protein -
ODR51_RS00375 53769..56741 + 2973 WP_001326173 MobH family relaxase -
ODR51_RS00380 56738..58603 + 1866 WP_000178857 conjugative transfer system coupling protein TraD virb4
ODR51_RS00385 58614..59198 + 585 WP_000332868 hypothetical protein -
ODR51_RS00390 59155..59784 + 630 WP_000743449 DUF4400 domain-containing protein tfc7
ODR51_RS00395 59794..60240 + 447 WP_000122507 hypothetical protein -
ODR51_RS00400 60250..60627 + 378 WP_000869297 hypothetical protein -
ODR51_RS00405 60627..61289 + 663 WP_001231464 hypothetical protein -
ODR51_RS00410 61470..61613 + 144 WP_001275801 hypothetical protein -
ODR51_RS00415 61625..61990 + 366 WP_001052530 hypothetical protein -
ODR51_RS00420 62135..62416 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
ODR51_RS00425 62413..63039 + 627 WP_001049717 TraE/TraK family type IV conjugative transfer system protein traE
ODR51_RS00430 63023..63940 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
ODR51_RS00435 63940..65253 + 1314 WP_024131605 TraB/VirB10 family protein traB
ODR51_RS00440 65250..65828 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
ODR51_RS00445 65832..66224 + 393 WP_000479535 TraA family conjugative transfer protein -
ODR51_RS00450 66509..67771 + 1263 WP_000608644 IS1380-like element ISEcp1 family transposase -
ODR51_RS00455 68095..69240 + 1146 WP_000976514 extended-spectrum class C beta-lactamase CMY-2 -
ODR51_RS00460 69334..69867 + 534 WP_001221666 lipocalin family protein -
ODR51_RS00465 69864..70181 - 318 WP_000118520 quaternary ammonium compound efflux SMR transporter SugE -
ODR51_RS00470 70438..70803 + 366 Protein_94 LuxR family transcriptional regulator -

Host bacterium

ID   16661 GenBank   NZ_ON390809
Plasmid name   pJZ30-tet(X4) Incompatibility group   IncA/C2
Plasmid size   172554 bp Coordinate of oriT [Strand]   58654..58804 [+]
Host baterium   Proteus vulgaris strain JZ30

Cargo genes

Drug resistance gene   tet(X4), floR, erm(42), blaCMY-2, ant(3'')-Ia, aac(3)-VIa, qacE, sul1
Virulence gene   htpB
Metal resistance gene   merE, merD, merB, merA, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -