Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100909
Name   oriT_pEC422_4 in_silico
Organism   Escherichia coli strain Ecol_422
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NZ_CP018958 (18003..18452 [-], 450 nt)
oriT length   450 nt
IRs (inverted repeats)      IR1: 201..215, 222..236  (ATTCATTGGTGAATC..GATTCACCAATGAAT)
 IR2: 308..315, 318..325  (GCAAAAAC..GTTTTTGC)
Location of nic site      334..335
Conserved sequence flanking the
  nic site    		  GTGGGGTGT|GG
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 450 nt

>oriT_pEC422_4
ATATGTATACCTCTTTATTTTCTTATCGCATCAAATTTATTTCACATATAAAAAAATGACAATTCATCGATGAATCGAATCGTGACGCAAGTTACGAAAATTACGATTCATGCAGCAAATCACATCACGAATTGAATCTAGAGTCAATTCGCTTTAACTCGTTGTTTTATTATTACTGATTCATCTATGAGTTGCGTTAAATTCATTGGTGAATCATATGCGATTCACCAATGAATCCTTTTTATAATGTAAAATAAATTAAAATACATTATTTAAAACATAAGTTAATGATTCAAATAGCAAATCAGCAAAAACTTGTTTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTTGAGCCTTTTAGTGGAGTGGGTTAAATTATTTACGGATAAAGTCACCAGAGGTGGAAAAATGAAAAAATGGATGTTAGCAATCT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   980 GenBank   WP_078207716
Name   TraI_pEC422_4 insolico UniProt ID   _
Length   1756 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 191839.44 Da        Isoelectric Point: 5.6862

>WP_078207716.1 conjugative transfer relaxase/helicase TraI [Escherichia coli]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRIMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFVASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDVMTVVVPGRAEPATLPVADSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLESAISHQKSALHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMETLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPASERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGETFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWENNPDALALVDNVYHRIAGISRDDGLITLEDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQEQAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVF
EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTELAVRDIAGQERDRADITEREAALPESVLRESQREQEAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

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)

AAA domain (AAA_30)

(968-1156)


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 17518..47108

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
BE933_RS00145 (BE933_00150) 12880..13134 + 255 WP_001230709 hypothetical protein -
BE933_RS00150 (BE933_00155) 13131..13373 + 243 WP_000151456 hypothetical protein -
BE933_RS00160 (BE933_00165) 13944..14237 + 294 WP_000673428 hypothetical protein -
BE933_RS00165 (BE933_00170) 14542..14829 + 288 WP_000606467 hypothetical protein -
BE933_RS00175 (BE933_00180) 15257..15490 + 234 WP_000093744 hypothetical protein -
BE933_RS00180 (BE933_00185) 15566..15868 + 303 WP_000379301 hypothetical protein -
BE933_RS00185 (BE933_00190) 16104..16289 + 186 Protein_27 hypothetical protein -
BE933_RS00190 (BE933_00195) 16400..17221 + 822 WP_016235962 DUF932 domain-containing protein -
BE933_RS00195 (BE933_00200) 17518..18165 - 648 WP_016235961 transglycosylase SLT domain-containing protein virB1
BE933_RS00200 (BE933_00205) 18451..18834 + 384 WP_016235960 conjugal transfer relaxosome DNA-binding protein TraM -
BE933_RS00205 (BE933_00210) 19028..19714 + 687 WP_000332487 PAS domain-containing protein -
BE933_RS00210 (BE933_00215) 19808..20035 + 228 WP_001254388 conjugal transfer relaxosome protein TraY -
BE933_RS00215 (BE933_00220) 20069..20434 + 366 WP_016235959 type IV conjugative transfer system pilin TraA -
BE933_RS00220 (BE933_00225) 20449..20760 + 312 WP_000012113 type IV conjugative transfer system protein TraL traL
BE933_RS00225 (BE933_00230) 20782..21348 + 567 WP_016235958 type IV conjugative transfer system protein TraE traE
BE933_RS00230 (BE933_00235) 21335..22063 + 729 WP_032179724 type-F conjugative transfer system secretin TraK traK
BE933_RS00235 (BE933_00240) 22063..23490 + 1428 WP_016235957 F-type conjugal transfer pilus assembly protein TraB traB
BE933_RS00240 (BE933_00245) 23480..24070 + 591 WP_016235956 conjugal transfer pilus-stabilizing protein TraP -
BE933_RS00245 (BE933_00250) 24024..24377 + 354 WP_071602423 conjugal transfer protein TrbD -
BE933_RS00250 (BE933_00255) 24374..24889 + 516 WP_000809905 type IV conjugative transfer system lipoprotein TraV traV
BE933_RS00255 (BE933_00260) 25024..25245 + 222 WP_001278694 conjugal transfer protein TraR -
BE933_RS00260 (BE933_00265) 25405..28032 + 2628 WP_001064239 type IV secretion system protein TraC virb4
BE933_RS00265 (BE933_00270) 28029..28415 + 387 WP_000214082 type-F conjugative transfer system protein TrbI -
BE933_RS00270 (BE933_00275) 28412..29044 + 633 WP_001203720 type-F conjugative transfer system protein TraW traW
BE933_RS00275 (BE933_00280) 29041..30033 + 993 WP_000830190 conjugal transfer pilus assembly protein TraU traU
BE933_RS00280 (BE933_00285) 30063..30368 + 306 WP_000224413 hypothetical protein -
BE933_RS00285 (BE933_00290) 30377..31015 + 639 WP_153302089 type-F conjugative transfer system pilin assembly protein TrbC trbC
BE933_RS00290 (BE933_00295) 31012..32862 + 1851 WP_032241672 type-F conjugative transfer system mating-pair stabilization protein TraN traN
BE933_RS00295 (BE933_00300) 32889..33146 + 258 WP_000864345 conjugal transfer protein TrbE -
BE933_RS00300 (BE933_00305) 33139..33882 + 744 WP_001403429 type-F conjugative transfer system pilin assembly protein TraF traF
BE933_RS00305 (BE933_00310) 33898..34236 + 339 WP_001287905 conjugal transfer protein TrbA -
BE933_RS00310 (BE933_00315) 34363..34647 + 285 WP_000623730 type-F conjugative transfer system pilin chaperone TraQ -
BE933_RS00315 (BE933_00320) 34634..35179 + 546 WP_000059832 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
BE933_RS00320 (BE933_00325) 35109..35450 + 342 WP_153302090 P-type conjugative transfer protein TrbJ -
BE933_RS00325 (BE933_00330) 35398..35823 + 426 WP_078207714 F-type conjugal transfer protein TrbF -
BE933_RS00330 (BE933_00335) 35810..37183 + 1374 WP_001137364 conjugal transfer pilus assembly protein TraH traH
BE933_RS00335 (BE933_00340) 37180..38793 + 1614 Protein_57 conjugal transfer mating pair stabilization protein TraG -
BE933_RS00340 (BE933_00345) 38879..39625 - 747 WP_001016257 IS21-like element ISEc12 family helper ATPase IstB -
BE933_RS00345 (BE933_00350) 39640..41181 - 1542 WP_002431311 IS21-like element ISEc12 family transposase -
BE933_RS00350 (BE933_00355) 41374..42582 + 1209 Protein_60 conjugal transfer protein TraG -
BE933_RS00355 (BE933_00360) 42615..43136 + 522 WP_000632668 conjugal transfer entry exclusion protein TraS -
BE933_RS00360 (BE933_00365) 43161..43892 + 732 WP_000850429 conjugal transfer complement resistance protein TraT -
BE933_RS00365 (BE933_00370) 44095..44832 + 738 WP_000199909 hypothetical protein -
BE933_RS00370 (BE933_00375) 44883..47108 + 2226 WP_078207715 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   1368 GenBank   NZ_CP018958
Plasmid name   pEC422_4 Incompatibility group   IncFIC(FII)
Plasmid size   53198 bp Coordinate of oriT [Strand]   18003..18452 [-]
Host baterium   Escherichia coli strain Ecol_422

Cargo genes

Drug resistance gene   -
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -