Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100643
Name   oriT_pSLT_VNP20009 in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium strain VNP20009
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NZ_CP008745 (60647..60905 [-], 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_pSLT_VNP20009
GCAGCGCCCCCAGGGGTGTTACTTAAAAACAGGCACAGCGACGCTAGCAGCGCCCCTGATATAATGCAATGTTTTTTATAAAAATAGTCAGTACTACCCCTGTATAGCGTCGTCATAGCGGTGCCGGCGACGTGCCTGCACCGCTATTTAATACATTAAAATAAATTAAATTACATTATTATGAACATAACTCACTGTTACTAAAAACAAATCAGAAAAATTTTAATTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   715 GenBank   WP_000986921
Name   TraI_pSLT_VNP20009 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: 60103..86460

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
DC51_RS23430 (DC51_p0095) 55259..57256 + 1998 WP_000117513 ParB/RepB/Spo0J family partition protein -
DC51_RS23435 (DC51_p0096) 57296..57730 + 435 WP_010999943 conjugation system SOS inhibitor PsiB -
DC51_RS23440 (DC51_p0097) 57727..58464 + 738 WP_000581933 plasmid SOS inhibition protein A -
DC51_RS26275 (DC51_p0098) 58499..58627 + 129 WP_000372429 hypothetical protein -
DC51_RS26010 (DC51_p0099) 58713..58871 + 159 WP_001704449 hypothetical protein -
DC51_RS26015 58974..59792 + 819 Protein_78 DUF932 domain-containing protein -
DC51_RS23455 (DC51_p0104) 60103..60573 - 471 WP_001526856 transglycosylase SLT domain-containing protein virB1
DC51_RS23460 (DC51_p0105) 60988..61368 + 381 WP_001151546 conjugal transfer relaxosome DNA-binding protein TraM -
DC51_RS23465 (DC51_p0106) 61561..62247 + 687 WP_000336297 PAS domain-containing protein -
DC51_RS25230 (DC51_p0107) 62341..62568 + 228 WP_001676655 conjugal transfer relaxosome protein TraY -
DC51_RS23470 (DC51_p0108) 62610..62972 + 363 WP_001274201 type IV conjugative transfer system pilin TraA -
DC51_RS23475 (DC51_p0109) 62987..63298 + 312 WP_000012129 type IV conjugative transfer system protein TraL traL
DC51_RS23480 (DC51_p0110) 63320..63886 + 567 WP_000399768 type IV conjugative transfer system protein TraE traE
DC51_RS23485 (DC51_p0111) 63873..64613 + 741 WP_001230719 type-F conjugative transfer system secretin TraK traK
DC51_RS23490 (DC51_p0112) 64613..66034 + 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
DC51_RS23495 (DC51_p0113) 66024..66621 + 598 Protein_88 conjugal transfer pilus-stabilizing protein TraP -
DC51_RS23500 (DC51_p0114) 66599..66844 + 246 WP_010999944 DUF2689 domain-containing protein virb4
DC51_RS23505 (DC51_p0115) 66841..67356 + 516 WP_001079995 type IV conjugative transfer system lipoprotein TraV traV
DC51_RS23510 (DC51_p0116) 67491..67712 + 222 WP_001278699 conjugal transfer protein TraR -
DC51_RS23515 (DC51_p0117) 67705..68172 + 468 WP_000549562 hypothetical protein -
DC51_RS23520 (DC51_p0119) 68289..68552 + 264 WP_001239255 hypothetical protein -
DC51_RS23525 (DC51_p0120) 68568..71216 + 2649 WP_000793310 type IV secretion system protein TraC virb4
DC51_RS23530 (DC51_p0121) 71191..71577 + 387 WP_000105164 type-F conjugative transfer system protein TrbI -
DC51_RS23535 (DC51_p0122) 71574..72206 + 633 WP_000871995 type-F conjugative transfer system protein TraW traW
DC51_RS23540 (DC51_p0123) 72203..73195 + 993 WP_000833320 conjugal transfer pilus assembly protein TraU traU
DC51_RS23545 (DC51_p0124) 73214..73522 + 309 WP_010999945 hypothetical protein -
DC51_RS23550 (DC51_p0125) 73507..74145 + 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
DC51_RS23555 (DC51_p0126) 74182..74601 + 420 WP_001229397 HNH endonuclease signature motif containing protein -
DC51_RS23560 (DC51_p0127) 74598..76424 + 1827 WP_000827528 type-F conjugative transfer system mating-pair stabilization protein TraN traN
DC51_RS23565 (DC51_p0128) 76435..76650 + 216 WP_000700023 conjugal transfer protein TrbE -
DC51_RS23570 (DC51_p0129) 76662..77411 + 750 WP_001226854 type-F conjugative transfer system pilin assembly protein TraF traF
DC51_RS23575 (DC51_p0131) 77625..77918 + 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
DC51_RS23580 (DC51_p0132) 77905..78453 + 549 WP_000055840 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
DC51_RS23585 (DC51_p0133) 78443..79825 + 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
DC51_RS23590 (DC51_p0134) 79822..82644 + 2823 WP_001007086 conjugal transfer mating-pair stabilization protein TraG traG
DC51_RS23595 (DC51_p0135) 82660..83154 + 495 WP_010999946 entry exclusion protein -
DC51_RS23600 (DC51_p0136) 83190..83921 + 732 WP_000782438 conjugal transfer complement resistance protein TraT -
DC51_RS23605 (DC51_p0137) 84298..86460 + 2163 WP_000009318 type IV conjugative transfer system coupling protein TraD virb4
DC51_RS23610 (DC51_p0138) 86469..86867 - 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
DC51_RS23615 (DC51_p0139) 86867..87094 - 228 WP_000450265 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   1103 GenBank   NZ_CP008745
Plasmid name   pSLT_VNP20009 Incompatibility group   IncFII
Plasmid size   93833 bp Coordinate of oriT [Strand]   60647..60905 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium strain VNP20009

Cargo genes

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