Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100792
Name   oriT_pSTY1-2009K-1640 in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium str. CDC 2009K-1640 isolate USDA-ARS-USMARC-1906
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NZ_CP014976 (60744..61002 [-], 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_pSTY1-2009K-1640
GCAGCGCCCCCAGGGGTGTTACTTAAAAACAGGCACAGCGACGCTAGCAGCGCCCCTGATATAATGCAATGTTTTTTATAAAAATAGTCAGTACTACCCCTGTATAGCGTCGTCATAGCGGTGCCGGCGACGTGCCTGCACCGCTATTTAATACATTAAAATAAATTAAATTACATTATTATGAACATAACTCACTGTTACTAAAAACAAATCAGAAAAATTTTAATTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   864 GenBank   WP_022743192
Name   Relaxase_pSTY1-2009K-1640 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: 60200..86647

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
AX07_RS24345 (AX07_24340) 55356..57353 + 1998 WP_000117513 ParB/RepB/Spo0J family partition protein -
AX07_RS24350 (AX07_24345) 57393..57827 + 435 WP_010999943 conjugation system SOS inhibitor PsiB -
AX07_RS24355 (AX07_24350) 57824..58561 + 738 WP_000581933 plasmid SOS inhibition protein A -
AX07_RS27365 58596..58724 + 129 WP_000372429 hypothetical protein -
AX07_RS27045 58810..58968 + 159 WP_001704449 hypothetical protein -
AX07_RS27050 59071..59889 + 819 Protein_80 DUF932 domain-containing protein -
AX07_RS24370 (AX07_24365) 60200..60670 - 471 WP_001526856 transglycosylase SLT domain-containing protein virB1
AX07_RS24375 (AX07_24370) 61085..61465 + 381 WP_001151546 conjugal transfer relaxosome DNA-binding protein TraM -
AX07_RS24380 (AX07_24375) 61658..62344 + 687 WP_000336297 PAS domain-containing protein -
AX07_RS26115 62439..62666 + 228 WP_001676655 conjugal transfer relaxosome protein TraY -
AX07_RS24385 (AX07_24380) 62708..63070 + 363 WP_001274201 type IV conjugative transfer system pilin TraA -
AX07_RS24390 (AX07_24385) 63085..63396 + 312 WP_000012129 type IV conjugative transfer system protein TraL traL
AX07_RS24395 (AX07_24390) 63418..63984 + 567 WP_000399768 type IV conjugative transfer system protein TraE traE
AX07_RS24400 (AX07_24395) 63971..64711 + 741 WP_001230719 type-F conjugative transfer system secretin TraK traK
AX07_RS24405 (AX07_24400) 64711..66132 + 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
AX07_RS24410 (AX07_24405) 66122..66718 + 597 WP_000527896 conjugal transfer pilus-stabilizing protein TraP -
AX07_RS24415 (AX07_24410) 66696..66941 + 246 WP_010999944 DUF2689 domain-containing protein virb4
AX07_RS24420 (AX07_24415) 66938..67453 + 516 WP_001079995 type IV conjugative transfer system lipoprotein TraV traV
AX07_RS24425 (AX07_24420) 67588..67809 + 222 WP_001278699 conjugal transfer protein TraR -
AX07_RS24430 (AX07_24425) 67802..68269 + 468 WP_000549562 hypothetical protein -
AX07_RS24435 (AX07_24430) 68386..68649 + 264 WP_001239256 hypothetical protein -
AX07_RS24440 (AX07_24435) 68665..71313 + 2649 WP_000793310 type IV secretion system protein TraC virb4
AX07_RS24445 (AX07_24440) 71288..71674 + 387 WP_000105164 type-F conjugative transfer system protein TrbI -
AX07_RS24450 (AX07_24445) 71671..72303 + 633 WP_000871995 type-F conjugative transfer system protein TraW traW
AX07_RS24455 (AX07_24450) 72300..73292 + 993 WP_000833320 conjugal transfer pilus assembly protein TraU traU
AX07_RS24460 (AX07_24455) 73311..73619 + 309 WP_010999945 hypothetical protein -
AX07_RS24465 (AX07_24460) 73604..74242 + 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
AX07_RS24470 (AX07_24465) 74279..74698 + 420 WP_001229397 HNH endonuclease signature motif containing protein -
AX07_RS24475 (AX07_24470) 74695..76521 + 1827 WP_000827528 type-F conjugative transfer system mating-pair stabilization protein TraN traN
AX07_RS24480 (AX07_24475) 76532..76747 + 216 WP_000700023 conjugal transfer protein TrbE -
AX07_RS24485 (AX07_24480) 76759..77508 + 750 WP_001226854 type-F conjugative transfer system pilin assembly protein TraF traF
AX07_RS24490 (AX07_24485) 77722..78015 + 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
AX07_RS24495 (AX07_24490) 78002..78550 + 549 WP_022743183 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
AX07_RS24500 (AX07_24495) 78540..79922 + 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
AX07_RS24505 (AX07_24500) 79919..82741 + 2823 WP_001007086 conjugal transfer mating-pair stabilization protein TraG traG
AX07_RS24510 (AX07_24505) 82757..83251 + 495 WP_010999946 entry exclusion protein -
AX07_RS24515 (AX07_24510) 83287..84018 + 732 WP_022743186 conjugal transfer complement resistance protein TraT -
AX07_RS24520 (AX07_24515) 84395..86647 + 2253 WP_058657852 type IV conjugative transfer system coupling protein TraD prgC
AX07_RS24525 (AX07_24520) 86656..87054 - 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
AX07_RS24530 (AX07_24525) 87054..87281 - 228 WP_000450265 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   1252 GenBank   NZ_CP014976
Plasmid name   pSTY1-2009K-1640 Incompatibility group   IncFII
Plasmid size   94019 bp Coordinate of oriT [Strand]   60744..61002 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium str. CDC 2009K-1640 isolate USDA-ARS-USMARC-1906

Cargo genes

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