Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100462
Name   oriT_pSD_174 in_silico
Organism   Salmonella enterica subsp. enterica serovar Dublin
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_019107 (56886..57436 [+], 551 nt)
oriT length   551 nt
IRs (inverted repeats)      IR1: 62..70, 71..79  (AACCCTTTC..GACAGGGTT)
  IR2: 143..150, 154..161  (TGGCCTGC..GGAGGCCA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 551 nt

>oriT_pSD_174
TGTAAAGAGGCTGTGAAAGAATAAGAGCATCAAGATTCCAGATAGATAGAGGGAAATTTGACAAATTCCAAAGATGGGTTAGCCTAGTGACAGAACTAGATTCCAGTATTGGAATAATCAGCTTTAAATTCCAGATAGATAGTTATGTGGATAGGAATTGGATAGGAATTGGGAGGGTATTGAGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   533 GenBank   YP_006955064
Name   TraI_pSD_174 insolico UniProt ID   F5BPR1
Length   990 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 990 a.a.        Molecular weight: 109356.90 Da        Isoelectric Point: 4.9395

>YP_006955064.1 conjugative transfer protein TraI (plasmid) [Salmonella enterica subsp. enterica serovar Dublin]
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


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 55020..66451

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HS771_RS00390 (pSD853_174_73) 51051..51284 - 234 WP_001191890 hypothetical protein -
HS771_RS00395 (pSD853_174_74) 51266..51883 - 618 WP_001249395 hypothetical protein -
HS771_RS00400 (pSD853_174_75) 52051..55023 + 2973 WP_001326173 MobH family relaxase -
HS771_RS00405 (pSD853_174_76) 55020..56885 + 1866 WP_000178857 conjugative transfer system coupling protein TraD virb4
HS771_RS00410 (pSD853_174_77) 56896..57480 + 585 WP_000332868 hypothetical protein -
HS771_RS00415 (pSD853_174_78) 57437..58066 + 630 WP_000743449 DUF4400 domain-containing protein tfc7
HS771_RS00420 (pSD853_174_79) 58076..58522 + 447 WP_000122507 hypothetical protein -
HS771_RS00425 (pSD853_174_80) 58532..58909 + 378 WP_000869297 hypothetical protein -
HS771_RS00430 (pSD853_174_81) 58909..59571 + 663 WP_001231464 hypothetical protein -
HS771_RS00435 (pSD853_174_82) 59752..59895 + 144 WP_001275801 hypothetical protein -
HS771_RS00440 (pSD853_174_83) 59907..60272 + 366 WP_001052530 hypothetical protein -
HS771_RS00445 (pSD853_174_84) 60417..60698 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
HS771_RS00450 (pSD853_174_85) 60695..61321 + 627 WP_001049717 TraE/TraK family type IV conjugative transfer system protein traE
HS771_RS00455 (pSD853_174_86) 61305..62222 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
HS771_RS00460 (pSD853_174_87) 62222..63535 + 1314 WP_024131605 TraB/VirB10 family protein traB
HS771_RS00465 (pSD853_174_88) 63532..64110 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
HS771_RS00470 (pSD853_174_89) 64114..64507 + 394 Protein_95 TraA family conjugative transfer protein -
HS771_RS00475 (pSD853_174_90) 64791..65750 + 960 Protein_96 IS1380-like element ISEcp1 family transposase -
HS771_RS00480 (pSD853_174_91) 65744..66451 - 708 WP_000637385 conjugal transfer protein TraC virb4
HS771_RS00485 (pSD853_174_92) 66448..67155 - 708 WP_001259346 DsbC family protein -

Host bacterium

ID   923 GenBank   NC_019107
Plasmid name   pSD_174 Incompatibility group   IncA/C2
Plasmid size   173673 bp Coordinate of oriT [Strand]   56886..57436 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Dublin

Cargo genes

Drug resistance gene   floR, tet(A), aph(6)-Id, aph(3'')-Ib, sul2, blaCMY-2, ant(3'')-Ia, qacE, sul1
Virulence gene   -
Metal resistance gene   merE, merD, merA, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -