Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100639
Name   oriT_p138736 in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium strain 138736
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NZ_CP007582 (59283..59541 [-], 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_p138736
GCAGCGCCCCCAGGGGTGTTACTTAAAAACAGGCACAGCGACGCTAGCAGCGCCCCTGATATAATGCAATGTTTTTTATAAAAATAGTCAGTACTACCCCTGTATAGCGTCGTCATAGCGGTGCCGGCGACGTGCCTGCACCGCTATTTAATACATTAAAATAAATTAAATTACATTATTATGAACATAACTCACTGTTACTAAAAACAAATCAGAAAAATTTTAATTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   711 GenBank   WP_022743192
Name   Relaxase_p138736 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: 58739..84367

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
CY43_RS27615 54015..54157 - 143 Protein_72 hypothetical protein -
CY43_RS24345 54484..54807 + 324 Protein_73 single-stranded DNA-binding protein SSB2 -
CY43_RS24350 (CY43_24335) 54810..55892 + 1083 Protein_74 chromosome partitioning protein ParB -
CY43_RS24355 (CY43_24340) 55932..56366 + 435 WP_010999943 conjugation system SOS inhibitor PsiB -
CY43_RS24360 (CY43_24345) 56363..57100 + 738 WP_000581933 plasmid SOS inhibition protein A -
CY43_RS27525 57135..57263 + 129 WP_000372429 hypothetical protein -
CY43_RS27200 57349..57507 + 159 WP_001704449 hypothetical protein -
CY43_RS27205 57610..58428 + 819 Protein_79 DUF932 domain-containing protein -
CY43_RS24375 (CY43_24370) 58739..59209 - 471 WP_001526856 transglycosylase SLT domain-containing protein virB1
CY43_RS24380 (CY43_24375) 59624..60004 + 381 WP_001151546 conjugal transfer relaxosome DNA-binding protein TraM -
CY43_RS24385 (CY43_24380) 60197..60883 + 687 WP_000336297 PAS domain-containing protein -
CY43_RS26260 60978..61205 + 228 WP_001676655 conjugal transfer relaxosome protein TraY -
CY43_RS24390 (CY43_24385) 61247..61609 + 363 WP_001274201 type IV conjugative transfer system pilin TraA -
CY43_RS24395 (CY43_24390) 61624..61935 + 312 WP_000012129 type IV conjugative transfer system protein TraL traL
CY43_RS24400 (CY43_24395) 61957..62523 + 567 WP_000399768 type IV conjugative transfer system protein TraE traE
CY43_RS24405 (CY43_24400) 62510..63250 + 741 WP_001230719 type-F conjugative transfer system secretin TraK traK
CY43_RS24410 (CY43_24405) 63250..64671 + 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
CY43_RS24415 (CY43_24410) 64661..65257 + 597 WP_000527896 conjugal transfer pilus-stabilizing protein TraP -
CY43_RS24420 (CY43_24415) 65235..65480 + 246 WP_010999944 DUF2689 domain-containing protein virb4
CY43_RS24425 (CY43_24420) 65477..65992 + 516 WP_001079995 type IV conjugative transfer system lipoprotein TraV traV
CY43_RS24430 (CY43_24425) 66127..66348 + 222 WP_001278699 conjugal transfer protein TraR -
CY43_RS24435 (CY43_24430) 66341..66808 + 468 WP_000549562 hypothetical protein -
CY43_RS24440 (CY43_24440) 66925..67188 + 264 WP_001239256 hypothetical protein -
CY43_RS24445 (CY43_24445) 67204..69024 + 1821 WP_040122033 TraC family protein virb4
CY43_RS24450 (CY43_24450) 68999..69385 + 387 WP_000105164 type-F conjugative transfer system protein TrbI -
CY43_RS24455 (CY43_24455) 69382..70014 + 633 WP_000871995 type-F conjugative transfer system protein TraW traW
CY43_RS24460 (CY43_24460) 70011..71003 + 993 WP_000833320 conjugal transfer pilus assembly protein TraU traU
CY43_RS24465 (CY43_24465) 71022..71330 + 309 WP_010999945 hypothetical protein -
CY43_RS24470 (CY43_24470) 71315..71953 + 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
CY43_RS24475 (CY43_24475) 71990..72409 + 420 WP_001229397 HNH endonuclease signature motif containing protein -
CY43_RS24480 (CY43_24480) 72406..74232 + 1827 WP_000827528 type-F conjugative transfer system mating-pair stabilization protein TraN traN
CY43_RS24485 (CY43_24485) 74243..74458 + 216 WP_000700023 conjugal transfer protein TrbE -
CY43_RS24490 (CY43_24490) 74470..75219 + 750 WP_001226854 type-F conjugative transfer system pilin assembly protein TraF traF
CY43_RS24495 (CY43_24495) 75433..75726 + 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
CY43_RS24500 (CY43_24500) 75713..76261 + 549 WP_022743183 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
CY43_RS24505 (CY43_24505) 76251..77633 + 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
CY43_RS24510 (CY43_24510) 77630..80452 + 2823 WP_031603544 conjugal transfer mating-pair stabilization protein TraG traG
CY43_RS24515 (CY43_24515) 80468..80962 + 495 WP_010999946 entry exclusion protein -
CY43_RS24520 (CY43_24520) 80998..81729 + 732 WP_022743186 conjugal transfer complement resistance protein TraT -
CY43_RS24525 (CY43_24525) 82106..84367 + 2262 WP_022743189 type IV conjugative transfer system coupling protein TraD prgC
CY43_RS24530 (CY43_24530) 84376..84774 - 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
CY43_RS24535 (CY43_24535) 84774..85001 - 228 WP_000450265 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   1099 GenBank   NZ_CP007582
Plasmid name   p138736 Incompatibility group   IncFII
Plasmid size   91739 bp Coordinate of oriT [Strand]   59283..59541 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium strain 138736

Cargo genes

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