Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100666
Name   oriT_pC5-A in_silico
Organism   Escherichia coli strain C5
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NZ_CP010123 (63390..63893 [+], 504 nt)
oriT length   504 nt
IRs (inverted repeats)      176..185, 188..197  (ATAGGGTCGT..ACGCCCCTAT)
 265..272, 275..282  (GCAAAAAC..GTTTTTGC)
Location of nic site      291..292
Conserved sequence flanking the
  nic site    		  GTGGGGTGT|GG
Note   predicted by the oriTfinder

  oriT sequence  


Download         Length: 504 nt

>oriT_pC5-A
TTTTACTCTAAATACGCATAGAGTATTCATAAGAAAGAAGAACGCTCCTAGCGGCGCTCCTAGGATCATCCTATAAAAAATTGCGATCCGCCGCTAGAGGCGGCACTAATATATCACAATGTTTTTCATAAAAAATGTCAGTACTGATCCTAATCAGAGTCGTCACAGGATCACCATAGGGTCGTCAACGACCCTATTTAATAATGTAAAATAAATTAAAATACATTATTTAGAACATAAGCTAATGATTCAGAAAACAAATCAGCAAAAACTTGTTTTTGCGTGGGGTGTGGTGCTTTTGGTGGTGAGAACCACCAACTAGTTGAGCCTTATTGTGGAGTAGGTTAAATTATTTCCGGATAATGTCACCAGAGGTGAAAAAATGAAAAAGTGGATGTTAGCAATCTGCCTGATGTTTATAAATGGGATCTGCGAAGCCGCCGATTGCTTTGATCTTGCAGGTCGGGATTACAAAATAGACCCGGATTTACTGAGAGCGATATC

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   738 GenBank   WP_073521273
Name   TraI_pC5-A insolico UniProt ID   A0A1L4J5E1
Length   1756 a.a. PDB ID   
Note   putative relaxase

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 192124.89 Da        Isoelectric Point: 5.9177

>WP_073521273.1 conjugative transfer relaxase/helicase TraI [Escherichia coli]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSVMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSSRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEIKMTEWMQT
LKETGFDIRAYRDAAEQRAETRTQAPGAVSLEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTIGILPPE
EGVIERARAGIDEAISREQLIPLDREKGLFTSWIHVLDELSVRALSRDIMKQNRVTVHPEKSVSRTAGYS
DAVSVLAQDRPPLAIVSGQGGAAGQRERVAELAMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQILITDSGQRTGTGSALMAMKDAGVNIYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQVILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVGDSLFTALKL
ESGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETSLETAISHQKSALHTPAQQAIHLALPVVESKNLAFSHVDLLTEAKSFAAEGTSFADLGREINA
QIKRGDLLHVDVAKGYGTDLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETPDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWVPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGGRKQMAGFESAYVALSRMKQHVQVYTDDRQGWTDAINNAVQKGTAHDVL
EPKADREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTTDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQERDRAAITEREAALPESVLREPQREREAVREVARENLLQERLQQMERDMVRDLQKE
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)

(969-1156)


  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 34961..61372

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
RG28_RS28465 (RG28_27090) 34961..37150 - 2190 WP_073521274 type IV conjugative transfer system coupling protein TraD virb4
RG28_RS28470 (RG28_27095) 37402..38133 - 732 WP_073521275 conjugal transfer complement resistance protein TraT -
RG28_RS28475 (RG28_27100) 38147..38656 - 510 WP_000628099 conjugal transfer entry exclusion protein TraS -
RG28_RS28480 (RG28_27105) 38653..41499 - 2847 WP_073521276 conjugal transfer mating-pair stabilization protein TraG traG
RG28_RS28485 (RG28_27110) 41496..42869 - 1374 WP_073521353 conjugal transfer pilus assembly protein TraH traH
RG28_RS32600 (RG28_27115) 42856..43248 - 393 WP_249530987 F-type conjugal transfer protein TrbF -
RG28_RS32605 43202..43517 - 316 Protein_46 P-type conjugative transfer protein TrbJ -
RG28_RS28495 (RG28_27120) 43507..44052 - 546 WP_073521277 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
RG28_RS28500 (RG28_27125) 44039..44323 - 285 WP_040089429 type-F conjugative transfer system pilin chaperone TraQ -
RG28_RS28505 (RG28_27130) 44404..44718 + 315 WP_000415566 protein ArtA -
RG28_RS28510 (RG28_27135) 44720..45067 - 348 WP_073521278 conjugal transfer protein TrbA -
RG28_RS28515 (RG28_27140) 45083..45826 - 744 WP_001030378 type-F conjugative transfer system pilin assembly protein TraF traF
RG28_RS28520 (RG28_27145) 45819..46076 - 258 WP_073521279 conjugal transfer protein TrbE -
RG28_RS28525 (RG28_27150) 46103..47965 - 1863 WP_249530988 type-F conjugative transfer system mating-pair stabilization protein TraN traN
RG28_RS28530 (RG28_27155) 48201..48581 - 381 WP_039052469 hypothetical protein -
RG28_RS28535 (RG28_27160) 48578..49216 - 639 WP_040089490 type-F conjugative transfer system pilin assembly protein TrbC trbC
RG28_RS28540 (RG28_27165) 49244..49696 - 453 WP_057698276 hypothetical protein -
RG28_RS28545 (RG28_27170) 49689..50024 - 336 WP_057698277 hypothetical protein -
RG28_RS28550 (RG28_27175) 50053..51045 - 993 WP_073521280 conjugal transfer pilus assembly protein TraU traU
RG28_RS28555 (RG28_27180) 51042..51674 - 633 WP_001203720 type-F conjugative transfer system protein TraW traW
RG28_RS28560 (RG28_27185) 51671..52057 - 387 WP_073521281 type-F conjugative transfer system protein TrbI -
RG28_RS28565 (RG28_27190) 52054..54684 - 2631 WP_073521282 type IV secretion system protein TraC virb4
RG28_RS31575 (RG28_27195) 54811..55173 - 363 WP_000836688 hypothetical protein -
RG28_RS28575 (RG28_27200) 55170..55574 - 405 WP_073521283 hypothetical protein -
RG28_RS28580 (RG28_27205) 55571..55789 - 219 WP_000556751 hypothetical protein -
RG28_RS28585 (RG28_27210) 55868..56344 - 477 WP_073521284 hypothetical protein -
RG28_RS28590 (RG28_27215) 56337..56558 - 222 WP_001756934 conjugal transfer protein TraR -
RG28_RS28595 (RG28_27220) 56693..57208 - 516 WP_073521285 type IV conjugative transfer system lipoprotein TraV traV
RG28_RS28600 (RG28_27225) 57205..57456 - 252 WP_073521286 conjugal transfer protein TrbG -
RG28_RS28605 (RG28_27230) 57449..57769 - 321 WP_001057291 DUF2689 domain-containing protein virb4
RG28_RS28610 (RG28_27235) 57756..58340 - 585 WP_040089506 conjugal transfer pilus-stabilizing protein TraP -
RG28_RS28615 (RG28_27240) 58351..59758 - 1408 Protein_71 F-type conjugal transfer pilus assembly protein TraB -
RG28_RS28620 (RG28_27245) 59758..60486 - 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
RG28_RS28625 (RG28_27250) 60473..61039 - 567 WP_000399797 type IV conjugative transfer system protein TraE traE
RG28_RS28630 (RG28_27255) 61061..61372 - 312 WP_000012125 type IV conjugative transfer system protein TraL traL
RG28_RS28635 (RG28_27260) 61387..61746 - 360 WP_019842731 type IV conjugative transfer system pilin TraA -
RG28_RS28640 (RG28_27265) 61780..62007 - 228 WP_001254386 conjugal transfer relaxosome protein TraY -
RG28_RS28645 (RG28_27270) 62101..62787 - 687 WP_073521287 PAS domain-containing protein -
RG28_RS28650 (RG28_27275) 62974..63357 - 384 WP_073521288 conjugal transfer relaxosome DNA-binding protein TraM -
RG28_RS28655 (RG28_27280) 63712..64281 + 570 Protein_79 transglycosylase SLT domain-containing protein -
RG28_RS28660 (RG28_27285) 64578..65399 - 822 WP_001234447 DUF932 domain-containing protein -
RG28_RS28665 (RG28_27290) 65508..65804 - 297 WP_001272251 hypothetical protein -
RG28_RS28670 (RG28_27295) 65828..66034 - 207 WP_000547959 hypothetical protein -

Host bacterium

ID   1126 GenBank   NZ_CP010123
Plasmid name   pC5-A Incompatibility group   IncFIC
Plasmid size   214445 bp Coordinate of oriT [Strand]   63390..63893 [+]
Host baterium   Escherichia coli strain C5

Cargo genes

Drug resistance gene   -
Virulence gene   virulence-associated protein VagC
Metal resistance gene   copper resistance
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -