Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100466
Name   oriT_pSH163_135 in_silico
Organism   Salmonella enterica subsp. enterica serovar Heidelberg
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_019116 (52964..53514 [+], 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_pSH163_135
TGTAAAGAGGCTGTGAAAGAATAAGAGCATCAAGATTCCAGATAGATAGAGGGAAATTTGACAAATTCCAAAGATGGGTTAGCCTAGTGACAGAACTAGATTCCAGTATTGGAATAATCAGCTTTAAATTCCAGATAGATAGTTATGTGGATAGGAATTGGATAGGAATTGGGAGGGTATTGAGG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   537 GenBank   YP_006956335
Name   TraI_pSH163_135 insolico UniProt ID   H9TK29
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_006956335.1 Conjugative transfer protein TraI, relaxase (plasmid) [Salmonella enterica subsp. enterica serovar Heidelberg]
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 H9TK29


T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 51098..62529

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HS880_RS00365 (pSH163_135_73) 47129..47362 - 234 WP_001191890 hypothetical protein -
HS880_RS00370 (pSH163_135_74) 47344..47961 - 618 WP_001249395 hypothetical protein -
HS880_RS00375 (pSH163_135_75) 48129..51101 + 2973 WP_001326173 MobH family relaxase -
HS880_RS00380 (pSH163_135_76) 51098..52963 + 1866 WP_000178857 conjugative transfer system coupling protein TraD virb4
HS880_RS00385 (pSH163_135_77) 52974..53558 + 585 WP_000332868 hypothetical protein -
HS880_RS00390 (pSH163_135_78) 53515..54144 + 630 WP_000743449 DUF4400 domain-containing protein tfc7
HS880_RS00395 (pSH163_135_79) 54154..54600 + 447 WP_000122507 hypothetical protein -
HS880_RS00400 (pSH163_135_80) 54610..54987 + 378 WP_000869297 hypothetical protein -
HS880_RS00405 (pSH163_135_81) 54987..55649 + 663 WP_001231464 hypothetical protein -
HS880_RS00410 (pSH163_135_82) 55830..55973 + 144 WP_001275801 hypothetical protein -
HS880_RS00415 (pSH163_135_83) 55973..56350 + 378 WP_001326174 hypothetical protein -
HS880_RS00420 (pSH163_135_84) 56495..56776 + 282 WP_000805625 type IV conjugative transfer system protein TraL traL
HS880_RS00425 (pSH163_135_85) 56773..57399 + 627 WP_001049717 TraE/TraK family type IV conjugative transfer system protein traE
HS880_RS00430 (pSH163_135_86) 57383..58300 + 918 WP_000794249 type-F conjugative transfer system secretin TraK traK
HS880_RS00435 (pSH163_135_87) 58300..59613 + 1314 WP_024131605 TraB/VirB10 family protein traB
HS880_RS00440 (pSH163_135_88) 59610..60188 + 579 WP_000793435 type IV conjugative transfer system lipoprotein TraV traV
HS880_RS00445 (pSH163_135_89) 60192..60584 + 393 WP_000479535 TraA family conjugative transfer protein -
HS880_RS00450 (pSH163_135_90) 60869..61828 + 960 Protein_90 IS1380-like element ISEcp1 family transposase -
HS880_RS00455 (pSH163_135_91) 61822..62529 - 708 WP_000637385 conjugal transfer protein TraC virb4
HS880_RS00460 (pSH163_135_92) 62526..63233 - 708 WP_001259346 DsbC family protein -

Host bacterium

ID   927 GenBank   NC_019116
Plasmid name   pSH163_135 Incompatibility group   IncA/C2
Plasmid size   135168 bp Coordinate of oriT [Strand]   52964..53514 [+]
Host baterium   Salmonella enterica subsp. enterica serovar Heidelberg

Cargo genes

Drug resistance gene   floR, tet(A), aph(6)-Id, aph(3'')-Ib, sul2, blaCMY-2, blaTEM-1B, cmlA1, ant(2'')-Ia
Virulence gene   -
Metal resistance gene   merE, merD, merB, merA, merP, merT, merR
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -