Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100775
Name   oriT_pSO2_STV in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium strain SO2 isolate SOHS 02-20
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NZ_CP014357 (60652..60910 [-], 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_pSO2_STV
GCAGCGCCCCCAGGGGTGTTACTTAAAAACAGGCACAGCGACGCTAGCAGCGCCCCTGATATAATGCAATGTTTTTTATAAAAATAGTCAGTACTACCCCTGTATAGCGTCGTCATAGCGGTGCCGGCGACGTGCCTGCACCGCTATTTAATACATTAAAATAAATTAAATTACATTATTATGAACATAACTCACTGTTACTAAAAACAAATCAGAAAAATTTTAATTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   847 GenBank   WP_000986921
Name   TraI_pSO2_STV insolico UniProt ID   _
Length   1752 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1752 a.a.        Molecular weight: 191683.72 Da        Isoelectric Point: 5.9311

>WP_000986921.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Salmonella]
MMSIAQVRSAGSAAGYYSDRDNYYVLGSMEERWAGKGAEQLGLQGTVDKEVFTRVLEGRLPDGADLSRQQ
DGGNKHRPGYDLTFSAPKSVSLMAMLAGDKRLTEAHNQAVDIAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVVNVTQHDGEWKTLSSDKVGKTGFIENVYANQIAFGKIYRAVLKEKVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVKMAEWMQT
LKDTGFDISAYRESADRRAEIQAAQPVPSQEQPDIQQAVTQAIAGLSDRKVQFTYTDVLARTVGMLPPEA
GVIEKARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSSDIMKQNRVTVHPEKSVPRTGSYSD
AVSVLAQDRPSLAIISGQGGAAGQRERVAELTMMAREQGREVQIIVADRRSQTNLKQDERLSGELITGRR
QLQEGMLFSPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKEAGVNSYRWQ
GRQQTPATVISEPDRNVRYARLAGDFVAAVKAGEESVAQVSGMREQAILAGMIRSELKTQGILGQQDTMM
TALSPVWLDSRNRYLRDMYREGMVMEQWNPEKRSHDRYVIDRVTAQSHSLTLRDAQGETQMVRISALDSS
WSLFRPEKMPVADGERLMVTGKIPGLRVSVGDRLQVSAVNDGVMTVTVPGRAEPASLPVGDSPFTALKLE
NGWVETPGHSVSDSAKVFASVTQMAMDNATLNSLARSGRDVRLYSSLDETRTAEKLSRHPSFTVVSEQIK
ARAGEVSLETAISRQKAGLHTPAQQAIHLALPVVESKNLAFSQVDLLTEAKSFAAEGTGFADLGREIDAQ
IKRGDLLYVDVAKGYGTDLLISRASYDAEKSILHHILEGKEAVTPLMERVPGELMETLTSGQRAATRMIL
ETKDRFTVVQGYAGVGKTTQFRAVMSAVNLLPESERPRVVGLGPTHRAVGEMRSAGVEAQTLASFLHDTQ
LQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSAA
DVAIMKEIVRQTPELRDAVYSLINRDVNKALSGLENVKPVQVPRLKGAWAPENSVTEFSRLQERELAKAA
QEAEKKGEAFPDVPVTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIQDALAKPGEQQVTVPVL
TTANIRDGELRRLSTWEAHPGALALVDNVYHRIAGISKEDGLITLEDKAGNTRLISPREAAAEGVTLYNP
ETIRVGAGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGKQTRVVRPGQDRAEQHIDLAYAITAHS
AQGASETFAIALEGTEGGRKQMAGFESAYVALSRMKQHVQVYTDDRQGWVKAINSAEQKGTAHDVLEPKS
EREMMNAERLFSTARELRDVAAGRAVLRNAGLAQGDSRARFIAPGRKYPQPYVALPAFDRNGKSAGIWLN
PLTTDDGAGLRGFTGEGRVKGSEEAQFVALQGSRNGESLLAGSMQDGVRIARENPDSGVVVRIVGDGRPW
NPVAITGGRVWGDIPDSNVQPGAGNGEPVTAEILAQRQAEEAVRRETERRADEIVRKMAEDKSDLPEEKT
AQAVREIAGQEQDRMTPPEREPPLPESVLREPQRERETIREVARENRGRERLQQMEQEMVRDLQKEKTPG
GD

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(967-1158)

TrwC relaxase (TrwC)

(11-282)

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

(632-711)

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

(574-626)

DNA helicase TraI (TraI_C)

(1430-1553)


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 60108..86464

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
SE17cs_RS24245 (SE17cs_04972) 55264..57261 + 1998 WP_000117513 ParB/RepB/Spo0J family partition protein -
SE17cs_RS24250 (SE17cs_04973) 57301..57735 + 435 WP_010999943 conjugation system SOS inhibitor PsiB -
SE17cs_RS24255 (SE17cs_04974) 57732..58469 + 738 WP_000581933 plasmid SOS inhibition protein A -
SE17cs_RS27105 58504..58632 + 129 WP_000372429 hypothetical protein -
SE17cs_RS26760 (SE17cs_04975) 58718..58876 + 159 WP_001704449 hypothetical protein -
SE17cs_RS26840 58979..59797 + 819 Protein_78 DUF932 domain-containing protein -
SE17cs_RS24270 (SE17cs_04978) 60108..60578 - 471 WP_001526856 transglycosylase SLT domain-containing protein virB1
SE17cs_RS24275 (SE17cs_04979) 60993..61373 + 381 WP_001151546 conjugal transfer relaxosome DNA-binding protein TraM -
SE17cs_RS24280 (SE17cs_04980) 61566..62252 + 687 WP_000336297 PAS domain-containing protein -
SE17cs_RS25930 (SE17cs_04981) 62346..62573 + 228 WP_001676655 conjugal transfer relaxosome protein TraY -
SE17cs_RS24285 (SE17cs_04982) 62615..62977 + 363 WP_001274201 type IV conjugative transfer system pilin TraA -
SE17cs_RS24290 (SE17cs_04983) 62992..63303 + 312 WP_012825259 type IV conjugative transfer system protein TraL traL
SE17cs_RS24295 (SE17cs_04984) 63325..63891 + 567 WP_000399768 type IV conjugative transfer system protein TraE traE
SE17cs_RS24300 (SE17cs_04985) 63878..64618 + 741 WP_001230719 type-F conjugative transfer system secretin TraK traK
SE17cs_RS24305 (SE17cs_04986) 64618..66039 + 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
SE17cs_RS24310 (SE17cs_04987) 66029..66625 + 597 WP_000527896 conjugal transfer pilus-stabilizing protein TraP -
SE17cs_RS24315 (SE17cs_04988) 66603..66848 + 246 WP_010999944 DUF2689 domain-containing protein virb4
SE17cs_RS24320 (SE17cs_04989) 66845..67360 + 516 WP_001079995 type IV conjugative transfer system lipoprotein TraV traV
SE17cs_RS24325 (SE17cs_04990) 67495..67716 + 222 WP_001278699 conjugal transfer protein TraR -
SE17cs_RS24330 (SE17cs_04991) 67709..68176 + 468 WP_000549562 hypothetical protein -
SE17cs_RS24335 (SE17cs_04993) 68293..68556 + 264 WP_001239255 hypothetical protein -
SE17cs_RS24340 (SE17cs_04994) 68572..71220 + 2649 WP_012825260 type IV secretion system protein TraC virb4
SE17cs_RS24345 (SE17cs_04995) 71195..71581 + 387 WP_000105164 type-F conjugative transfer system protein TrbI -
SE17cs_RS24350 (SE17cs_04996) 71578..72210 + 633 WP_000871995 type-F conjugative transfer system protein TraW traW
SE17cs_RS24355 (SE17cs_04997) 72207..73199 + 993 WP_000833320 conjugal transfer pilus assembly protein TraU traU
SE17cs_RS24360 (SE17cs_04998) 73218..73526 + 309 WP_010999945 hypothetical protein -
SE17cs_RS24365 (SE17cs_04999) 73511..74149 + 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
SE17cs_RS24370 (SE17cs_05000) 74186..74605 + 420 WP_001229397 HNH endonuclease signature motif containing protein -
SE17cs_RS24375 (SE17cs_05001) 74602..76428 + 1827 WP_000827528 type-F conjugative transfer system mating-pair stabilization protein TraN traN
SE17cs_RS24380 (SE17cs_05002) 76439..76654 + 216 WP_000700023 conjugal transfer protein TrbE -
SE17cs_RS24385 (SE17cs_05003) 76666..77415 + 750 WP_001226854 type-F conjugative transfer system pilin assembly protein TraF traF
SE17cs_RS24390 (SE17cs_05004) 77629..77922 + 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
SE17cs_RS24395 (SE17cs_05005) 77909..78457 + 549 WP_000055840 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
SE17cs_RS24400 (SE17cs_05006) 78447..79829 + 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
SE17cs_RS24405 (SE17cs_05007) 79826..82648 + 2823 WP_001007086 conjugal transfer mating-pair stabilization protein TraG traG
SE17cs_RS24410 (SE17cs_05008) 82664..83158 + 495 WP_010999946 entry exclusion protein -
SE17cs_RS24415 (SE17cs_05009) 83194..83925 + 732 WP_000782438 conjugal transfer complement resistance protein TraT -
SE17cs_RS24420 (SE17cs_05010) 84302..86464 + 2163 WP_000009318 type IV conjugative transfer system coupling protein TraD virb4
SE17cs_RS24425 (SE17cs_05011) 86473..86871 - 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
SE17cs_RS24430 (SE17cs_05012) 86871..87098 - 228 WP_000450265 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   1235 GenBank   NZ_CP014357
Plasmid name   pSO2_STV Incompatibility group   IncFII
Plasmid size   93837 bp Coordinate of oriT [Strand]   60652..60910 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium strain SO2 isolate SOHS 02-20

Cargo genes

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