Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100287
Name   oriT_pVM01 in_silico
Organism   Escherichia coli
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_010409 (126811..127100 [+], 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_pVM01
CGCACCGCTAGCAGCGCCCCTAGCGGTATCCTATAAAAAAACACACCGCGCCGCTAGCAGCACCCCTAATATAAAATAATGTTTTTTATAAAAATAGTCAGTACCACCCCTACAAAGCGGTGTCGGCGCGTTGTTGTAGCCGCGCCGACACCGCTTTTTTAAATATCATAAAGAGAGTAAGAGAAACTAATTTTTCATAACTCTCTATTTATAAAGAAAAATCAGCAAAAACTTGTTTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTTGAGCCT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   358 GenBank   YP_001711935
Name   TraI_pVM01 insolico UniProt ID   B1P7Q9
Length   1756 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 192143.94 Da        Isoelectric Point: 6.0143

>YP_001711935.1 conjugal transfer nickase/helicase TraI (plasmid) [Escherichia coli]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRSSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQILITDSGQRTGTGSALMAMKDAGVNIYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSYDRYVIDRVTAQSNSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVSDSPFMALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KTRAGETSLETAISHQKSALHTPAQQAIHLALPVVESKNLAFSQVDLLTEAKSFAAEGTSFTDLGGEINA
QIKRGDLLYVDVAKGYGTDLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QMQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRLEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIGLAYAI
TAHGAQGASETFAIALEGTEGNRKQMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKSDREVMNAERLFSTARELRDVVAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPRTITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVRDIAGLERDRSAISEREAALPESVLREPQRVREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

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

(633-712)

DNA helicase TraI (TraI_C)

(1434-1557)

AAA domain (AAA_30)

(969-1156)

TrwC relaxase (TrwC)

(10-283)

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

(575-626)


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 100030..127662

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HS504_RS00460 (pVM01_p087) 100030..102183 - 2154 WP_000009325 type IV conjugative transfer system coupling protein TraD virb4
HS504_RS00465 (pVM01_p088) 102436..103167 - 732 WP_000850422 conjugal transfer complement resistance protein TraT -
HS504_RS00470 (pVM01_p089) 103181..103690 - 510 WP_000628107 conjugal transfer entry exclusion protein TraS -
HS504_RS00475 (pVM01_p090) 103687..106512 - 2826 WP_001007037 conjugal transfer mating-pair stabilization protein TraG traG
HS504_RS00480 (pVM01_p091) 106509..107882 - 1374 WP_000944319 conjugal transfer pilus assembly protein TraH traH
HS504_RS00485 107869..108261 - 393 Protein_98 F-type conjugal transfer protein TrbF -
HS504_RS00490 (pVM01_p093) 108248..108589 - 342 WP_001442101 P-type conjugative transfer protein TrbJ -
HS504_RS00495 (pVM01_p094) 108519..109064 - 546 WP_000052614 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HS504_RS00500 (pVM01_p095) 109051..109287 - 237 WP_001346259 type-F conjugative transfer system pilin chaperone TraQ -
HS504_RS00505 (pVM01_p096) 109448..110191 - 744 WP_001030376 type-F conjugative transfer system pilin assembly protein TraF traF
HS504_RS00510 (pVM01_p097) 110184..110441 - 258 WP_000864341 conjugal transfer protein TrbE -
HS504_RS00515 (pVM01_p098) 110468..112318 - 1851 WP_000827530 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HS504_RS00520 (pVM01_p099) 112315..112953 - 639 WP_001104087 type-F conjugative transfer system pilin assembly protein TrbC trbC
HS504_RS00525 (pVM01_p100) 112981..113433 - 453 WP_000069429 hypothetical protein -
HS504_RS00530 (pVM01_p101) 113463..113924 - 462 WP_000277843 hypothetical protein -
HS504_RS00535 (pVM01_p102) 113950..114942 - 993 WP_000830839 conjugal transfer pilus assembly protein TraU traU
HS504_RS00540 (pVM01_p103) 114939..115571 - 633 WP_001203720 type-F conjugative transfer system protein TraW traW
HS504_RS00545 (pVM01_p104) 115568..115954 - 387 WP_000099690 type-F conjugative transfer system protein TrbI -
HS504_RS00550 (pVM01_p105) 115951..118581 - 2631 WP_000069766 type IV secretion system protein TraC virb4
HS504_RS00555 (pVM01_p106) 118708..119055 - 348 WP_000802783 hypothetical protein -
HS504_RS00560 (pVM01_p107) 119083..119301 - 219 WP_000556754 hypothetical protein -
HS504_RS00565 (pVM01_p108) 119381..119854 - 474 WP_000549598 hypothetical protein -
HS504_RS00570 119847..120020 - 174 WP_024262213 conjugal transfer protein TraR -
HS504_RS00575 (pVM01_p110) 120139..120654 - 516 WP_000724021 type IV conjugative transfer system lipoprotein TraV traV
HS504_RS00580 (pVM01_p111) 120651..120971 - 321 WP_001057280 conjugal transfer protein TrbD -
HS504_RS00585 (pVM01_p112) 120958..121548 - 591 WP_000002785 conjugal transfer pilus-stabilizing protein TraP -
HS504_RS00590 (pVM01_p113) 121538..122965 - 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
HS504_RS00595 (pVM01_p114) 122965..123693 - 729 WP_001230786 type-F conjugative transfer system secretin TraK traK
HS504_RS00600 (pVM01_p115) 123680..124246 - 567 WP_000399792 type IV conjugative transfer system protein TraE traE
HS504_RS00605 (pVM01_p116) 124268..124579 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
HS504_RS00610 (pVM01_p117) 124594..124953 - 360 WP_000994785 type IV conjugative transfer system pilin TraA -
HS504_RS00615 (pVM01_p118) 124986..125387 - 402 WP_001369361 conjugal transfer relaxosome DNA-bindin protein TraY -
HS504_RS00620 (pVM01_p119) 125480..126169 - 690 WP_000283372 conjugal transfer transcriptional regulator TraJ -
HS504_RS00625 (pVM01_p120) 126356..126739 - 384 WP_001151524 conjugal transfer relaxosome DNA-binding protein TraM -
HS504_RS00630 (pVM01_p121) 127060..127662 + 603 WP_000243703 transglycosylase SLT domain-containing protein virB1
HS504_RS00635 (pVM01_p122) 127959..128780 - 822 WP_001234469 DUF932 domain-containing protein -
HS504_RS00640 128900..129097 - 198 WP_052318758 hypothetical protein -
HS504_RS00805 129075..129329 - 255 WP_000547972 hypothetical protein -
HS504_RS00810 129399..129572 + 174 Protein_131 hypothetical protein -
HS504_RS00815 129570..129800 - 231 WP_071587244 hypothetical protein -
HS504_RS00645 130020..130145 - 126 WP_250697071 type I toxin-antitoxin system Hok family toxin -
HS504_RS00820 130087..130236 - 150 Protein_134 plasmid maintenance protein Mok -
HS504_RS00775 130258..130446 + 189 WP_001299721 hypothetical protein -
HS504_RS00650 (pVM01_p126) 130415..131177 - 763 Protein_136 plasmid SOS inhibition protein A -
HS504_RS00655 (pVM01_p127) 131174..131608 - 435 WP_000845953 conjugation system SOS inhibitor PsiB -

Host bacterium

ID   749 GenBank   NC_010409
Plasmid name   pVM01 Incompatibility group   IncFIB
Plasmid size   151002 bp Coordinate of oriT [Strand]   126811..127100 [+]
Host baterium   Escherichia coli

Cargo genes

Drug resistance gene   sitABCD
Virulence gene   Plasmid pVM01 is essential for virulence in avian pathogenic Escherichia coli (APEC) strain E3 in chickens after aerosol exposure and contains the virulence-associated genes iucA, iss and tsh in distinct regions.
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -