Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103062
Name   oriT_pYD786-2 in_silico
Organism   Escherichia coli strain YD786
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KU254579 (37168..37291 [-], 124 nt)
oriT length   124 nt
IRs (inverted repeats)      101..106, 119..124  (TTTAAT..ATTAAA)
 91..99, 113..121  (AATAATGTA..TACATTATT)
 90..95, 107..112  (AAATAA..TTATTT)
 39..46, 49..56  (GCAAAAAC..GTTTTTGC)
 3..10, 15..22  (TTGGTGGT..ACCACCAA)
Location of nic site      _
Conserved sequence flanking the
  nic site    		  _
Note   Predicted by oriTfinder 2.0

  oriT sequence  


Download         Length: 124 nt

>oriT_pYD786-2
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGCTTTTTGAATCATTAGCTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2292 GenBank   WP_103687900
Name   traI_HTG80_RS00045_pYD786-2 insolico UniProt ID   _
Length   1756 a.a. PDB ID   
Note   Predicted by oriTfinder 2.0

  Relaxase protein sequence


Download         Length: 1756 a.a.        Molecular weight: 192060.79 Da        Isoelectric Point: 5.8861

>WP_103687900.1 MULTISPECIES: conjugative transfer relaxase/helicase TraI [Enterobacteriaceae]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNKHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLLEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNTYRW
QGGEQRLATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDAQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVTSVSEDAMTVVVPGRAEPASLPVSDSPFTALKL
ENGWVETPGHSVSDSATVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGEISLETAISLQKAGLHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTSFVDLGREIDA
QIKRGDLLHVDVAKGYGTDLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRVVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQESAWAPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDVPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISKDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDTIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPGQERAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKQMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVF
EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTSDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTELAVREIAGQERDRAAITEREAALPESVLREPQREREAVREVARENLLQERLQQMERDMVRDLQKE
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)

(969-1156)

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

(575-626)


  Protein structure



No available structure.




Auxiliary protein

ID   952 GenBank   WP_001254386
Name   WP_001254386_pYD786-2 insolico UniProt ID   A0A3Z6KJB5
Length   75 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 75 a.a.        Molecular weight: 9005.11 Da        Isoelectric Point: 10.1422

>WP_001254386.1 MULTISPECIES: conjugal transfer relaxosome protein TraY [Gammaproteobacteria]
MRRRNARGGISRTVSVYLDEDTNNRLIKAKDRSGRSKTIEVQIRLRDHLKRFPDFYNEEIFREVTEESES
TFKEL

  Protein domains


Predicted by InterproScan.

TraY domain (TraY)

(14-61)


  Protein structure


Source ID Structure
AlphaFold DB A0A3Z6KJB5

ID   953 GenBank   WP_000124981
Name   WP_000124981_pYD786-2 insolico UniProt ID   A0A630FTW9
Length   127 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  Auxiliary protein sequence


Download         Length: 127 a.a.        Molecular weight: 14542.59 Da        Isoelectric Point: 5.0278

>WP_000124981.1 MULTISPECIES: conjugal transfer relaxosome DNA-binding protein TraM [Gammaproteobacteria]
MARVNLYISNEVHEKINMIVEKRRQEGARDKDISLSGTASMLLELGLRVYDAQMERKESAFNQTEFNKLL
LECVVKTQSTVAKILGIESLSPHVSGNPKFEYASMVDDIREKVSVEMDRFFPKNDDE

  Protein domains


Predicted by InterproScan.

TraM protein, DNA-binding (Tra_M)

(1-126)


  Protein structure


Source ID Structure
AlphaFold DB A0A630FTW9


T4CP

ID   2000 GenBank   WP_130989118
Name   traD_HTG80_RS00050_pYD786-2 insolico UniProt ID   _
Length   740 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 740 a.a.        Molecular weight: 84076.74 Da        Isoelectric Point: 5.0504

>WP_130989118.1 type IV conjugative transfer system coupling protein TraD [Escherichia coli]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTSGKEDPFW
QGSGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTYLRNSPAANLVEEKIEKTAISIRAVLTNYV
KAIRYLQGIEHNGEPFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNR
RVWFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHK
IAEFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKL
SLKYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQP
QQPQQPQQPQQPQQPQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAA
YEAWQQENHPDIQQQMQRREEVNINVHRERGEDVEPGDDF

  Protein domains


Predicted by InterproScan.

F sex factor protein N terminal (TraD_N)

(32-128)

Type IV secretion-system coupling protein DNA-binding domain (TrwB_AAD_bind)

(173-562)

  Protein structure



No available structure.



ID   2001 GenBank   WP_000069764
Name   traC_HTG80_RS00130_pYD786-2 insolico UniProt ID   _
Length   876 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 876 a.a.        Molecular weight: 99302.93 Da        Isoelectric Point: 5.8486

>WP_000069764.1 MULTISPECIES: type IV secretion system protein TraC [Enterobacteriaceae]
MSNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAI
PINGANESIVEALDHMLRTKLPRGVPFCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMNAA
ATQFPLPEGMNLPLTLRHYRVFFSYCSPSKKKSRADILEMENLVKIIRASLQGASITTQAVDAQAFIDIV
GEMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLREKGRNSTARILNFHLARNPEIAF
LWNMADNYSNLLNPELSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWG
ELRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGK
GLFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFRGMNNTNYNMAVCGTSG
AGKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLS
VMASPNGNLDEVHEGLLLQAVRASWLAKENRARIDDVVDFLKNASDSEQYAESPTIRSRLDEMIVLLDQY
TANGTYGQYFNSDEPSLRDDAKMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGW
RLLDFKNHKVGEFIEKGYRTARRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKY
NQLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEG
LSIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

TraC protein (TraC_F_IV)

(39-277)

TraG P-loop domain (P-loop_TraG)

(468-772)

Family of unknown function (DUF5934) (DUF5934)

(290-447)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 11273..37863

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTG80_RS00050 11273..13495 - 2223 WP_130989118 type IV conjugative transfer system coupling protein TraD virb4
HTG80_RS00055 13747..14478 - 732 WP_000850424 conjugal transfer complement resistance protein TraT -
HTG80_RS00060 14492..15001 - 510 WP_000628099 conjugal transfer entry exclusion protein TraS -
HTG80_RS00065 14998..17823 - 2826 WP_001007030 conjugal transfer mating-pair stabilization protein TraG traG
HTG80_RS00070 17820..19193 - 1374 WP_001137358 conjugal transfer pilus assembly protein TraH traH
HTG80_RS00075 19193..19555 - 363 WP_010379880 P-type conjugative transfer protein TrbJ -
HTG80_RS00080 19485..20030 - 546 WP_000060037 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HTG80_RS00085 20017..20301 - 285 WP_000624108 type-F conjugative transfer system pilin chaperone TraQ -
HTG80_RS00090 20420..20767 - 348 WP_001287893 conjugal transfer protein TrbA -
HTG80_RS00095 20783..21526 - 744 WP_001030376 type-F conjugative transfer system pilin assembly protein TraF traF
HTG80_RS00100 21519..21776 - 258 WP_000864325 conjugal transfer protein TrbE -
HTG80_RS00105 21803..23611 - 1809 WP_001567342 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HTG80_RS00110 23608..24246 - 639 WP_029400171 type-F conjugative transfer system pilin assembly protein TrbC trbC
HTG80_RS00115 24255..25247 - 993 WP_000830839 conjugal transfer pilus assembly protein TraU traU
HTG80_RS00120 25244..25876 - 633 WP_001203720 type-F conjugative transfer system protein TraW traW
HTG80_RS00125 25873..26259 - 387 WP_029400173 type-F conjugative transfer system protein TrbI -
HTG80_RS00130 26256..28886 - 2631 WP_000069764 type IV secretion system protein TraC virb4
HTG80_RS00135 29013..29360 - 348 WP_000802783 hypothetical protein -
HTG80_RS00140 29388..29605 - 218 Protein_28 hypothetical protein -
HTG80_RS00145 29685..30161 - 477 WP_000549579 hypothetical protein -
HTG80_RS00150 30154..30375 - 222 WP_001278695 conjugal transfer protein TraR -
HTG80_RS00155 30510..31025 - 516 WP_000809874 type IV conjugative transfer system lipoprotein TraV traV
HTG80_RS00160 31022..31342 - 321 WP_001057307 conjugal transfer protein TrbD -
HTG80_RS00165 31329..31919 - 591 WP_000002784 conjugal transfer pilus-stabilizing protein TraP -
HTG80_RS00170 31909..33336 - 1428 WP_000146657 F-type conjugal transfer pilus assembly protein TraB traB
HTG80_RS00175 33336..34064 - 729 WP_001230798 type-F conjugative transfer system secretin TraK traK
HTG80_RS00180 34051..34617 - 567 WP_000399792 type IV conjugative transfer system protein TraE traE
HTG80_RS00185 34639..34950 - 312 WP_000012103 type IV conjugative transfer system protein TraL traL
HTG80_RS00190 34965..35324 - 360 WP_000340272 type IV conjugative transfer system pilin TraA -
HTG80_RS00195 35358..35585 - 228 WP_001254386 conjugal transfer relaxosome protein TraY -
HTG80_RS00200 35679..36365 - 687 WP_000332484 PAS domain-containing protein -
HTG80_RS00205 36556..36939 - 384 WP_000124981 conjugal transfer relaxosome DNA-binding protein TraM -
HTG80_RS00210 37216..37863 + 648 WP_000614934 transglycosylase SLT domain-containing protein virB1
HTG80_RS00215 38160..38981 - 822 WP_021573168 DUF932 domain-containing protein -
HTG80_RS00220 39098..39385 - 288 WP_000107538 hypothetical protein -
HTG80_RS00225 39636..40640 + 1005 WP_024257664 IS110 family transposase -
HTG80_RS00440 41064..41225 + 162 Protein_46 hypothetical protein -
HTG80_RS00445 41235..41465 - 231 WP_001426396 hypothetical protein -
HTG80_RS00235 41685..41810 - 126 WP_001372321 type I toxin-antitoxin system Hok family toxin -
HTG80_RS00450 41752..41901 - 150 Protein_49 plasmid maintenance protein Mok -
HTG80_RS00240 42080..42842 - 763 Protein_50 plasmid SOS inhibition protein A -

Host bacterium

ID   3505 GenBank   NZ_KU254579
Plasmid name   pYD786-2 Incompatibility group   IncFII
Plasmid size   68812 bp Coordinate of oriT [Strand]   37168..37291 [-]
Host baterium   Escherichia coli strain YD786

Cargo genes

Drug resistance gene   fosA6, floR
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -