Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100671
Name   oriT_pD6-A in_silico
Organism   Escherichia coli strain D6
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NZ_CP010149 (57089..57378 [+], 290 nt)
oriT length   290 nt
IRs (inverted repeats)      225..232, 235..242 n  (GCAAAAAC..GTTTTTGC)
Location of nic site      251..252
Conserved sequence flanking the
  nic site    		  GTGGGGTGT|GG
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 290 nt

>oriT_pD6-A
CGCACCGCTAGCAGCGCCCCTAGCGGTATCCTATAAAAAAACACACCGCGCCGCTAGCAGCACCCCTAATATAAAATAATGTTTTTTATAAAAATAGTCAGTACCACCCCTACAAAGCGGTGTCGGCGCGTTGTTGTAGCCGCGCCGACACCGCTTTTTTAAATATCATAAAGAGAGTAAGAGAAACTAATTTTTCATAACTCTCTATTTATAAAGAAAAATCAGCAAAAACTTGTTTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTTGAGCCT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   743 GenBank   WP_000986962
Name   TraI_pD6-A insolico UniProt ID   _
Length   1756 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 192018.92 Da        Isoelectric Point: 5.8722

>WP_000986962.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGKLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQTPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMAFTPGNTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGRPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSNSLTLRDAQDETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVSDSPFMALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKTGLHTPAQQAIHLALPVVESKNLAFSMVDLLTEAKSFAAEGTSFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLLQRSGETPNFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPDALALVDSVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQIRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKSDREVMNAERLFSTARELRDVVAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPRTITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVRDIAGLERDRSAISEREAALPESVLREPQRVREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

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

(575-626)

AAA domain (AAA_30)

(969-1156)

DNA helicase TraI (TraI_C)

(1434-1557)

TrwC relaxase (TrwC)

(10-283)

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

(633-712)


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 31567..57940

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
RG39_RS24395 (RG39_23205) 30933..31160 + 228 WP_000450520 toxin-antitoxin system antitoxin VapB -
RG39_RS24400 (RG39_23210) 31160..31558 + 399 WP_000911313 type II toxin-antitoxin system VapC family toxin -
RG39_RS24405 (RG39_23215) 31567..33720 - 2154 WP_000009324 type IV conjugative transfer system coupling protein TraD virb4
RG39_RS24410 (RG39_23220) 33973..34704 - 732 WP_023565183 conjugal transfer complement resistance protein TraT -
RG39_RS24415 (RG39_23225) 34736..35233 - 498 WP_000605857 entry exclusion protein -
RG39_RS24420 (RG39_23230) 35249..38071 - 2823 WP_001007018 conjugal transfer mating-pair stabilization protein TraG traG
RG39_RS24425 (RG39_23235) 38068..39441 - 1374 WP_001517790 conjugal transfer pilus assembly protein TraH traH
RG39_RS24430 (RG39_23240) 39441..39821 - 381 WP_001389370 F-type conjugal transfer protein TrbF -
RG39_RS24435 (RG39_23245) 39808..40149 - 342 WP_001443031 P-type conjugative transfer protein TrbJ -
RG39_RS24440 (RG39_23250) 40079..40624 - 546 WP_000059851 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
RG39_RS24445 (RG39_23255) 40611..40895 - 285 WP_000624109 type-F conjugative transfer system pilin chaperone TraQ -
RG39_RS24450 (RG39_23260) 40976..41290 + 315 WP_001324103 hypothetical protein -
RG39_RS24455 (RG39_23265) 41292..41639 - 348 WP_001287910 conjugal transfer protein TrbA -
RG39_RS24460 (RG39_23270) 41655..42398 - 744 WP_001030393 type-F conjugative transfer system pilin assembly protein TraF traF
RG39_RS24465 (RG39_23275) 42391..42648 - 258 WP_000864318 conjugal transfer protein TrbE -
RG39_RS24470 (RG39_23280) 42675..44483 - 1809 WP_000821841 type-F conjugative transfer system mating-pair stabilization protein TraN traN
RG39_RS24475 (RG39_23285) 44480..45118 - 639 WP_000777700 type-F conjugative transfer system pilin assembly protein TrbC trbC
RG39_RS24480 (RG39_23290) 45127..46119 - 993 WP_000830183 conjugal transfer pilus assembly protein TraU traU
RG39_RS24485 (RG39_23295) 46116..46748 - 633 WP_001203720 type-F conjugative transfer system protein TraW traW
RG39_RS24490 (RG39_23300) 46745..47131 - 387 WP_000099686 type-F conjugative transfer system protein TrbI -
RG39_RS24495 (RG39_23305) 47128..49755 - 2628 WP_001064245 type IV secretion system protein TraC virb4
RG39_RS24500 (RG39_23310) 49915..50136 - 222 WP_001278689 conjugal transfer protein TraR -
RG39_RS24505 (RG39_23315) 50271..50786 - 516 WP_000809838 type IV conjugative transfer system lipoprotein TraV traV
RG39_RS24510 (RG39_23320) 50783..51034 - 252 WP_001038342 conjugal transfer protein TrbG -
RG39_RS24515 (RG39_23325) 51046..51243 - 198 WP_001324648 conjugal transfer protein TrbD -
RG39_RS24520 (RG39_23330) 51230..51820 - 591 WP_001376242 conjugal transfer pilus-stabilizing protein TraP -
RG39_RS24525 (RG39_23335) 51810..53237 - 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
RG39_RS24530 (RG39_23340) 53237..53965 - 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
RG39_RS24535 (RG39_23345) 53952..54518 - 567 WP_000399792 type IV conjugative transfer system protein TraE traE
RG39_RS24540 (RG39_23350) 54540..54851 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
RG39_RS24545 (RG39_23355) 54866..55231 - 366 WP_000994779 type IV conjugative transfer system pilin TraA -
RG39_RS24550 (RG39_23360) 55264..55659 - 396 WP_001309237 conjugal transfer relaxosome DNA-bindin protein TraY -
RG39_RS24555 (RG39_23365) 55758..56447 - 690 WP_000283385 conjugal transfer transcriptional regulator TraJ -
RG39_RS24560 (RG39_23370) 56634..57017 - 384 WP_001151524 conjugal transfer relaxosome DNA-binding protein TraM -
RG39_RS24570 (RG39_23375) 57350..57940 + 591 WP_001376243 transglycosylase SLT domain-containing protein virB1
RG39_RS24575 (RG39_23380) 58237..59058 - 822 WP_001234426 DUF932 domain-containing protein -
RG39_RS24580 (RG39_23385) 59176..59463 - 288 WP_000107535 hypothetical protein -
RG39_RS27140 (RG39_23390) 59488..59694 - 207 WP_000547968 hypothetical protein -
RG39_RS27145 59764..59936 + 173 Protein_73 hypothetical protein -
RG39_RS27150 59934..60164 - 231 WP_071586998 hypothetical protein -
RG39_RS24600 (RG39_23400) 60384..60509 - 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
RG39_RS27155 60451..60600 - 150 Protein_76 plasmid maintenance protein Mok -
RG39_RS26715 (RG39_23405) 60622..60810 + 189 WP_001299721 hypothetical protein -
RG39_RS24610 (RG39_23410) 60779..61541 - 763 Protein_78 plasmid SOS inhibition protein A -
RG39_RS24615 (RG39_23415) 61538..61972 - 435 WP_000845936 conjugation system SOS inhibitor PsiB -
RG39_RS24620 62027..62224 - 198 Protein_80 hypothetical protein -
RG39_RS24625 (RG39_23420) 62252..62485 - 234 WP_000005987 DUF905 family protein -

Host bacterium

ID   1131 GenBank   NZ_CP010149
Plasmid name   pD6-A Incompatibility group   IncFIC
Plasmid size   199494 bp Coordinate of oriT [Strand]   57089..57378 [+]
Host baterium   Escherichia coli strain D6

Cargo genes

Drug resistance gene   tetracycline resistance
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -