Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   113980
Name   oriT_pN13-01141 in_silico
Organism   Salmonella enterica subsp. enterica serovar Dublin strain N13-01141
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_MK205417 (50754..50904 [+], 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_pN13-01141
TGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   8978 GenBank   WP_001326173
Name   mobH_HTU96_RS00355_pN13-01141 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   10416 GenBank   WP_077779971
Name   traD_HTU96_RS00360_pN13-01141 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: 48838..57928

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTU96_RS00345 44869..45102 - 234 WP_001191890 hypothetical protein -
HTU96_RS00350 45084..45701 - 618 WP_001249395 hypothetical protein -
HTU96_RS00355 45869..48841 + 2973 WP_001326173 MobH family relaxase -
HTU96_RS00360 48838..50703 + 1866 WP_077779971 conjugative transfer system coupling protein TraD virb4
HTU96_RS00365 50714..51298 + 585 WP_000332868 hypothetical protein -
HTU96_RS00370 51255..51884 + 630 WP_000743449 DUF4400 domain-containing protein tfc7
HTU96_RS00375 51894..52340 + 447 WP_000122507 hypothetical protein -
HTU96_RS00380 52350..52727 + 378 WP_000869297 hypothetical protein -
HTU96_RS00385 52727..53389 + 663 WP_001231464 hypothetical protein -
HTU96_RS00390 53570..53713 + 144 WP_001275801 hypothetical protein -
HTU96_RS00395 53713..54090 + 378 WP_001326174 hypothetical protein -
HTU96_RS00400 54235..54516 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
HTU96_RS00405 54513..55139 + 627 WP_001049717 TraE/TraK family type IV conjugative transfer system protein traE
HTU96_RS00410 55123..56040 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
HTU96_RS00415 56040..57353 + 1314 WP_024131605 TraB/VirB10 family protein traB
HTU96_RS00420 57350..57928 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
HTU96_RS00425 57932..58324 + 393 WP_000479535 TraA family conjugative transfer protein -
HTU96_RS00430 58609..59871 + 1263 WP_000608644 IS1380-like element ISEcp1 family transposase -
HTU96_RS00435 60195..61340 + 1146 WP_000976514 extended-spectrum class C beta-lactamase CMY-2 -
HTU96_RS00440 61434..61907 + 474 Protein_88 lipocalin family protein -

Host bacterium

ID   14415 GenBank   NZ_MK205417
Plasmid name   pN13-01141 Incompatibility group   IncA/C2
Plasmid size   83375 bp Coordinate of oriT [Strand]   50754..50904 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Dublin strain N13-01141

Cargo genes

Drug resistance gene   floR, tet(A), aph(6)-Id, aph(3'')-Ib, sul2, blaCMY-2
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -