Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100543
Name   oriT_pYT3 in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_022372 (40778..41328 [+], 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_pYT3
GAGCAGAGCTATGTGTGACAAGAAGTATAGAAATTACGAGGTAGCCATCATGGTCGATGTGAACCCTTTCGACAGGGTTATGAATGAATTGAAAAGTCGTGGCCGCAAGAACGCTCACATCCTGAGCATCCTCCAATTCGACTGGCCTGCATCGGAGGCCATCATCGAGAAGCTGAGCTGCTACATCACAGACGGGATTAAGGCTAATCAGGAGCCTGTGATTTACCCGATCATTGAAGAAGCTCTGCATCGCTACAGCCAGCTCGTGTTTCATGAGCAGAGAGAGAAATATGAAGACCCGGCCAGAATTGGGGCATTTCTGGAAACCCTGATCACCGAAACCTGCCGGGCGTTGGAAGTGCAAATTGTCGATAGTGGCGGTGATTCATGGTCTGTCGATTCAGGAGAGTCGTTCTCACTGTGGCTTTCTTCCCATCCAGGAGAACTATCCATTAACCCGCAGCCCCATGAGGATGAGACCTCTTTGCGTGGCTTGCTGTATGAGCTCATCACCTGTGAGAGCGTGAAAACTGTTTTAAGGAGAACCGACT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   614 GenBank   YP_008574717
Name   TraI_pYT3 insolico UniProt ID   F2Z7Z0
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_008574717.1 type IV conjugative transfer system protein TraI (plasmid) [Salmonella enterica subsp. enterica serovar Typhimurium]
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 F2Z7Z0


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 38912..48002

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HXC46_RS00275 (pYT3_0270) 34943..35176 - 234 WP_001191890 hypothetical protein -
HXC46_RS00280 (pYT3_0275) 35158..35775 - 618 WP_001249395 hypothetical protein -
HXC46_RS00285 (pYT3_0280) 35943..38915 + 2973 WP_001326173 MobH family relaxase -
HXC46_RS00290 (pYT3_0285) 38912..40777 + 1866 WP_000178857 conjugative transfer system coupling protein TraD virb4
HXC46_RS00295 (pYT3_0290) 40788..41372 + 585 WP_000332868 hypothetical protein -
HXC46_RS00300 (pYT3_0295) 41329..41958 + 630 WP_000743449 DUF4400 domain-containing protein tfc7
HXC46_RS00305 (pYT3_0300) 41968..42414 + 447 WP_000122507 hypothetical protein -
HXC46_RS00310 (pYT3_0305) 42424..42801 + 378 WP_000869297 hypothetical protein -
HXC46_RS00315 (pYT3_0310) 42801..43463 + 663 WP_001231464 hypothetical protein -
HXC46_RS00320 (pYT3_0320) 43787..44164 + 378 WP_001326174 hypothetical protein -
HXC46_RS00325 (pYT3_0325) 44309..44590 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
HXC46_RS00330 (pYT3_0330) 44587..45213 + 627 WP_001049717 TraE/TraK family type IV conjugative transfer system protein traE
HXC46_RS00335 (pYT3_0335) 45197..46114 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
HXC46_RS00340 (pYT3_0340) 46114..47427 + 1314 WP_024131605 TraB/VirB10 family protein traB
HXC46_RS00345 (pYT3_0345) 47424..48002 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
HXC46_RS00350 (pYT3_0350) 48006..48398 + 393 WP_000479535 TraA family conjugative transfer protein -
HXC46_RS00355 (pYT3_0355) 48683..49945 + 1263 WP_000608644 IS1380-like element ISEcp1 family transposase -
HXC46_RS00360 (pYT3_0360) 50269..51414 + 1146 WP_000976514 extended-spectrum class C beta-lactamase CMY-2 -
HXC46_RS00365 (pYT3_0365) 51508..52041 + 534 WP_001221666 lipocalin family protein -
HXC46_RS00370 (pYT3_0370) 52038..52355 - 318 WP_000118520 quaternary ammonium compound efflux SMR transporter SugE -
HXC46_RS00375 52612..52977 + 366 Protein_75 LuxR family transcriptional regulator -

Host bacterium

ID   1003 GenBank   NC_022372
Plasmid name   pYT3 Incompatibility group   IncFIB
Plasmid size   121723 bp Coordinate of oriT [Strand]   40778..41328 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium

Cargo genes

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