Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100789
Name   oriT_pSTY1-1808 in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium str. USDA-ARS-USMARC-1808 isolate ST1126-1
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NZ_CP014970 (60730..60988 [-], 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_pSTY1-1808
GCAGCGCCCCCAGGGGTGTTACTTAAAAACAGGCACAGCGACGCTAGCAGCGCCCCTGATATAATGCAATGTTTTTTATAAAAATAGTCAGTACTACCCCTGTATAGCGTCGTCATAGCGGTGCCGGCGACGTGCCTGCACCGCTATTTAATACATTAAAATAAATTAAATTACATTATTATGAACATAACTCACTGTTACTAAAAACAAATCAGAAAAATTTTAATTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   861 GenBank   WP_022743192
Name   Relaxase_pSTY1-1808 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: 60186..86642

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AW93_RS24365 (AW93_00360) 55342..57339 + 1998 WP_000117513 ParB/RepB/Spo0J family partition protein -
AW93_RS24370 (AW93_00365) 57379..57813 + 435 WP_010999943 conjugation system SOS inhibitor PsiB -
AW93_RS24375 (AW93_00370) 57810..58547 + 738 WP_000581933 plasmid SOS inhibition protein A -
AW93_RS27640 58582..58710 + 129 WP_000372429 hypothetical protein -
AW93_RS27210 58796..58954 + 159 WP_001704449 hypothetical protein -
AW93_RS27300 59057..59875 + 819 Protein_80 DUF932 domain-containing protein -
AW93_RS24390 (AW93_00385) 60186..60656 - 471 WP_001526856 transglycosylase SLT domain-containing protein virB1
AW93_RS24395 (AW93_00390) 61071..61451 + 381 WP_001151546 conjugal transfer relaxosome DNA-binding protein TraM -
AW93_RS24400 (AW93_00395) 61644..62330 + 687 WP_000336297 PAS domain-containing protein -
AW93_RS26115 62425..62652 + 228 WP_001676655 conjugal transfer relaxosome protein TraY -
AW93_RS24405 (AW93_00400) 62694..63056 + 363 WP_001274201 type IV conjugative transfer system pilin TraA -
AW93_RS24410 (AW93_00405) 63071..63382 + 312 WP_000012129 type IV conjugative transfer system protein TraL traL
AW93_RS24415 (AW93_00410) 63404..63970 + 567 WP_000399768 type IV conjugative transfer system protein TraE traE
AW93_RS24420 (AW93_00415) 63957..64697 + 741 WP_001230719 type-F conjugative transfer system secretin TraK traK
AW93_RS24425 (AW93_00420) 64697..66118 + 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
AW93_RS24430 (AW93_00425) 66108..66704 + 597 WP_000527896 conjugal transfer pilus-stabilizing protein TraP -
AW93_RS24435 (AW93_00430) 66682..66927 + 246 WP_010999944 DUF2689 domain-containing protein virb4
AW93_RS24440 (AW93_00435) 66924..67439 + 516 WP_001079995 type IV conjugative transfer system lipoprotein TraV traV
AW93_RS24445 (AW93_00440) 67574..67795 + 222 WP_001278699 conjugal transfer protein TraR -
AW93_RS24450 (AW93_00445) 67788..68255 + 468 WP_000549562 hypothetical protein -
AW93_RS24455 (AW93_00450) 68372..68635 + 264 WP_001239256 hypothetical protein -
AW93_RS24460 (AW93_00455) 68651..71299 + 2649 WP_000793310 type IV secretion system protein TraC virb4
AW93_RS24465 (AW93_00460) 71274..71660 + 387 WP_000105164 type-F conjugative transfer system protein TrbI -
AW93_RS24470 (AW93_00465) 71657..72289 + 633 WP_000871995 type-F conjugative transfer system protein TraW traW
AW93_RS24475 (AW93_00470) 72286..73278 + 993 WP_000833320 conjugal transfer pilus assembly protein TraU traU
AW93_RS24480 (AW93_00475) 73297..73605 + 309 WP_010999945 hypothetical protein -
AW93_RS24485 (AW93_00480) 73590..74228 + 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
AW93_RS24490 (AW93_00485) 74265..74684 + 420 WP_001229397 HNH endonuclease signature motif containing protein -
AW93_RS24495 (AW93_00490) 74681..76507 + 1827 WP_000827528 type-F conjugative transfer system mating-pair stabilization protein TraN traN
AW93_RS24500 (AW93_00495) 76518..76733 + 216 WP_000700023 conjugal transfer protein TrbE -
AW93_RS24505 (AW93_00500) 76745..77494 + 750 WP_001226854 type-F conjugative transfer system pilin assembly protein TraF traF
AW93_RS24510 (AW93_00505) 77708..78001 + 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
AW93_RS24515 (AW93_00510) 77988..78536 + 549 WP_022743183 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
AW93_RS24520 (AW93_00515) 78526..79908 + 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
AW93_RS24525 (AW93_00520) 79905..82727 + 2823 WP_001007086 conjugal transfer mating-pair stabilization protein TraG traG
AW93_RS24530 (AW93_00525) 82743..83237 + 495 WP_010999946 entry exclusion protein -
AW93_RS24535 (AW93_00530) 83273..84004 + 732 WP_022743186 conjugal transfer complement resistance protein TraT -
AW93_RS24540 (AW93_00535) 84381..86642 + 2262 WP_022743189 type IV conjugative transfer system coupling protein TraD prgC
AW93_RS24545 (AW93_00540) 86651..87049 - 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
AW93_RS24550 (AW93_00545) 87049..87276 - 228 WP_000450265 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   1249 GenBank   NZ_CP014970
Plasmid name   pSTY1-1808 Incompatibility group   IncFII
Plasmid size   94014 bp Coordinate of oriT [Strand]   60730..60988 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium str. USDA-ARS-USMARC-1808 isolate ST1126-1

Cargo genes

Drug resistance gene   -
Virulence gene   rck, pefD, pefC, pefA, pefB, fdeC, spvC, spvB
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -