Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103114
Name   oriT_pHS36-NDM in_silico
Organism   Salmonella enterica subsp. enterica serovar Stanley strain LS001
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KU726616 (89140..89290 [-], 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_pHS36-NDM
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2335 GenBank   WP_001326173
Name   TraI_2_HTH28_RS00485_pHS36-NDM 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   2061 GenBank   WP_000637384
Name   traC_HTH28_RS00380_pHS36-NDM 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   2062 GenBank   WP_000178857
Name   traD_HTH28_RS00480_pHS36-NDM 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: 82116..91206

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTH28_RS00850 77142..77506 - 365 Protein_80 LuxR family transcriptional regulator -
HTH28_RS00395 (pHS36-NDM_00082) 77763..78080 + 318 WP_000118520 quaternary ammonium compound efflux SMR transporter SugE -
HTH28_RS00400 (pHS36-NDM_00083) 78077..78610 - 534 WP_001221666 lipocalin family protein -
HTH28_RS00405 (pHS36-NDM_00084) 78704..79849 - 1146 WP_015058212 class C beta-lactamase CMY-6 -
HTH28_RS00410 (pHS36-NDM_00086) 80173..81435 - 1263 WP_000608644 IS1380-like element ISEcp1 family transposase -
HTH28_RS00415 (pHS36-NDM_00087) 81720..82112 - 393 WP_000479535 TraA family conjugative transfer protein -
HTH28_RS00420 (pHS36-NDM_00088) 82116..82694 - 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
HTH28_RS00425 (pHS36-NDM_00089) 82691..84004 - 1314 WP_024131605 TraB/VirB10 family protein traB
HTH28_RS00430 (pHS36-NDM_00090) 84004..84921 - 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
HTH28_RS00435 (pHS36-NDM_00091) 84905..85531 - 627 WP_001049717 TraE/TraK family type IV conjugative transfer system protein traE
HTH28_RS00440 (pHS36-NDM_00092) 85528..85809 - 282 WP_000805625 type IV conjugative transfer system protein TraL traL
HTH28_RS00445 (pHS36-NDM_00094) 85954..86319 - 366 WP_001052530 hypothetical protein -
HTH28_RS00450 (pHS36-NDM_00095) 86331..86474 - 144 WP_001275801 hypothetical protein -
HTH28_RS00455 (pHS36-NDM_00096) 86655..87317 - 663 WP_001231464 hypothetical protein -
HTH28_RS00460 (pHS36-NDM_00097) 87317..87694 - 378 WP_000869297 hypothetical protein -
HTH28_RS00465 (pHS36-NDM_00098) 87704..88150 - 447 WP_000122507 hypothetical protein -
HTH28_RS00470 (pHS36-NDM_00099) 88160..88789 - 630 WP_000743449 DUF4400 domain-containing protein tfc7
HTH28_RS00475 (pHS36-NDM_00100) 88746..89330 - 585 WP_000332868 hypothetical protein -
HTH28_RS00480 (pHS36-NDM_00101) 89341..91206 - 1866 WP_000178857 conjugative transfer system coupling protein TraD virb4
HTH28_RS00485 (pHS36-NDM_00102) 91203..94175 - 2973 WP_001326173 MobH family relaxase -
HTH28_RS00490 (pHS36-NDM_00103) 94343..94960 + 618 WP_001249395 hypothetical protein -
HTH28_RS00495 (pHS36-NDM_00104) 94942..95175 + 234 WP_001191890 hypothetical protein -

Host bacterium

ID   3557 GenBank   NZ_KU726616
Plasmid name   pHS36-NDM Incompatibility group   IncA/C2
Plasmid size   137952 bp Coordinate of oriT [Strand]   89140..89290 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Stanley strain LS001

Cargo genes

Drug resistance gene   blaNDM-1, sul1, qacE, aadA2, dfrA12, blaCMY-6
Virulence gene   htpB
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -