Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100328
Name   oriT_pVir68 in_silico
Organism   Escherichia coli Vir68
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_012944 (56493..56953 [-], 461 nt)
oriT length   461 nt
IRs (inverted repeats)      141..150, 153..162  (ATAGGGTCGT..ACGACCCTAT)
 230..237, 240..247  (GCAAAAAC..GTTTTTGC)
Location of nic site      256..257
Conserved sequence flanking the
  nic site    		  GTGGGGTGT|GG
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 461 nt

>oriT_pVir68
CCTAGCAGCGCCCCTAGGGGCATACTATAAAAAAACGCACGGCGCTGCTAGGGGCGGCCCTAATATATCCAAATGTTTTTCATGAAAATTGTCAGCACTGACCCTAACAAGGGTCGTCATAGGGTCGCTATAGGGTCGCTATAGGGTCGTCAACGACCCTATTTAATAATGTAAAATAAATTAAAATACATTATTTAGAACATAAACTAATGATTTAAAAAACAAATCAGCAAAAACTTGTTTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTTGAGCCTTTTTGTGGAGTGGGTTAAATTATTTACGGATAAAGTCACCAGAGGTGGAAAAATGAAAAAATGGATGTTAGCCATCTGCCTGATGTTTATAAATGAGAACTGCCTAGCCACTGATTGCTTTGATCTTGCAGGCAGGGATTACAAAATAGATCCTGATTTACTGAGA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   399 GenBank   YP_003034058
Name   TraI_pVir68 insolico UniProt ID   C5ZZM7
Length   1763 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1763 a.a.        Molecular weight: 192853.74 Da        Isoelectric Point: 5.8080

>YP_003034058.1 conjugal transfer nickase/helicase TraI (plasmid) [Escherichia coli Vir68]
MSKGYTFMMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGKLPDG
ADLSRMQDGSNKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSET
VLTGNLVMALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREK
LKEQVEALGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVR
MAEWMQTLKETGFDIRAYRDAADQRAETRTQTPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLART
VGILPPENGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSV
PRTAGYSDAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLS
GELITGRRQLQEGMAFTPGNTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDA
GVNTYRWQGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGV
LGRPEITMTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSNSLTLRDAQGETQVV
RISSLDSSWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVSDS
PFMALKLENGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSF
TVVSEQIKARAGETLLETAISLQKTGLHTPAQQAIHLALPVVESKNLAFSMVDLLTEAKSFAAEGTSFTE
LGGEINAQIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQ
RAATRMILETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTL
ASFLHDTQLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFR
LQQTRSAADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQ
EAKLAEAQQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDALEKAGE
LGKEQVMVPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISKDDGLITLEDAEGNTRLISPRE
AVAEGVTLYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVFGDSVTLSDGQQTRVIRPGQERAEQH
IDLAYAITAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDDRQGWTDAINNAVQK
GTAHDVFEPKPDREVMNAQRLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFD
RNGKSAGIWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGV
VVRIAGEGRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMA
ENKPDLPDGRTEQAVREIAGQERERAVTSEREAALPESVLREPQREREAVREVVRENLLQERLQQMERDM
VRDLQKEKTLGGD

  Protein domains


Predicted by InterproScan.

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

(640-719)

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

(582-633)

DNA helicase TraI (TraI_C)

(1441-1564)

AAA domain (AAA_30)

(975-1163)

TrwC relaxase (TrwC)

(17-290)


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 56097..82309

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
PVIR_RS00260 (pVir_48) 52429..52863 + 435 WP_012775868 conjugation system SOS inhibitor PsiB -
PVIR_RS00265 (pVir_49) 52860..53622 + 763 Protein_50 plasmid SOS inhibition protein A -
PVIR_RS00745 53796..53945 + 150 Protein_51 plasmid maintenance protein Mok -
PVIR_RS00270 53887..54012 + 126 WP_096937776 type I toxin-antitoxin system Hok family toxin -
PVIR_RS00275 54313..54572 - 260 Protein_53 hypothetical protein -
PVIR_RS00280 (pVir_50) 54574..54861 + 288 WP_012775870 hypothetical protein -
PVIR_RS00285 (pVir_51) 54980..55801 + 822 WP_168445116 DUF932 domain-containing protein -
PVIR_RS00290 (pVir_53) 56097..56699 - 603 WP_012775872 transglycosylase SLT domain-containing protein virB1
PVIR_RS00295 (pVir_54) 57032..57403 + 372 WP_012775873 conjugal transfer relaxosome DNA-binding protein TraM -
PVIR_RS00300 (pVir_55) 57603..58289 + 687 WP_000332492 PAS domain-containing protein -
PVIR_RS00305 58384..58611 + 228 WP_001254386 conjugal transfer relaxosome protein TraY -
PVIR_RS00310 (pVir_56) 58645..59010 + 366 WP_012775875 type IV conjugative transfer system pilin TraA -
PVIR_RS00315 (pVir_57) 59025..59336 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
PVIR_RS00320 (pVir_58) 59358..59924 + 567 WP_000399792 type IV conjugative transfer system protein TraE traE
PVIR_RS00325 (pVir_59) 59911..60639 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
PVIR_RS00330 (pVir_60) 60639..62066 + 1428 WP_000146655 F-type conjugal transfer pilus assembly protein TraB traB
PVIR_RS00335 (pVir_61) 62056..62646 + 591 WP_000002787 conjugal transfer pilus-stabilizing protein TraP -
PVIR_RS00340 62633..62830 + 198 WP_001324648 conjugal transfer protein TrbD -
PVIR_RS00345 (pVir_62) 62842..63093 + 252 WP_001038342 conjugal transfer protein TrbG -
PVIR_RS00350 (pVir_63) 63090..63605 + 516 WP_000809838 type IV conjugative transfer system lipoprotein TraV traV
PVIR_RS00355 63740..63961 + 222 WP_112912743 conjugal transfer protein TraR -
PVIR_RS00360 (pVir_64) 64121..66748 + 2628 WP_001064245 type IV secretion system protein TraC virb4
PVIR_RS00365 (pVir_65) 66745..67131 + 387 WP_000099690 type-F conjugative transfer system protein TrbI -
PVIR_RS00370 (pVir_66) 67128..67760 + 633 WP_001203720 type-F conjugative transfer system protein TraW traW
PVIR_RS00375 (pVir_67) 67757..68749 + 993 WP_000830183 conjugal transfer pilus assembly protein TraU traU
PVIR_RS00380 (pVir_68) 68758..69396 + 639 WP_062894220 type-F conjugative transfer system pilin assembly protein TrbC trbC
PVIR_RS00385 (pVir_69) 69393..71201 + 1809 WP_012775877 type-F conjugative transfer system mating-pair stabilization protein TraN traN
PVIR_RS00390 (pVir_70) 71228..71485 + 258 WP_000864318 conjugal transfer protein TrbE -
PVIR_RS00395 (pVir_71) 71478..72221 + 744 WP_001030377 type-F conjugative transfer system pilin assembly protein TraF traF
PVIR_RS00400 (pVir_72) 72237..72584 + 348 WP_001287910 conjugal transfer protein TrbA -
PVIR_RS00405 (pVir_72a) 72586..72900 - 315 WP_000415566 protein ArtA -
PVIR_RS00410 (pVir_73) 72981..73265 + 285 WP_000624109 type-F conjugative transfer system pilin chaperone TraQ -
PVIR_RS00415 (pVir_74) 73252..73797 + 546 WP_000059851 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
PVIR_RS00420 (pVir_75) 73727..74068 + 342 WP_001443031 P-type conjugative transfer protein TrbJ -
PVIR_RS00425 (pVir_76) 74055..74435 + 381 WP_001389370 F-type conjugal transfer protein TrbF -
PVIR_RS00430 (pVir_77) 74435..75808 + 1374 WP_001517790 conjugal transfer pilus assembly protein TraH traH
PVIR_RS00435 (pVir_78) 75805..78627 + 2823 WP_001007018 conjugal transfer mating-pair stabilization protein TraG traG
PVIR_RS00440 (pVir_79) 78643..79140 + 498 WP_000605857 entry exclusion protein -
PVIR_RS00445 (pVir_80) 79172..79903 + 732 WP_023565183 conjugal transfer complement resistance protein TraT -
PVIR_RS00450 (pVir_81) 80156..82309 + 2154 WP_000009324 type IV conjugative transfer system coupling protein TraD virb4
PVIR_RS00455 82318..82716 - 399 WP_000911313 type II toxin-antitoxin system VapC family toxin -
PVIR_RS00460 82716..82943 - 228 WP_000450520 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   789 GenBank   NC_012944
Plasmid name   pVir68 Incompatibility group   IncFIB
Plasmid size   138362 bp Coordinate of oriT [Strand]   56493..56953 [-]
Host baterium   Escherichia coli Vir68

Cargo genes

Drug resistance gene   -
Virulence gene   The tibA and tibC genes were identified on pVir68, located within a 37-kb region that also contained cdt-ABC and hly-AC.
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -