Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100448
Name   oriT_pHK08 in_silico
Organism   Escherichia coli
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_019072 (32605..33154 [-], 550 nt)
oriT length   550 nt
IRs (inverted repeats)      243..255, 257..269  (TATTTAATAATTC..GAATTATTAAATA)
 311..318, 321..328  (GCAAAAAC..GTTTTTGC)
Location of nic site      337..338
Conserved sequence flanking the
  nic site    		  GTAGTGTGT|GG
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 550 nt

>oriT_pHK08
TTACTCTGGCCATAAGATAAAACCTTTCATTATTAAGCAATGAACTTTTCACTATAAATATGCATATAGTGTTTACAAGTAAGAAAGACACTCCTAGCAGCGCCTCTAGGATCATCCTATAAAAAAATGCGATCCGGCGCTAGGGGCGTCCCTAATATATATCAATGTTTTTCATGAAAATTGTCAGTACTGATCCTAATAAGAGTCGCTATAGGGTCGTAACAGGATCGCCAACGACTCTCTATTTAATAATTCAGAATTATTAAATATAAATAGCGTTTGTTAATTACATGATTTAAAACGTAAATCAGCAAAAACTTGTTTTTGCGTAGTGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTTGAGCCTTTTTGTGGAGTGGGTTAAATTATTTACGGATAAAGTCACCAGAGGTGGAAAAATGAAAAAATGGATGTTAGTAATCTGCCTGATGTTTATAAATGGGATCTGCGAAGCCGCCGATTGCTTTGATCTTGCAGGTCGGGATTACAAAATAGACCCGGATTTACTGAGAGCGATATC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   519 GenBank   YP_006953453
Name   TraI_pHK08 insolico UniProt ID   _
Length   1756 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191683.22 Da        Isoelectric Point: 5.6912

>YP_006953453.1 conjugal transfer DNA-nicking and unwinding protein TraI (plasmid) [Escherichia coli]
MLSFSVVKSAGSAGNYYTDKDNYYVLGSMGERWAGQGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQDPQLHTHVVVANVTQHNGEWKTLSSDKVGKTGFSENVLANRIAFGKIYQSELRQRVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAEIRTQAPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLQEGMVFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYDRLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVADSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETSLETAISLQKTGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPASERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVVIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGETFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPDALALVDSVYHRIAGISKDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPDREVMNAQRLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDSSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQERDRADITEREAALPESVLRESQREQEAVREVARENLLQERLQQIERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

DNA helicase TraI (TraI_C)

(1434-1557)

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

(633-712)

TrwC relaxase (TrwC)

(10-283)

AAA domain (AAA_30)

(968-1156)

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: 32217..60261

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HS812_RS00180 (D616_p63045) 27539..27853 + 315 WP_000872086 hypothetical protein -
HS812_RS00465 28043..28156 + 114 Protein_41 DUF5431 family protein -
HS812_RS00185 28101..28223 + 123 WP_223412041 Hok/Gef family protein -
HS812_RS00190 28524..28773 - 250 Protein_43 hypothetical protein -
HS812_RS00195 (D616_p63050) 29069..29392 + 324 WP_000533253 hypothetical protein -
HS812_RS00200 (D616_p63051) 29451..29693 + 243 WP_000540588 hypothetical protein -
HS812_RS00470 29963..30223 + 261 WP_071600428 hypothetical protein -
HS812_RS00210 (D616_p63054) 30694..30990 + 297 WP_015058998 hypothetical protein -
HS812_RS00215 (D616_p63055) 31100..31921 + 822 WP_001234437 DUF932 domain-containing protein -
HS812_RS00220 (D616_p63057) 32217..32819 - 603 WP_000243715 transglycosylase SLT domain-containing protein virB1
HS812_RS00225 (D616_p63058) 33142..33525 + 384 WP_001354030 conjugal transfer relaxosome DNA-binding protein TraM -
HS812_RS00230 (D616_p63059) 33719..34390 + 672 WP_000283561 conjugal transfer transcriptional regulator TraJ -
HS812_RS00235 (D616_p63060) 34527..34754 + 228 WP_000089263 conjugal transfer relaxosome protein TraY -
HS812_RS00240 (D616_p63061) 34787..35146 + 360 WP_001098992 type IV conjugative transfer system pilin TraA -
HS812_RS00245 (D616_p63062) 35161..35472 + 312 WP_000012113 type IV conjugative transfer system protein TraL traL
HS812_RS00250 (D616_p63063) 35494..36060 + 567 WP_000399780 type IV conjugative transfer system protein TraE traE
HS812_RS00255 (D616_p63064) 36047..36775 + 729 WP_001230772 type-F conjugative transfer system secretin TraK traK
HS812_RS00260 (D616_p63065) 36775..38226 + 1452 WP_000146675 F-type conjugal transfer pilus assembly protein TraB traB
HS812_RS00265 (D616_p63066) 38216..38782 + 567 WP_000896599 conjugal transfer pilus-stabilizing protein TraP -
HS812_RS00270 (D616_p63067) 38769..39089 + 321 WP_001057307 conjugal transfer protein TrbD -
HS812_RS00275 (D616_p63068) 39086..39601 + 516 WP_000809881 type IV conjugative transfer system lipoprotein TraV traV
HS812_RS00280 (D616_p63069) 39736..39957 + 222 WP_001278683 conjugal transfer protein TraR -
HS812_RS00285 (D616_p63070) 39950..40426 + 477 WP_000549587 hypothetical protein -
HS812_RS00290 (D616_p63071) 40506..40724 + 219 WP_000556745 hypothetical protein -
HS812_RS00295 (D616_p63072) 40752..41099 + 348 WP_000836682 hypothetical protein -
HS812_RS00300 (D616_p63073) 41225..43855 + 2631 WP_012917677 type IV secretion system protein TraC virb4
HS812_RS00305 (D616_p63074) 43852..44238 + 387 WP_000214084 type-F conjugative transfer system protein TrbI -
HS812_RS00310 (D616_p63075) 44235..44867 + 633 WP_001203728 type-F conjugative transfer system protein TraW traW
HS812_RS00315 (D616_p63076) 44864..45856 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
HS812_RS00320 (D616_p63077) 45886..46191 + 306 WP_000224416 hypothetical protein -
HS812_RS00325 (D616_p63078) 46200..46838 + 639 WP_001080256 type-F conjugative transfer system pilin assembly protein TrbC trbC
HS812_RS00330 (D616_p63079) 46835..48685 + 1851 WP_000821856 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HS812_RS00335 (D616_p63080) 48712..48969 + 258 WP_000864353 conjugal transfer protein TrbE -
HS812_RS00340 (D616_p63081) 48962..49705 + 744 WP_001030371 type-F conjugative transfer system pilin assembly protein TraF traF
HS812_RS00345 (D616_p63082) 49719..50063 + 345 WP_000556796 conjugal transfer protein TrbA -
HS812_RS00350 (D616_p63083) 50182..50466 + 285 WP_000624194 type-F conjugative transfer system pilin chaperone TraQ -
HS812_RS00355 (D616_p63084) 50453..50998 + 546 WP_000059831 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HS812_RS00360 (D616_p63085) 50928..51275 + 348 WP_001309242 P-type conjugative transfer protein TrbJ -
HS812_RS00365 (D616_p63086) 51256..51648 + 393 WP_000660699 F-type conjugal transfer protein TrbF -
HS812_RS00370 (D616_p63087) 51635..53008 + 1374 WP_000944331 conjugal transfer pilus assembly protein TraH traH
HS812_RS00375 (D616_p63088) 53005..55827 + 2823 WP_001007039 conjugal transfer mating-pair stabilization protein TraG traG
HS812_RS00380 (D616_p63089) 55843..56328 + 486 WP_000605870 hypothetical protein -
HS812_RS00385 (D616_p63090) 56377..57108 + 732 WP_000782451 conjugal transfer complement resistance protein TraT -
HS812_RS00390 (D616_p63091) 57311..58048 + 738 WP_000199905 hypothetical protein -
HS812_RS00395 (D616_p63092) 58099..60261 + 2163 WP_015058999 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   909 GenBank   NC_019072
Plasmid name   pHK08 Incompatibility group   IncFII
Plasmid size   69812 bp Coordinate of oriT [Strand]   32605..33154 [-]
Host baterium   Escherichia coli

Cargo genes

Drug resistance gene   blaCTX-M-14
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   AcrIIA7