Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100570
Name   oriT_pDM0133 in_silico
Organism   Escherichia coli
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_024956 (80197..80486 [+], 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_pDM0133
CGCACCGCTAGCAGCGCCCCTAGCGGTATCCTATAAAAAAACACACCGCGCCGCTAGCAGCACCCCTAATATAAAATAATGTTTTTTATAAAAATAGTCAGTACCACCCCTACAAAACGGTGTCGGCGCGTTGTTGTAGCCGCGCCGACACCGCTTTTTTAAATATCATAAAGAGAGTAAGAGAAACTAATTTTTCATAACACTCTATTTATAAAGAAAAATCAGCAAAAACTTGTTTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTTGAGCCT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   642 GenBank   YP_009060129
Name   TraI_pDM0133 insolico UniProt ID   A0A023UKI9
Length   1623 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1623 a.a.        Molecular weight: 177770.04 Da        Isoelectric Point: 5.9510

>YP_009060129.1 conjugative transfer relaxase protein TraI (plasmid) [Escherichia coli]
MLTGNLVMALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREK
LKEQVEALGYETEVVGKHGMWEMPGVPVEAFSGRSQTIREAVGEDASLKSRDVAALDTRKSKQHVDPEIK
MVEWMQTLKETGFDIRAYRDAADQRADLRTLTPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLART
VGILPPENGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSV
PRTAGYSDAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNMKQDERLS
GELITGRRQLLEGMTFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLIIDSGQRTGTGSALMAMKDA
GVNTYRWQGGEQRPATIISEPDRNVRYARLAGDFAVSVKAGEESVAQVSGVREQAMLTQTIRSELKTQGV
LGHPEVTMTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVV
RISSLDSSWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVSSVSEDAMTVVVPGRAEPATLPVSDS
PFTALKLENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSF
TVVSEQIKTRAGETSLETAISHQKSALHTPAQQAIHLALPVVESKKLAFSMVDLLTEAKSFAAEGTGFTE
LGGEINAQIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVMPLMERVPGELMEKLTSGQ
RAATRMILETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTL
ASFLHDTQLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFR
LQQTRSAADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQ
EAKLAEAQQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDVREKAGE
LGKEQVMVPVLNTANIRDGELRRLSTWETHRDALVLVDNVYHRIAGISKDDGLITLQDAEGNTRLISPRE
AVAEGVTLYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTREIRPGQEQAEQH
IDLAYAITAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQK
GTAHDVFEPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFD
RNGKSAGIWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGV
VVRIAGEGRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMA
ENKPDLPDGKTEQAVREIAGQERDRAAITEREAALPEGVLREPQRVREAVREIARENLLQERLQQMERDM
VRDLQKEKTLGGD

  Protein domains


Predicted by InterproScan.

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

(442-493)

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

(500-579)

TrwC relaxase (TrwC)

(3-150)

DNA helicase TraI (TraI_C)

(1301-1424)

AAA domain (AAA_30)

(836-1023)


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 54646..81048

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTC35_RS00255 (D616_p117041) 54012..54239 + 228 WP_000450532 toxin-antitoxin system antitoxin VapB -
HTC35_RS00260 (D616_p117042) 54239..54637 + 399 WP_000911324 type II toxin-antitoxin system VapC family toxin -
HTC35_RS00265 (D616_p117043) 54646..56799 - 2154 WP_000009350 type IV conjugative transfer system coupling protein TraD virb4
HTC35_RS00270 (D616_p117044) 57052..57783 - 732 WP_000850422 conjugal transfer complement resistance protein TraT -
HTC35_RS00275 57808..58329 - 522 WP_000632670 conjugal transfer entry exclusion protein TraS -
HTC35_RS00280 (D616_p117046) 58362..61178 - 2817 WP_001007054 conjugal transfer mating-pair stabilization protein TraG traG
HTC35_RS00285 (D616_p117047) 61175..62548 - 1374 WP_021553026 conjugal transfer pilus assembly protein TraH traH
HTC35_RS00290 62535..62929 - 395 Protein_59 F-type conjugal transfer protein TrbF -
HTC35_RS00295 (D616_p117049) 62916..63257 - 342 WP_001443031 P-type conjugative transfer protein TrbJ -
HTC35_RS00300 (D616_p117050) 63187..63732 - 546 WP_000059850 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HTC35_RS00305 (D616_p117051) 63719..64003 - 285 WP_000624109 type-F conjugative transfer system pilin chaperone TraQ -
HTC35_RS00310 64084..64398 + 315 WP_000415567 hypothetical protein -
HTC35_RS00315 64400..64747 - 348 WP_001287913 conjugal transfer protein TrbA -
HTC35_RS00320 (D616_p117052) 64763..65506 - 744 WP_001030367 type-F conjugative transfer system pilin assembly protein TraF traF
HTC35_RS00325 65499..65756 - 258 WP_000864318 conjugal transfer protein TrbE -
HTC35_RS00330 (D616_p117053) 65783..67591 - 1809 WP_000821847 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HTC35_RS00335 (D616_p117054) 67588..68226 - 639 WP_000777688 type-F conjugative transfer system pilin assembly protein TrbC trbC
HTC35_RS00340 (D616_p117055) 68235..69227 - 993 WP_000830187 conjugal transfer pilus assembly protein TraU traU
HTC35_RS00345 (D616_p117056) 69224..69856 - 633 WP_001203720 type-F conjugative transfer system protein TraW traW
HTC35_RS00350 (D616_p117057) 69853..70239 - 387 WP_000097319 type-F conjugative transfer system protein TrbI -
HTC35_RS00355 (D616_p117058) 70236..72863 - 2628 WP_001064247 type IV secretion system protein TraC virb4
HTC35_RS00360 (D616_p117059) 73023..73244 - 222 WP_001278689 conjugal transfer protein TraR -
HTC35_RS00365 (D616_p117060) 73379..73894 - 516 WP_000809841 type IV conjugative transfer system lipoprotein TraV traV
HTC35_RS00370 (D616_p117061) 73891..74142 - 252 WP_001038342 conjugal transfer protein TrbG -
HTC35_RS00375 (D616_p117062) 74154..74345 - 192 WP_032072783 conjugal transfer protein TrbD -
HTC35_RS00380 (D616_p117063) 74338..74928 - 591 WP_000002792 conjugal transfer pilus-stabilizing protein TraP -
HTC35_RS00385 (D616_p117064) 74918..76345 - 1428 WP_000146692 F-type conjugal transfer pilus assembly protein TraB traB
HTC35_RS00390 (D616_p117065) 76345..77073 - 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
HTC35_RS00395 (D616_p117066) 77060..77626 - 567 WP_000399792 type IV conjugative transfer system protein TraE traE
HTC35_RS00400 (D616_p117067) 77648..77959 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
HTC35_RS00405 (D616_p117068) 77974..78339 - 366 WP_000994779 type IV conjugative transfer system pilin TraA -
HTC35_RS00410 78372..78773 - 402 WP_001369361 conjugal transfer relaxosome DNA-bindin protein TraY -
HTC35_RS00415 (D616_p117070) 78866..79555 - 690 WP_000283385 conjugal transfer transcriptional regulator TraJ -
HTC35_RS00420 (D616_p117071) 79742..80125 - 384 WP_001151524 conjugal transfer relaxosome DNA-binding protein TraM -
HTC35_RS00425 (D616_p117072) 80446..81048 + 603 WP_000243709 transglycosylase SLT domain-containing protein virB1
HTC35_RS00430 81344..82165 - 822 WP_001234469 DUF932 domain-containing protein -
HTC35_RS00435 (D616_p117073) 82286..82573 - 288 WP_000107535 hypothetical protein -
HTC35_RS00440 82598..82804 - 207 WP_000547939 hypothetical protein -
HTC35_RS00530 82874..83047 + 174 Protein_90 hypothetical protein -
HTC35_RS00535 83045..83275 - 231 WP_001426396 hypothetical protein -
HTC35_RS00445 83495..83620 - 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
HTC35_RS00540 83562..83711 - 150 Protein_93 plasmid maintenance protein Mok -
HTC35_RS00450 (D616_p117075) 83890..84652 - 763 Protein_94 plasmid SOS inhibition protein A -
HTC35_RS00455 (D616_p117076) 84649..85083 - 435 WP_000845895 conjugation system SOS inhibitor PsiB -

Host bacterium

ID   1030 GenBank   NC_024956
Plasmid name   pDM0133 Incompatibility group   IncFIC(FII)
Plasmid size   94587 bp Coordinate of oriT [Strand]   80197..80486 [+]
Host baterium   Escherichia coli

Cargo genes

Drug resistance gene   tet(A), sul1, qacE, ant(3'')-Ia
Virulence gene   -
Metal resistance gene   merR, merT, merP, merA, merD, merE
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -