Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100252
Name   oriT_pAPEC-O2-R in_silico
Organism   Escherichia coli
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_006671 (39494..39955 [+], 462 nt)
oriT length   462 nt
IRs (inverted repeats)      142..151, 154..163  (ATAGGGTCGT..ACGACCCTAT)
 231..238, 241..248  (GCAAAAAC..GTTTTTGC)
Location of nic site      257..258
Conserved sequence flanking the
  nic site    		  GTGGGGTGT|GG
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 462 nt

>oriT_pAPEC-O2-R
AAGAAGAGCACCCCTAGCAGCGCCCCTAGGGGCATACTATAAAAAAACGCACGGCGCTGCTAGGGGCGGCCCTAATATATCCAAATGTTTTTCATGAAAATTGTCAGTACTGACCCTAACAAGGGTCGTCATAGGGTCGCCATAGGGTCGTCAACGACCCTATTTAATAATGTAAAATAAATTAAAATACATTATTTATAACATAAGCTAATGATTCAAAAAACAAATCAGCAAAAACTTGTTTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTTGAGCCTTTTTGTGGAGTGGGTTAAATTATTTACGGATAAAGTCACCAGAGGTGGAAAAATGAAAAAATGGATGTTAGCCATCTGCTTGATGTTTATAAATGAGATCTGCCATGCCACTGATTGCTTTGATCTTGCAGGCCGGGATTACAAAATAGATCCTGATTTACTGAGA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   323 GenBank   YP_190115
Name   TraI_pAPEC-O2-R insolico UniProt ID   Q5JBP8
Length   1756 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191818.65 Da        Isoelectric Point: 6.0139

>YP_190115.1 conjugal transfer nickase/helicase TraI (plasmid) [Escherichia coli]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGINVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVTSVSEDAMTVVVPGRAEPASLPVADSPFTALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKTGLHTPAQQAIHLALPVVESKNLAFSMVDLLTEAKSFAAEGTSFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLSASERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRLEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISRDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVF
EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVRDIAGLERDRSAISEREAALPESVLREPQRVREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

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

(633-712)

TrwC relaxase (TrwC)

(10-283)

AAA domain (AAA_30)

(969-1156)

DNA helicase TraI (TraI_C)

(1434-1557)

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: 13576..40351

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HS182_RS00075 (O2R_17) 13576..15774 - 2199 WP_011402783 type IV conjugative transfer system coupling protein TraD virb4
HS182_RS00080 (O2R_18) 16027..16758 - 732 WP_000850424 conjugal transfer complement resistance protein TraT -
HS182_RS00085 16790..17293 - 504 WP_000605510 hypothetical protein -
HS182_RS00090 (O2R_20) 17308..20130 - 2823 WP_011251382 conjugal transfer mating-pair stabilization protein TraG traG
HS182_RS00095 (O2R_21) 20127..21500 - 1374 WP_001137358 conjugal transfer pilus assembly protein TraH traH
HS182_RS00100 (O2R_22) 21500..21862 - 363 WP_011251381 P-type conjugative transfer protein TrbJ -
HS182_RS00105 (O2R_23) 21792..22337 - 546 WP_000052618 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HS182_RS00110 (O2R_24) 22324..22608 - 285 WP_000624110 type-F conjugative transfer system pilin chaperone TraQ -
HS182_RS00115 (O2R_25) 22727..23074 - 348 WP_011251380 conjugal transfer protein TrbA -
HS182_RS00120 (O2R_26) 23090..23833 - 744 WP_001030390 type-F conjugative transfer system pilin assembly protein TraF traF
HS182_RS00125 (O2R_27) 23826..24083 - 258 WP_000864328 conjugal transfer protein TrbE -
HS182_RS00130 (O2R_28) 24110..25918 - 1809 WP_011251379 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HS182_RS00135 (O2R_29) 25915..26553 - 639 WP_000777692 type-F conjugative transfer system pilin assembly protein TrbC trbC
HS182_RS00140 (O2R_30) 26562..27554 - 993 WP_001712363 conjugal transfer pilus assembly protein TraU traU
HS182_RS00145 (O2R_31) 27551..28183 - 633 WP_011251377 type-F conjugative transfer system protein TraW traW
HS182_RS00150 (O2R_32) 28180..28566 - 387 WP_011251376 type-F conjugative transfer system protein TrbI -
HS182_RS00155 (O2R_33) 28563..31193 - 2631 WP_011251375 type IV secretion system protein TraC virb4
HS182_RS00160 (O2R_34) 31319..31681 - 363 WP_000836686 hypothetical protein -
HS182_RS00165 (O2R_35) 31709..31924 - 216 WP_000556749 hypothetical protein -
HS182_RS00170 (O2R_36) 32004..32477 - 474 WP_000549595 hypothetical protein -
HS182_RS00175 (O2R_37) 32470..32643 - 174 WP_024262213 conjugal transfer protein TraR -
HS182_RS00180 (O2R_38) 32761..33276 - 516 WP_000809838 type IV conjugative transfer system lipoprotein TraV traV
HS182_RS00185 (O2R_39) 33273..33524 - 252 WP_001038341 conjugal transfer protein TrbG -
HS182_RS00190 (O2R_40) 33521..33838 - 318 WP_001057292 conjugal transfer protein TrbD virb4
HS182_RS00195 (O2R_41) 33835..34407 - 573 WP_000002794 conjugal transfer pilus-stabilizing protein TraP -
HS182_RS00200 (O2R_42) 34397..35824 - 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
HS182_RS00205 (O2R_43) 35824..36552 - 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
HS182_RS00210 (O2R_44) 36539..37105 - 567 WP_011251373 type IV conjugative transfer system protein TraE traE
HS182_RS00215 (O2R_45) 37127..37438 - 312 WP_000012106 type IV conjugative transfer system protein TraL traL
HS182_RS00220 (O2R_46) 37453..37812 - 360 WP_000340272 type IV conjugative transfer system pilin TraA -
HS182_RS00225 (O2R_47) 37846..38073 - 228 WP_001254385 conjugal transfer relaxosome protein TraY -
HS182_RS00230 (O2R_48) 38167..38853 - 687 WP_011251372 PAS domain-containing protein -
HS182_RS00235 (O2R_49) 39044..39427 - 384 WP_000124979 conjugal transfer relaxosome DNA-binding protein TraM -
HS182_RS00240 (O2R_50) 39704..40351 + 648 WP_000615259 transglycosylase SLT domain-containing protein virB1
HS182_RS00245 (O2R_51) 40648..41469 - 822 WP_001234469 DUF932 domain-containing protein -
HS182_RS00250 41590..41877 - 288 WP_000107535 hypothetical protein -
HS182_RS00255 (O2R_53) 41902..42108 - 207 WP_000547971 hypothetical protein -
HS182_RS00590 42178..42351 + 174 Protein_51 hypothetical protein -
HS182_RS00595 42349..42579 - 231 WP_001426396 hypothetical protein -
HS182_RS00260 (O2R_56) 42798..42923 - 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
HS182_RS00600 42865..43014 - 150 Protein_54 plasmid maintenance protein Mok -
HS182_RS00580 43036..43224 + 189 WP_001299721 hypothetical protein -
HS182_RS00265 (O2R_58) 43193..43955 - 763 Protein_56 plasmid SOS inhibition protein A -
HS182_RS00270 (O2R_59) 43952..44386 - 435 WP_000845873 conjugation system SOS inhibitor PsiB -

Host bacterium

ID   714 GenBank   NC_006671
Plasmid name   pAPEC-O2-R Incompatibility group   IncFII
Plasmid size   101375 bp Coordinate of oriT [Strand]   39494..39955 [+]
Host baterium   Escherichia coli

Cargo genes

Drug resistance gene   tet(A), dfrA1, catB3, aadA5, qacE, sul1, blaTEM-1A
Virulence gene   -
Metal resistance gene   silE, silS, silR, silC, silF, silB, silA, silP
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -