Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100765
Name   oriT_F128-(DHB4) in_silico
Organism   Escherichia coli K-12 strain K-12 DHB4
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NZ_CP014271 (137766..138055 [-], 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_F128-(DHB4)
CGCACCGCTAGCAGCGCCCCTAGCGGTATCCTATAAAAAAACACACCGCGCCGCTAGCAGCACCCCTAATATAAAATAATGTTTTTTATAAAAATAGTCAGTACCACCCCTACAAAACGGTGTCGGCGCGTTGTTGTAGCCGCGCCGACACCGCTTTTTTAAATATCATAAAGAGAGTAAGAGAAACTAATTTTTCATAACACTCTATTTATAAAGAAAAATCAGCAAAAACTTGTTTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAGAACCACCAACCTGTTGAGCCT

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   837 GenBank   WP_000987005
Name   TraI_F128-(DHB4) insolico UniProt ID   _
Length   1756 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 192015.91 Da        Isoelectric Point: 5.8951

>WP_000987005.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQTIREAVGEDASLKSRDVAALDTRKSKQHVDPEIKMAEWMQT
LKETGFDIRAYRDAADQRADLRTLTPGPASQDGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNMKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGLPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVSDSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KTRAGETSLETAISHQKSALHTPAQQAIHLALPVVESKKLAFSMVDLLTEAKSFAAEGTGFTELGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVMPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDVREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALVLVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTREIRPGQEQAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVF
EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQERDRAAITEREAALPEGVLREPQRVREAVREIARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

TrwC relaxase (TrwC)

(10-283)

DNA helicase TraI (TraI_C)

(1434-1557)

AAA domain (AAA_30)

(969-1156)

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

(575-625)

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: 137204..163605

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
DHB4_RS23300 (DHB4_23295) 133200..133634 + 435 WP_000845928 conjugation system SOS inhibitor PsiB -
DHB4_RS23305 (DHB4_23300) 133631..134393 + 763 Protein_140 plasmid SOS inhibition protein A -
DHB4_RS27380 134567..134716 + 150 Protein_141 DUF5431 family protein -
DHB4_RS23315 (DHB4_23310) 134658..134783 + 126 WP_096937776 type I toxin-antitoxin system Hok family toxin -
DHB4_RS27095 (DHB4_23315) 135084..135380 - 297 Protein_143 hypothetical protein -
DHB4_RS27100 (DHB4_23320) 135450..135656 + 207 WP_000547965 hypothetical protein -
DHB4_RS23330 (DHB4_23325) 135681..135968 + 288 WP_000107542 hypothetical protein -
DHB4_RS23335 (DHB4_23330) 136087..136908 + 822 WP_001234417 DUF932 domain-containing protein -
DHB4_RS23340 (DHB4_23335) 137204..137806 - 603 WP_077763528 transglycosylase SLT domain-containing protein virB1
DHB4_RS23345 (DHB4_23340) 138127..138510 + 384 WP_001151527 conjugal transfer relaxosome DNA-binding protein TraM -
DHB4_RS23350 (DHB4_23345) 138697..139386 + 690 WP_000283385 conjugal transfer transcriptional regulator TraJ -
DHB4_RS23355 (DHB4_23350) 139485..139880 + 396 WP_001309237 conjugal transfer relaxosome DNA-bindin protein TraY -
DHB4_RS23360 (DHB4_23355) 139913..140278 + 366 WP_000994779 type IV conjugative transfer system pilin TraA -
DHB4_RS23365 (DHB4_23360) 140293..140604 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
DHB4_RS23370 (DHB4_23365) 140626..141192 + 567 WP_000399792 type IV conjugative transfer system protein TraE traE
DHB4_RS23375 (DHB4_23370) 141179..141907 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
DHB4_RS23380 (DHB4_23375) 141907..143334 + 1428 WP_000146685 F-type conjugal transfer pilus assembly protein TraB traB
DHB4_RS23385 (DHB4_23380) 143324..143914 + 591 WP_000002792 conjugal transfer pilus-stabilizing protein TraP -
DHB4_RS23390 (DHB4_23385) 143901..144098 + 198 WP_001443030 conjugal transfer protein TrbD -
DHB4_RS23395 (DHB4_23390) 144110..144361 + 252 WP_001038342 conjugal transfer protein TrbG -
DHB4_RS23400 (DHB4_23395) 144358..144873 + 516 WP_010892541 type IV conjugative transfer system lipoprotein TraV traV
DHB4_RS25700 145008..145229 + 222 WP_001278689 conjugal transfer protein TraR -
DHB4_RS23405 (DHB4_23400) 145389..148016 + 2628 WP_001064243 type IV secretion system protein TraC virb4
DHB4_RS23410 (DHB4_23405) 148013..148399 + 387 WP_000099690 type-F conjugative transfer system protein TrbI -
DHB4_RS23415 (DHB4_23410) 148396..149028 + 633 WP_001203720 type-F conjugative transfer system protein TraW traW
DHB4_RS23420 (DHB4_23415) 149025..150017 + 993 WP_000830185 conjugal transfer pilus assembly protein TraU traU
DHB4_RS23425 (DHB4_23420) 150026..150664 + 639 WP_000777688 type-F conjugative transfer system pilin assembly protein TrbC trbC
DHB4_RS23430 (DHB4_23425) 150661..152469 + 1809 WP_000821835 type-F conjugative transfer system mating-pair stabilization protein TraN traN
DHB4_RS23435 (DHB4_23430) 152496..152753 + 258 WP_000864318 conjugal transfer protein TrbE -
DHB4_RS23440 (DHB4_23435) 152746..153489 + 744 WP_001030367 type-F conjugative transfer system pilin assembly protein TraF traF
DHB4_RS23445 (DHB4_23440) 153505..153852 + 348 WP_001287913 conjugal transfer protein TrbA -
DHB4_RS23450 (DHB4_23445) 153854..154168 - 315 WP_000415566 protein ArtA -
DHB4_RS23455 (DHB4_23450) 154249..154533 + 285 WP_000624109 type-F conjugative transfer system pilin chaperone TraQ -
DHB4_RS23460 (DHB4_23455) 154520..155065 + 546 WP_000059850 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
DHB4_RS23465 (DHB4_23460) 154995..155336 + 342 WP_001443031 P-type conjugative transfer protein TrbJ -
DHB4_RS23470 (DHB4_23465) 155323..155703 + 381 WP_001366201 F-type conjugal transfer protein TrbF -
DHB4_RS23475 (DHB4_23470) 155703..157076 + 1374 WP_021553026 conjugal transfer pilus assembly protein TraH traH
DHB4_RS23480 (DHB4_23475) 157073..159889 + 2817 WP_001007055 conjugal transfer mating-pair stabilization protein TraG traG
DHB4_RS25705 159922..160443 + 522 WP_000632670 conjugal transfer entry exclusion protein TraS -
DHB4_RS23490 (DHB4_23485) 160468..161199 + 732 WP_000850422 conjugal transfer complement resistance protein TraT -
DHB4_RS23495 (DHB4_23490) 161452..163605 + 2154 WP_000009350 type IV conjugative transfer system coupling protein TraD virb4
DHB4_RS23500 (DHB4_23495) 163614..164012 - 399 WP_000911324 type II toxin-antitoxin system VapC family toxin -
DHB4_RS23505 (DHB4_23500) 164012..164239 - 228 WP_000450532 toxin-antitoxin system antitoxin VapB -

Host bacterium

ID   1225 GenBank   NZ_CP014271
Plasmid name   F128-(DHB4) Incompatibility group   IncFIC
Plasmid size   232954 bp Coordinate of oriT [Strand]   137766..138055 [-]
Host baterium   Escherichia coli K-12 strain K-12 DHB4

Cargo genes

Drug resistance gene   -
Virulence gene   yagV/ecpE, yagW/ecpD, yagX/ecpC, yagY/ecpB, yagZ/ecpA, ykgK/ecpR
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -