Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100548
Name   oriT_pDT104 in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium str. DT104 unnamed
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_022570 (60749..61007 [-], 259 nt)
oriT length   259 nt
IRs (inverted repeats)      115..128, 134..147  (ATAGCGGTGCCGGC..GCCTGCACCGCTAT)
Location of nic site      241..242
Conserved sequence flanking the
  nic site    		  GTGGGGTGT|GG
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 259 nt

>oriT_pDT104
GCAGCGCCCCCAGGGGTGTTACTTAAAAACAGGCACAGCGACGCTAGCAGCGCCCCTGATATAATGCAATGTTTTTTATAAAAATAGTCAGTACTACCCCTGTATAGCGTCGTCATAGCGGTGCCGGCGACGTGCCTGCACCGCTATTTAATACATTAAAATAAATTAAATTACATTATTATGAACATAACTCACTGTTACTAAAAACAAATCAGAAAAATTTTAATTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   620 GenBank   WP_022743192
Name   Relaxase_pDT104 insolico UniProt ID   _
Length   1752 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 191680.70 Da        Isoelectric Point: 5.9879

>WP_022743192.1 conjugative transfer relaxase/helicase TraI [Salmonella enterica]
MMSIAQVRSAGSAAGYYSDRDNYYVLGSMEERWAGKGAEQLGLQGTVDKEVFTRVLEGRLPDGADLSRQQ
DGGNKHRPGYDLTFSAPKSVSLMAMLAGDKRLTEAHNQAVDIAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVVNVTQHDGEWKTLSSDKVGKTGFIENVYANQIAFGKIYRAVLKEKVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVKMAEWMQT
LKDTGFDISAYRESADRRAEIQAAQPVPSQEQPDIQQAVTQAIAGLSDRKVQFTYTDVLARTVGMLPPEA
GVIEKARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSSDIMKQNRVTVHPEKSVPRTGSYSD
AVSVLAQDRPSLAIISGQGGAAGQRERVAELTMMAREQGREVQIIVADRRSQTNLKQDERLSGELITGRR
QLQEGMLFSPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKEAGVNSYRWQ
GRQQTPATVISEPDRNVRYARLAGDFVAAVKAGEESVAQVSGMREQAILAGMIRSELKTQGILGQQDTMM
TALSPVWLDSRNRYLRDMYREGMVMEQWNPEKRSHDRYVIDRVTAQSHSLTLRDAQGETQMVRISALDSS
WSLFRPEKMPVADGERLMVTGKIPGLRVSVGDRLQVSAVNDGVMTVTVPGRAEPASLPVGDSPFTALKLE
NGWVETPGHSVSDSAKVFASVTQMAMDNATLNSLARSGRDVRLYSSLDETRTAEKLSRHPSFTVVSEQIK
ARAGEVSLETAISRQKAGLHTPAQQAIHLALPVVESKNLAFSQVDLLTEAKSFAAEGTGFADLGREIDAQ
IKRGDLLYVDVAKGYGTDLLISRASYDAEKSILHHILEGKEAVTPLMERVPGELMETLTSGQRAATRMIL
ETKDRFTVVQGYAGVGKTTQFRAVMSAVNLLPESERPRVVGLGPTHRAVGEMRSAGVEAQTLASFLHDTQ
LQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSAA
DVAIMKEIVRQTPELRDAVYSLINRDVNKALSGLENVKPVQVPRLKGAWAPENSVTEFSRLQERELAKAA
QEAEKKGEAFPDVPVTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIQDALAKPGEQQVTVPVL
TTANIRDGELRRLSTWEAHPGALALVDNVYHRIAGISKEDGLITLEDKAGNTRLISPREAAAEGVTLYNP
ETIRVGAGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGKQTRVVRPGQDRAEQHIDLAYAITAHS
AQGASETFAIALEGTEGGRKQMAGFESAYVALSRMKQHVQVYTDDRQGWVKAINSAEQKGTAHDVLEPKS
EREMKNAERLFSTARELRDVAAGRAVLRNAGLAQGDSRARFIAPGRKYPQPYVALPAFDRNGKSAGIWLN
PLTTDDGAGLRGFTGEGRVKGSEEAQFVALQGSRNGESLLAGSMQDGVRIARENPDSGVVVRIVGDGRPW
NPVAITGGRVWGDIPDSNVQPGAGNGEPVTAEILAQRQAEEAVRRETERRADEIVRKMAEDKSDLPEEKT
AQAVREIAGQEQDRMTPPEREPPLPESVLREPQRERETIREVARENRGRERLQQMEQEMVRDLQKEKTPG
GD

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(967-1158)

DNA relaxase TraI 2B/2B-like domain (TraI_2B)

(632-711)

single-stranded DNA binding TraI N-terminal subdomain (ssDNA_TraI_N)

(574-626)

TrwC relaxase (TrwC)

(11-282)

DNA helicase TraI (TraI_C)

(1430-1553)


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 60205..86661

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
DT104_RS24375 (DT104_p0681) 55361..57358 + 1998 WP_000117513 ParB/RepB/Spo0J family partition protein -
DT104_RS24380 (DT104_p0691) 57398..57832 + 435 WP_010999943 conjugation system SOS inhibitor PsiB -
DT104_RS24385 (DT104_p0701) 57829..58566 + 738 WP_000581933 plasmid SOS inhibition protein A -
DT104_RS27065 58815..58973 + 159 WP_001704449 hypothetical protein -
DT104_RS24390 59076..59477 + 402 Protein_74 DUF945 domain-containing protein -
DT104_RS27035 59539..59894 + 356 Protein_75 DUF945 domain-containing protein -
DT104_RS24400 (DT104_p0721) 60205..60675 - 471 WP_001526856 transglycosylase SLT domain-containing protein virB1
DT104_RS24405 (DT104_p0731) 61090..61470 + 381 WP_001151546 conjugal transfer relaxosome DNA-binding protein TraM -
DT104_RS24410 (DT104_p0741) 61663..62349 + 687 WP_000336297 PAS domain-containing protein -
DT104_RS26300 (DT104_p0751) 62444..62671 + 228 WP_001676655 conjugal transfer relaxosome protein TraY -
DT104_RS24415 (DT104_p0761) 62713..63075 + 363 WP_001274201 type IV conjugative transfer system pilin TraA -
DT104_RS24420 (DT104_p0771) 63090..63401 + 312 WP_000012129 type IV conjugative transfer system protein TraL traL
DT104_RS24425 (DT104_p0781) 63423..63989 + 567 WP_000399768 type IV conjugative transfer system protein TraE traE
DT104_RS24430 (DT104_p0791) 63976..64716 + 741 WP_001230719 type-F conjugative transfer system secretin TraK traK
DT104_RS24435 (DT104_p0801) 64716..66137 + 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
DT104_RS24440 (DT104_p0811) 66127..66723 + 597 WP_000527896 conjugal transfer pilus-stabilizing protein TraP -
DT104_RS24445 (DT104_p0821) 66701..66946 + 246 WP_010999944 DUF2689 domain-containing protein virb4
DT104_RS24450 (DT104_p0831) 66943..67458 + 516 WP_001079995 type IV conjugative transfer system lipoprotein TraV traV
DT104_RS24455 (DT104_p0841) 67593..67814 + 222 WP_001278699 conjugal transfer protein TraR -
DT104_RS24460 (DT104_p0851) 67807..68274 + 468 WP_000549562 hypothetical protein -
DT104_RS24465 68391..68654 + 264 WP_001239256 hypothetical protein -
DT104_RS24470 (DT104_p0861) 68670..71318 + 2649 WP_000793310 type IV secretion system protein TraC virb4
DT104_RS24475 (DT104_p0871) 71293..71679 + 387 WP_000105164 type-F conjugative transfer system protein TrbI -
DT104_RS24480 (DT104_p0881) 71676..72308 + 633 WP_000871995 type-F conjugative transfer system protein TraW traW
DT104_RS24485 (DT104_p0891) 72305..73297 + 993 WP_000833320 conjugal transfer pilus assembly protein TraU traU
DT104_RS24490 (DT104_p0901) 73316..73624 + 309 WP_010999945 hypothetical protein -
DT104_RS24495 (DT104_p0911) 73609..74247 + 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
DT104_RS24500 74284..74703 + 420 WP_001229397 HNH endonuclease signature motif containing protein -
DT104_RS24505 (DT104_p0921) 74700..76526 + 1827 WP_000827528 type-F conjugative transfer system mating-pair stabilization protein TraN traN
DT104_RS24510 (DT104_p0931) 76537..76752 + 216 WP_000700023 conjugal transfer protein TrbE -
DT104_RS24515 (DT104_p0941) 76764..77513 + 750 WP_001226854 type-F conjugative transfer system pilin assembly protein TraF traF
DT104_RS24520 (DT104_p0951) 77727..78020 + 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
DT104_RS24525 (DT104_p0961) 78007..78555 + 549 WP_022743183 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
DT104_RS24530 (DT104_p0971) 78545..79927 + 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
DT104_RS24535 (DT104_p0981) 79924..82746 + 2823 WP_001007086 conjugal transfer mating-pair stabilization protein TraG traG
DT104_RS24540 (DT104_p0991) 82762..83256 + 495 WP_010999946 entry exclusion protein -
DT104_RS24545 (DT104_p1001) 83292..84023 + 732 WP_022743186 conjugal transfer complement resistance protein TraT -
DT104_RS24550 (DT104_p1011) 84400..86661 + 2262 WP_022743189 type IV conjugative transfer system coupling protein TraD prgC
DT104_RS24555 86670..87068 - 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
DT104_RS24560 87068..87298 - 231 WP_001526804 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   1008 GenBank   NC_022570
Plasmid name   pDT104 Incompatibility group   IncFII
Plasmid size   94034 bp Coordinate of oriT [Strand]   60749..61007 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium str. DT104 unnamed

Cargo genes

Drug resistance gene   -
Virulence gene   Salmonella plasmid virulence
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -