Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100283
Name   oriT_pAPEC-O1-ColBM in_silico
Organism   Escherichia coli APEC O1
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_009837 (18095..18384 [+], 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_pAPEC-O1-ColBM
AGGCTCAACAGGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTTTCTTTATAAATAGAGTGTTATGAAAAATTAGTTTCTCTTACTCTCTTTATGATATTTAAAAAAGCGGTGTCGGCGCGGCTACAACAACGCGCCGACACCGTTTTGTAGGGGTGGTACTGACTATTTTTATAAAAAACATTATTTTATATTAGGGGTGCTGCTAGCGGCGCGGTGTGTTTTTTTATAGGATACCGCTAGGGGCGCTGCTAGCGGTGCG

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   354 GenBank   WP_000986968
Name   TraI_pAPEC-O1-ColBM insolico UniProt ID   _
Length   1756 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191859.74 Da        Isoelectric Point: 6.1369

>WP_000986968.1 conjugative transfer relaxase/helicase TraI [Escherichia coli]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGKLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQTPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMAFTPGNTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGRPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSNSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPASLPVSDSPFMALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKTGLHTPAQQAIHLALPVVESKNLAFSMVDLLTEAKSFAAEGTSFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLLQRSGETPNFSNTLFLLDESSMVGNTDMARAYSLIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWVPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIGLAYAI
TAHGAQGASETFAIALEGTEGNRKQMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKSDREVMNAERLFSTARELRDVVAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPNSSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVRDIAGLERDRSAISEREAALPESVLREPQRVREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(969-1156)

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

(575-626)

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1434-1557)

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: 17533..43842

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
APECO1_RS25780 (APECO1_O1CoBM17) 13497..13931 + 435 WP_000845949 conjugation system SOS inhibitor PsiB -
APECO1_RS25785 (APECO1_O1CoBM18) 13928..14690 + 763 Protein_18 plasmid SOS inhibition protein A -
APECO1_RS31660 (APECO1_O1CoBM19) 14659..14847 - 189 WP_001299721 hypothetical protein -
APECO1_RS32130 (APECO1_O1CoBM20) 14869..15018 + 150 Protein_20 plasmid maintenance protein Mok -
APECO1_RS25795 (APECO1_O1CoBM20) 14960..15085 + 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
APECO1_RS32135 15305..15535 + 231 WP_001426396 hypothetical protein -
APECO1_RS32140 15533..15706 - 174 Protein_23 hypothetical protein -
APECO1_RS30720 15776..15982 + 207 WP_000547939 hypothetical protein -
APECO1_RS25805 (APECO1_O1CoBM23) 16007..16294 + 288 WP_000107535 hypothetical protein -
APECO1_RS25810 (APECO1_O1CoBM24) 16415..17236 + 822 WP_001234469 DUF932 domain-containing protein -
APECO1_RS25815 (APECO1_O1CoBM25) 17533..18135 - 603 WP_000243709 transglycosylase SLT domain-containing protein virB1
APECO1_RS25820 (APECO1_O1CoBM26) 18456..18839 + 384 WP_001151524 conjugal transfer relaxosome DNA-binding protein TraM -
APECO1_RS25825 (APECO1_O1CoBM27) 19026..19715 + 690 WP_000283385 conjugal transfer transcriptional regulator TraJ -
APECO1_RS25830 (APECO1_O1CoBM28) 19808..20209 + 402 WP_012006553 conjugal transfer relaxosome DNA-bindin protein TraY -
APECO1_RS25835 (APECO1_O1CoBM29) 20242..20607 + 366 WP_000994779 type IV conjugative transfer system pilin TraA -
APECO1_RS25840 (APECO1_O1CoBM30) 20622..20933 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
APECO1_RS25845 (APECO1_O1CoBM31) 20955..21521 + 567 WP_000399792 type IV conjugative transfer system protein TraE traE
APECO1_RS25850 (APECO1_O1CoBM32) 21508..22236 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
APECO1_RS25855 (APECO1_O1CoBM33) 22236..23663 + 1428 WP_000146692 F-type conjugal transfer pilus assembly protein TraB traB
APECO1_RS25860 (APECO1_O1CoBM34) 23653..24243 + 591 WP_000002792 conjugal transfer pilus-stabilizing protein TraP -
APECO1_RS25865 (APECO1_O1CoBM35) 24230..24427 + 198 WP_001324648 conjugal transfer protein TrbD -
APECO1_RS25870 (APECO1_O1CoBM36) 24439..24690 + 252 WP_001038342 conjugal transfer protein TrbG -
APECO1_RS25875 (APECO1_O1CoBM37) 24687..25202 + 516 WP_000809841 type IV conjugative transfer system lipoprotein TraV traV
APECO1_RS29740 (APECO1_O1CoBM38) 25337..25558 + 222 WP_001278689 conjugal transfer protein TraR -
APECO1_RS25885 (APECO1_O1CoBM39) 25718..28345 + 2628 WP_001064247 type IV secretion system protein TraC virb4
APECO1_RS25890 (APECO1_O1CoBM40) 28342..28728 + 387 WP_000097319 type-F conjugative transfer system protein TrbI -
APECO1_RS25895 (APECO1_O1CoBM41) 28725..29357 + 633 WP_001203720 type-F conjugative transfer system protein TraW traW
APECO1_RS25900 (APECO1_O1CoBM42) 29354..30346 + 993 WP_000830187 conjugal transfer pilus assembly protein TraU traU
APECO1_RS25905 (APECO1_O1CoBM43) 30355..30993 + 639 WP_000777688 type-F conjugative transfer system pilin assembly protein TrbC trbC
APECO1_RS25910 (APECO1_O1CoBM44) 30990..32798 + 1809 WP_000821847 type-F conjugative transfer system mating-pair stabilization protein TraN traN
APECO1_RS25915 (APECO1_O1CoBM45) 32825..33082 + 258 WP_000864318 conjugal transfer protein TrbE -
APECO1_RS25920 (APECO1_O1CoBM46) 33075..33818 + 744 WP_001030367 type-F conjugative transfer system pilin assembly protein TraF traF
APECO1_RS25925 (APECO1_O1CoBM47) 33834..34181 + 348 WP_001287911 conjugal transfer protein TrbA -
APECO1_RS25930 (APECO1_O1CoBM48) 34183..34458 - 276 WP_001513501 hypothetical protein -
APECO1_RS25935 (APECO1_O1CoBM49) 34584..34820 + 237 WP_000270010 type-F conjugative transfer system pilin chaperone TraQ -
APECO1_RS25940 (APECO1_O1CoBM50) 34807..35352 + 546 WP_000059833 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
APECO1_RS29745 (APECO1_O1CoBM51) 35282..35623 + 342 WP_001442101 P-type conjugative transfer protein TrbJ -
APECO1_RS32145 35610..36002 + 393 Protein_54 F-type conjugal transfer protein TrbF -
APECO1_RS29755 35989..37363 + 1375 Protein_55 conjugal transfer pilus assembly protein TraH -
APECO1_RS25950 (APECO1_O1CoBM53) 37360..40185 + 2826 WP_001007037 conjugal transfer mating-pair stabilization protein TraG traG
APECO1_RS25955 (APECO1_O1CoBM54) 40182..40691 + 510 WP_000628107 conjugal transfer entry exclusion protein TraS -
APECO1_RS25960 (APECO1_O1CoBM55) 40705..41436 + 732 WP_000850422 conjugal transfer complement resistance protein TraT -
APECO1_RS25965 (APECO1_O1CoBM56) 41689..43842 + 2154 WP_000009325 type IV conjugative transfer system coupling protein TraD virb4
APECO1_RS25970 43851..44249 - 399 WP_000911333 tRNA(fMet)-specific endonuclease VapC -
APECO1_RS25975 44249..44476 - 228 WP_000450520 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   745 GenBank   NC_009837
Plasmid name   pAPEC-O1-ColBM Incompatibility group   IncFIC
Plasmid size   174241 bp Coordinate of oriT [Strand]   18095..18384 [+]
Host baterium   Escherichia coli APEC O1

Cargo genes

Drug resistance gene   sitABCD
Virulence gene   vat, iroN, iroE, iroD, iroC, iroB, iutA, iucC, iucB, iucA
Metal resistance gene   yfeC
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -