Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100995
Name   oriT_pSLT in_silico
Organism   Salmonella enterica subsp. enterica serovar Typhimurium str. DT2
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NZ_LN999012 (60659..60917 [-], 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
GCAGCGCCCCCAGGGGTGTTACTTAAAAACAGGCACAGCGACGCTAGCAGCGCCCCTGATATAATGCAATGTTTTTTATAAAAATAGTCAGTACTACCCCTGTATAGCGTCGTCATAGCGGTGCCGGCGACGTGCCTGCACCGCTATTTAATACATTAAAATAAATTAAATTACATTATTATGAACATAACTCACTGTTACTAAAAACAAATCAGAAAAATTTTAATTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   1065 GenBank   WP_000986921
Name   TraI_pSLT 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: 60115..86471

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
STMDT2_RS23610 (STMDT2_p00073) 55271..57268 + 1998 WP_000117513 ParB/RepB/Spo0J family partition protein -
STMDT2_RS23615 (STMDT2_p00074) 57308..57742 + 435 WP_010999943 conjugation system SOS inhibitor PsiB -
STMDT2_RS23620 (STMDT2_p00075) 57739..58476 + 738 WP_000581933 plasmid SOS inhibition protein A -
STMDT2_RS26415 58511..58639 + 129 WP_000372429 hypothetical protein -
STMDT2_RS26100 (STMDT2_p00076) 58725..58883 + 159 WP_001704449 hypothetical protein -
STMDT2_RS26105 58986..59804 + 819 Protein_79 DUF932 domain-containing protein -
STMDT2_RS23635 (STMDT2_p00079) 60115..60585 - 471 WP_001526856 transglycosylase SLT domain-containing protein virB1
STMDT2_RS23640 (STMDT2_p00080) 61000..61380 + 381 WP_001151546 conjugal transfer relaxosome DNA-binding protein TraM -
STMDT2_RS23645 (STMDT2_p00081) 61573..62259 + 687 WP_000336297 PAS domain-containing protein -
STMDT2_RS25275 (STMDT2_p00082) 62353..62580 + 228 WP_001676655 conjugal transfer relaxosome protein TraY -
STMDT2_RS23650 (STMDT2_p00083) 62622..62984 + 363 WP_001274201 type IV conjugative transfer system pilin TraA -
STMDT2_RS23655 (STMDT2_p00084) 62999..63310 + 312 WP_000012129 type IV conjugative transfer system protein TraL traL
STMDT2_RS23660 (STMDT2_p00085) 63332..63898 + 567 WP_000399768 type IV conjugative transfer system protein TraE traE
STMDT2_RS23665 (STMDT2_p00086) 63885..64625 + 741 WP_001230719 type-F conjugative transfer system secretin TraK traK
STMDT2_RS23670 (STMDT2_p00087) 64625..66046 + 1422 WP_000146700 F-type conjugal transfer pilus assembly protein TraB traB
STMDT2_RS23675 (STMDT2_p00088) 66036..66632 + 597 WP_000527896 conjugal transfer pilus-stabilizing protein TraP -
STMDT2_RS23680 (STMDT2_p00089) 66610..66855 + 246 WP_010999944 DUF2689 domain-containing protein virb4
STMDT2_RS23685 (STMDT2_p00090) 66852..67367 + 516 WP_001079995 type IV conjugative transfer system lipoprotein TraV traV
STMDT2_RS23690 (STMDT2_p00091) 67502..67723 + 222 WP_001278699 conjugal transfer protein TraR -
STMDT2_RS23695 (STMDT2_p00092) 67716..68183 + 468 WP_000549562 hypothetical protein -
STMDT2_RS23700 (STMDT2_p00094) 68300..68563 + 264 WP_001239255 hypothetical protein -
STMDT2_RS23705 (STMDT2_p00095) 68579..71227 + 2649 WP_000793310 type IV secretion system protein TraC virb4
STMDT2_RS23710 (STMDT2_p00096) 71202..71588 + 387 WP_000105164 type-F conjugative transfer system protein TrbI -
STMDT2_RS23715 (STMDT2_p00097) 71585..72217 + 633 WP_000871995 type-F conjugative transfer system protein TraW traW
STMDT2_RS23720 (STMDT2_p00098) 72214..73206 + 993 WP_000833320 conjugal transfer pilus assembly protein TraU traU
STMDT2_RS23725 (STMDT2_p00099) 73225..73533 + 309 WP_010999945 hypothetical protein -
STMDT2_RS23730 (STMDT2_p00100) 73518..74156 + 639 WP_000554823 type-F conjugative transfer system pilin assembly protein TrbC trbC
STMDT2_RS23735 (STMDT2_p00101) 74193..74612 + 420 WP_001229397 HNH endonuclease signature motif containing protein -
STMDT2_RS23740 (STMDT2_p00102) 74609..76435 + 1827 WP_000827528 type-F conjugative transfer system mating-pair stabilization protein TraN traN
STMDT2_RS23745 (STMDT2_p00103) 76446..76661 + 216 WP_000700023 conjugal transfer protein TrbE -
STMDT2_RS23750 (STMDT2_p00104) 76673..77422 + 750 WP_001226854 type-F conjugative transfer system pilin assembly protein TraF traF
STMDT2_RS23755 (STMDT2_p00105) 77636..77929 + 294 WP_001233881 type-F conjugative transfer system pilin chaperone TraQ -
STMDT2_RS23760 (STMDT2_p00106) 77916..78464 + 549 WP_000055840 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
STMDT2_RS23765 (STMDT2_p00107) 78454..79836 + 1383 WP_001161719 conjugal transfer pilus assembly protein TraH traH
STMDT2_RS23770 (STMDT2_p00108) 79833..82655 + 2823 WP_001007086 conjugal transfer mating-pair stabilization protein TraG traG
STMDT2_RS23775 (STMDT2_p00109) 82671..83165 + 495 WP_010999946 entry exclusion protein -
STMDT2_RS23780 (STMDT2_p00110) 83201..83932 + 732 WP_000782438 conjugal transfer complement resistance protein TraT -
STMDT2_RS23785 (STMDT2_p00111) 84309..86471 + 2163 WP_063977673 type IV conjugative transfer system coupling protein TraD virb4
STMDT2_RS23790 (STMDT2_p00112) 86480..86878 - 399 WP_000911322 type II toxin-antitoxin system VapC family toxin -
STMDT2_RS23795 (STMDT2_p00113) 86878..87105 - 228 WP_000450265 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   1453 GenBank   NZ_LN999012
Plasmid name   pSLT Incompatibility group   IncFII
Plasmid size   93844 bp Coordinate of oriT [Strand]   60659..60917 [-]
Host baterium   Salmonella enterica subsp. enterica serovar Typhimurium str. DT2

Cargo genes

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