Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   106859
Name   oriT_p8538-NDM-1 in_silico
Organism   Providencia vermicola strain P8538
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_CP048797 (47529..47679 [+], 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_p8538-NDM-1
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   4527 GenBank   WP_001326173
Name   mobH_G3341_RS19870_p8538-NDM-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   4594 GenBank   WP_000178857
Name   traD_G3341_RS19875_p8538-NDM-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.



ID   4595 GenBank   WP_000637384
Name   traC_G3341_RS19975_p8538-NDM-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.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 45613..54703

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
G3341_RS19860 (G3341_19860) 41644..41877 - 234 WP_001191890 hypothetical protein -
G3341_RS19865 (G3341_19865) 41859..42476 - 618 WP_001249395 hypothetical protein -
G3341_RS19870 (G3341_19870) 42644..45616 + 2973 WP_001326173 MobH family relaxase -
G3341_RS19875 (G3341_19875) 45613..47478 + 1866 WP_000178857 conjugative transfer system coupling protein TraD virb4
G3341_RS19880 (G3341_19880) 47528..48073 + 546 WP_000228720 hypothetical protein -
G3341_RS19885 (G3341_19885) 48030..48659 + 630 WP_000743449 DUF4400 domain-containing protein tfc7
G3341_RS20595 48707..48883 + 177 WP_169342285 hypothetical protein -
G3341_RS19895 (G3341_19895) 49125..49502 + 378 WP_000869297 hypothetical protein -
G3341_RS19900 (G3341_19900) 49733..50164 + 432 WP_001694500 hypothetical protein -
G3341_RS20505 50345..50488 + 144 WP_001275801 hypothetical protein -
G3341_RS19905 (G3341_19905) 50500..50865 + 366 WP_001052530 hypothetical protein -
G3341_RS19910 (G3341_19910) 51010..51291 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
G3341_RS19915 (G3341_19915) 51288..51914 + 627 WP_001049717 TraE/TraK family type IV conjugative transfer system protein traE
G3341_RS19920 (G3341_19920) 51898..52815 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
G3341_RS19925 (G3341_19925) 52815..54128 + 1314 WP_024131605 TraB/VirB10 family protein traB
G3341_RS19930 (G3341_19930) 54125..54703 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
G3341_RS19935 (G3341_19935) 54707..55099 + 393 WP_000479535 TraA family conjugative transfer protein -
G3341_RS19940 (G3341_19940) 55384..56646 + 1263 WP_000608644 IS1380-like element ISEcp1 family transposase -
G3341_RS19945 (G3341_19945) 56970..58115 + 1146 WP_015058212 class C beta-lactamase CMY-6 -
G3341_RS19950 (G3341_19950) 58209..58742 + 534 WP_001221666 lipocalin family protein -
G3341_RS19955 (G3341_19955) 58739..59056 - 318 WP_000118520 quaternary ammonium compound efflux SMR transporter SugE -
G3341_RS20925 (G3341_19960) 59313..59678 + 366 Protein_88 LuxR family transcriptional regulator -

Host bacterium

ID   7296 GenBank   NZ_CP048797
Plasmid name   p8538-NDM-1 Incompatibility group   IncA/C2
Plasmid size   151684 bp Coordinate of oriT [Strand]   47529..47679 [+]
Host baterium   Providencia vermicola strain P8538

Cargo genes

Drug resistance gene   blaCMY-6, aac(6')-Ib, qacE, sul1, rmtC, blaNDM-1
Virulence gene   htpB
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -