Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113978
Name   oriT_pN13-01070-1 in_silico
Organism   Salmonella enterica subsp. enterica serovar Dublin strain N13-01070
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MK205416 (44261..44411 [-], 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_pN13-01070-1
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8976 GenBank   WP_001326173
Name   mobH_HTU78_RS00350_pN13-01070-1 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   10414 GenBank   WP_077779971
Name   traD_HTU78_RS00345_pN13-01070-1 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: 69253.76 Da        Isoelectric Point: 6.9403

>WP_077779971.1 MULTISPECIES: conjugative transfer system coupling protein TraD [Enterobacteriaceae]
MTMSYDPLAYEMPWRPNYEKNAVAGWLAASGAALAVEQVSTMPPEPFYWMTGICGVMAMARLPKAIKLHL
LQKHLKGRDLEFISIAELQKYIKDTPDDMWLGSGFLWENRHAQRVFEILKRDWTSIVGRESTVKKVVRKI
QGKKKELPIGQPWIHGVEPKEEKLMQPLKHTEGHSLIVGTTGSGKTRMFDILISQAILRGEAVIIIDPKG
DKEMRDNARRACEAMGQPERFVSFHPVFPEESVRIDPLRNFTRVTEIASRLAALIPSEAGADPFKSFGWQ
ALNNIAQGLVITHDRPNLTKLRRFLEGGAAGLVIKAVQAYSERVMPDWEAEAAAYLEKVKNGSREKIAFA
LMKFYYDIIQPEHPNSDLEGLLSMFQHDQTHFSKMVANLLPIMNMLTSGELGPLLSPDSSDLSDERQITD
SAKIINNAQVAYLGLDSLTDNMVGSAMGSIFLSDLTAVAGDRYNYGVNNRPVNIFVDEAAEVINDPFIQL
LNKGRGAKLRLFVATQTFADFAARLGSKDKALQVLGNINNTFALRIVDGETQEYIADNLPKTRLKYVMRT
QGQNSDGKEPIMHGGNQGERLMEEEADLFPAQLLGMLPNLEYIAKISGGTIVKGRLPILTQ

  Protein domains


Predicted by InterproScan.

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(170-302)

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: 37237..46327

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTU78_RS00265 32500..33204 + 705 WP_001067855 IS6-like element IS26 family transposase -
HTU78_RS00270 33150..33731 - 582 WP_058663077 lipocalin family protein -
HTU78_RS00275 33825..34970 - 1146 WP_000976514 extended-spectrum class C beta-lactamase CMY-2 -
HTU78_RS00280 35294..36556 - 1263 WP_000608644 IS1380-like element ISEcp1 family transposase -
HTU78_RS00285 36841..37233 - 393 WP_000479535 TraA family conjugative transfer protein -
HTU78_RS00290 37237..37815 - 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
HTU78_RS00295 37812..39125 - 1314 WP_024131605 TraB/VirB10 family protein traB
HTU78_RS00300 39125..40042 - 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
HTU78_RS00305 40026..40652 - 627 WP_001049717 TraE/TraK family type IV conjugative transfer system protein traE
HTU78_RS00310 40649..40930 - 282 WP_000805625 type IV conjugative transfer system protein TraL traL
HTU78_RS00315 41075..41452 - 378 WP_001326174 hypothetical protein -
HTU78_RS00320 41776..42438 - 663 WP_001231464 hypothetical protein -
HTU78_RS00325 42438..42815 - 378 WP_000869297 hypothetical protein -
HTU78_RS00330 42825..43271 - 447 WP_000122507 hypothetical protein -
HTU78_RS00335 43281..43910 - 630 WP_000743449 DUF4400 domain-containing protein tfc7
HTU78_RS00340 43867..44451 - 585 WP_000332868 hypothetical protein -
HTU78_RS00345 44462..46327 - 1866 WP_077779971 conjugative transfer system coupling protein TraD virb4
HTU78_RS00350 46324..49296 - 2973 WP_001326173 MobH family relaxase -
HTU78_RS00355 49464..50081 + 618 WP_001249395 hypothetical protein -
HTU78_RS00360 50063..50296 + 234 WP_001191890 hypothetical protein -

Host bacterium

ID   14413 GenBank   NZ_MK205416
Plasmid name   pN13-01070-1 Incompatibility group   IncA/C2
Plasmid size   107296 bp Coordinate of oriT [Strand]   44261..44411 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Dublin strain N13-01070

Cargo genes

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