Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   103264
Name   oriT_pECF12 in_silico
Organism   Escherichia coli strain DH286F
Sequence Completeness      -
NCBI accession of oriT (coordinates [strand])   NZ_KY865322 (40577..40700 [+], 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_pECF12
GGTTGGTGGTTCTCACCACCAAAAGCACCACACCCCACGCAAAAACAAGTTTTTGCTGATTTGCTTTTTGAATCATTAGCTTATGTTTTAAATAATGTATTTTAATTTATTTTACATTATTAAA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file


Relaxase

ID   2440 GenBank   WP_172690587
Name   traI_HTM59_RS00465_pECF12 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: 192022.96 Da        Isoelectric Point: 6.0017

>WP_172690587.1 conjugative transfer relaxase/helicase TraI [Escherichia coli]
MMSIAQVRSAGSAGNYYTDKDNYYVLGSMGERWAGRGAEQLGLQGSVDKDVFTRLLEGRLPDGADLSRMQ
DGSNRHRPGYDLTFSAPKSVSMMAMLGGDKRLIDAHNQAVDFAVRQVEALASTRVMTDGQSETVLTGNLV
MALFNHDTSRDQEPQLHTHAVVANVTQHNGEWKTLSSDKVGKTGFIENVYANQIAFGRLYREKLKEQVEA
LGYETEVVGKHGMWEMPGVPVEAFSGRSQAIREAVGEDASLKSRDVAALDTRKSKQHVDPEVRMAEWMQT
LKETGFDIRAYRDAADQRAETRTQAPGAVSQEGPDVQQAVTQAIAGLSERKVQFTYTDVLARTVGILPPE
NGVIERARAGIDEAISREQLIPLDREKGLFTSGIHVLDELSVRALSRDIMKQNRVTVHPEKSVPRTAGYS
DAVSVLAQDRPSLAIVSGQGGAAGQRERVAELVMMAREQGREVQIIAADRRSQMNLKQDERLSGELITGR
RQLPEGMAFTPGSTVIVDQGEKLSLKETLTLLDGAARHNVQVLITDSGQRTGTGSALMAMKDAGVNIYRW
QGGEQRPATIISEPDRNVRYARLAGDFAASVKAGEESVAQVSGVREQAILTQAIRSELKTQGVLGHPEVT
MTALSPVWLDSRSRYLRDMYRPGMVMEQWNPETRSHDRYVIDRVTAQSHSLTLRDVQGETQVVRISSLDS
SWSLFRPEKMPVADGERLRVTGKIPGLRVSGGDRLQVASVSEDAMTVVVPGRAEPATLPVADSPFTALKL
ENGWVETPGHSVSDSAKVFASVTQMAMDNATLNGLARSGRDVRLYSSLDETRTAEKLARHPSFTVVSEQI
KARAGETLLETAISLQKAGIHTPAQQAIHLALPVLESKNLAFSMVDLLTEAKSFAAEGTSFTDLGGEINA
QIKRGDLLYVDVAKGYGTGLLVSRASYEAEKSILRHILEGKEAVTPLMERVPGELMEKLTSGQRAATRMI
LETSDRFTVVQGYAGVGKTTQFRAVMSAVNMLPESERPRIVGLGPTHRAVGEMRSAGVDAQTLASFLHDT
QLQQRSGETPDFSNTLFLLDESSMVGNTDMARAYALIAAGGGRAVASGDTDQLQAIAPGQPFRLQQTRSA
ADVAIMKEIVRQTPELREAVYSLINRDVERALSGLESVKPSQVPRQEGAWVPEHSVTEFSHSQEAKLAEA
QQKAMLKGEAFPDIPMTLYEAIVRDYTGRTPEAREQTLIVTHLNEDRRVLNSMIHDAREKAGELGKEQVM
VPVLNTANIRDGELRRLSTWETHRDALALVDNVYHRIAGISRDDGLITLQDAEGNTRLISPREAVAEGVT
LYTPDKIRVGTGDRMRFTKSDRERGYVANSVWTVTAVSGDSVTLSDGQQTRVIRPAQEQAEQHIDLAYAI
TAHGAQGASETFAIALEGTEGNRKLMAGFESAYVALSRMKQHVQVYTDNRQGWTDAINNAVQKGTAHDVL
EPKPDREVMNAERLFSTARELRDVAAGRAVLRQAGLAGGDSPARFIAPGRKYPQPYVALPAFDRNGKSAG
IWLNPLTSDDGNGLRGFSGEGRVKGSGDAQFVALQGSRNGESLLADNMQDGVRIARDNPDSGVVVRIAGE
GRPWNPGAITGGRVWGDIPDNSVQPGAGNGEPVTAEVLAQRQAEEAIRRETERRADEIVRKMAENKPDLP
DGKTEQAVREIAGQVRERAAITERETALPESVLREPQREREAVREVARENLLQERLQQMERDMVRDLQKE
KTLGGD

  Protein domains


Predicted by InterproScan.

AAA domain (AAA_30)

(969-1156)

DNA helicase TraI (TraI_C)

(1434-1557)

TrwC relaxase (TrwC)

(10-283)

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

(575-626)

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

(633-712)


  Protein structure



No available structure.




Auxiliary protein

ID   1038 GenBank   WP_000124981
Name   WP_000124981_pECF12 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

ID   1039 GenBank   WP_001254386
Name   WP_001254386_pECF12 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


T4CP

ID   2207 GenBank   WP_015059012
Name   traC_HTM59_RS00355_pECF12 insolico UniProt ID   _
Length   875 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 875 a.a.        Molecular weight: 99393.22 Da        Isoelectric Point: 6.3465

>WP_015059012.1 MULTISPECIES: type IV secretion system protein TraC [Gammaproteobacteria]
MNNPLEAVTQAVNSLVTALKLPDESAKANEVLGEMSFPQFSRLLPYRDYNQESGLFMNDTTMGFMLEAIP
INGANESIVEALDHMLRTKLPRGVPFCIHLMSSQLVGDRIEYGLREFSWSGEQAERFNAITRAYYMNAAA
TQFPLPEGMNLPLTLRHYRVFFSYCSPSKKKSRADILEMENLVKIIRASLQGASITTQAVDAQAFIDIVG
EMINHNPDSLYPKRRQLDPYSDLNYQCVEDSFDLKVRADYLTLGLRENGRNSTARILNFHLARNPEIAFL
WNMADNYSNLLNPEMSISCPFILTLTLVVEDQVKTHSEANLKYMDLEKKSKTSYAKWFPSVEKEAKEWGE
LRQRLGSGQSSVVSYFLNITAFCKDNNETALEVEQDILNSFRKNGFELISPRFNHMRNFLTCLPFMAGKG
LFKQLKEAGVVQRAESFNVANLMPLVADNPLTPAGLLAPTYRNQLAFIDIFFKGMNNTNYNMAVCGTSGA
GKTGLIQPLIRSVLDSGGFAVVFDMGDGYKSLCENMGGVYLDGETLRFNPFANITDIDQSAERVRDQLSV
MASPNGNLDEVHEGLLLQAVRASWLAKKKQARIDDVVDFLKNARDNDQYVESPTIRSRLDEMIVLLDQYT
ANGTYGRYFNSDEPSLRDDARMVVLELGGLEDRPSLLVAVMFSLIIYIENRMYRTPRNLKKLNVIDEGWR
LLDFKNRKVGEFIQKGYRTCRRHTGAYITITQNIVDFDSDKASSAARAAWGNSSYKIILKQSAKEFAKYN
QLYPDQFLPLQRDMIGKFGAAKDQWFSSFLLQVENHSSWHRLFVDPLSRAMYSSDGPDFEFVQQKRKEGL
SIHEAVWQLAWKKSGPEMASLEAWLEEHEKYRSVA

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5934) (DUF5934)

(290-446)

TraG P-loop domain (P-loop_TraG)

(467-771)

TraC protein (TraC_F_IV)

(38-276)

  Protein structure



No available structure.



ID   2208 GenBank   WP_021573169
Name   traD_HTM59_RS00460_pECF12 insolico UniProt ID   _
Length   735 a.a. PDB ID   _
Note   Predicted by oriTfinder 2.0

  T4CP protein sequence


Download         Length: 735 a.a.        Molecular weight: 83553.19 Da        Isoelectric Point: 5.0504

>WP_021573169.1 MULTISPECIES: type IV conjugative transfer system coupling protein TraD [Gammaproteobacteria]
MSFNAKDMTQGGQIASMRIRMFSQIANIMLYCLFIFFWILVGLVLWVKISWQTFVNGCIYWWCTTLEGMR
DLIKSQPVYEIQYYGKTFRMNAAQVLHDKYMIWCGEQLWSAFVLATVVALVICLITFFVVSWILGRQGKQ
QSENEVTGGRQLTDNPKDVARMLKKDGKDSDIRIGDLPIIRDSEIQNFCLHGTVGAGKSEVIRRLANYAR
QRGDMVVIYDRSGEFVKSYYDPSIDKILNPLDARCAAWDLWKECLTQPDFDNTANTLIPMGTKEDPFWQG
SGRTIFAEAAYLMRNDPNRSYSKLVDTLLSIKIEKLRTFLRNSPAANLVEEKIEKTAISIRAVLTNYVKA
IRYLQGIEHNGESFTIRDWMRGVREDQKNGWLFISSNADTHASLKPVISMWLSIAIRGLLAMGENRNRRV
WFFCDELPTLHKLPDLVEILPEARKFGGCYVFGIQSYAQLEDIYGEKAAATLFDVMNTRAFFRSPSHKIA
EFAAGEIGEKEHLKASEQYSYGADPVRDGVSTGKDMERQTLVSYSDIQSLPDLTCYVTLPGPYPAVKLSL
KYQARPKVAPEFIPRDINPEMENRLSAVLAAREAEGRQMASLFEPDVPEVVSGEDVTQAEQPQQPQQPQQ
PQQPQQPQQPQQPVSPAINDKKSDSGVNVPAGGIEQELKMKPEEEMEQQLPPGISESGEVVDMAAYEAWQ
QENHPDIQQQMQRREEVNINVHRERGEDVEPGDDF

  Protein domains


Predicted by InterproScan.

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

(173-560)

F sex factor protein N terminal (TraD_N)

(32-128)

  Protein structure



No available structure.




T4SS

T4SS were predicted by using oriTfinder2.

Region 1: 40005..68175

Locus tag Coordinates Strand Size (bp) Protein ID Product Description
HTM59_RS00510 35094..35390 - 297 Protein_49 hypothetical protein -
HTM59_RS00255 35890..36120 + 231 WP_000218642 hypothetical protein -
HTM59_RS00260 36172..37533 + 1362 WP_000170695 DUF3560 domain-containing protein -
HTM59_RS00265 37580..38143 + 564 WP_015059007 class I SAM-dependent methyltransferase -
HTM59_RS00525 38143..38400 + 258 Protein_53 hypothetical protein -
HTM59_RS00275 38480..38776 + 297 WP_001272251 hypothetical protein -
HTM59_RS00280 38887..39708 + 822 WP_001234445 DUF932 domain-containing protein -
HTM59_RS00285 40005..40652 - 648 WP_015059008 transglycosylase SLT domain-containing protein virB1
HTM59_RS00290 40929..41312 + 384 WP_000124981 conjugal transfer relaxosome DNA-binding protein TraM -
HTM59_RS00295 41503..42189 + 687 WP_015059009 PAS domain-containing protein -
HTM59_RS00300 42283..42510 + 228 WP_001254386 conjugal transfer relaxosome protein TraY -
HTM59_RS00305 42544..42909 + 366 WP_021519752 type IV conjugative transfer system pilin TraA -
HTM59_RS00310 42924..43235 + 312 WP_000012106 type IV conjugative transfer system protein TraL traL
HTM59_RS00315 43257..43823 + 567 WP_000399794 type IV conjugative transfer system protein TraE traE
HTM59_RS00320 43810..44538 + 729 WP_001230787 type-F conjugative transfer system secretin TraK traK
HTM59_RS00325 44538..45965 + 1428 WP_032297072 F-type conjugal transfer pilus assembly protein TraB traB
HTM59_RS00330 45955..46545 + 591 WP_000002778 conjugal transfer pilus-stabilizing protein TraP -
HTM59_RS00335 46532..46729 + 198 WP_001324648 conjugal transfer protein TrbD -
HTM59_RS00340 46741..46992 + 252 WP_001038341 conjugal transfer protein TrbG -
HTM59_RS00345 46989..47504 + 516 WP_000809902 type IV conjugative transfer system lipoprotein TraV traV
HTM59_RS00350 47639..47860 + 222 WP_001278692 conjugal transfer protein TraR -
HTM59_RS00355 48020..50647 + 2628 WP_015059012 type IV secretion system protein TraC virb4
HTM59_RS00360 50644..51030 + 387 WP_015059013 type-F conjugative transfer system protein TrbI -
HTM59_RS00365 51027..51659 + 633 WP_001203735 type-F conjugative transfer system protein TraW traW
HTM59_RS00370 51656..52648 + 993 WP_000830838 conjugal transfer pilus assembly protein TraU traU
HTM59_RS00375 52675..52983 + 309 WP_000412447 hypothetical protein -
HTM59_RS00380 53046..53567 + 522 WP_015059014 hypothetical protein -
HTM59_RS00385 53594..54232 + 639 WP_000087532 type-F conjugative transfer system pilin assembly protein TrbC trbC
HTM59_RS00390 54229..54600 + 372 WP_000056336 hypothetical protein -
HTM59_RS00395 54626..55048 + 423 WP_001229309 HNH endonuclease signature motif containing protein -
HTM59_RS00400 55045..56895 + 1851 WP_015059015 type-F conjugative transfer system mating-pair stabilization protein TraN traN
HTM59_RS00405 56922..57179 + 258 WP_053913405 conjugal transfer protein TrbE -
HTM59_RS00410 57172..57915 + 744 WP_015059017 type-F conjugative transfer system pilin assembly protein TraF traF
HTM59_RS00415 58076..58312 + 237 WP_000270010 type-F conjugative transfer system pilin chaperone TraQ -
HTM59_RS00420 58299..58844 + 546 WP_000059817 type-F conjugative transfer system pilin assembly thiol-disulfide isomerase TrbB traF
HTM59_RS00425 58834..59148 + 315 WP_001384255 P-type conjugative transfer protein TrbJ -
HTM59_RS00430 59102..59494 + 393 WP_000126338 F-type conjugal transfer protein TrbF -
HTM59_RS00435 59481..60854 + 1374 WP_000944325 conjugal transfer pilus assembly protein TraH traH
HTM59_RS00440 60851..63667 + 2817 WP_015059018 conjugal transfer mating-pair stabilization protein TraG traG
HTM59_RS00445 63700..64221 + 522 WP_000632668 conjugal transfer entry exclusion protein TraS -
HTM59_RS00450 64246..64977 + 732 WP_021559024 conjugal transfer complement resistance protein TraT -
HTM59_RS00455 65180..65917 + 738 WP_015059020 hypothetical protein -
HTM59_RS00460 65968..68175 + 2208 WP_021573169 type IV conjugative transfer system coupling protein TraD virb4

Host bacterium

ID   3707 GenBank   NZ_KY865322
Plasmid name   pECF12 Incompatibility group   IncFII
Plasmid size   77822 bp Coordinate of oriT [Strand]   40577..40700 [+]
Host baterium   Escherichia coli strain DH286F

Cargo genes

Drug resistance gene   fosA3, tet(A), aph(6)-Id, aph(3'')-Ib, sul2, blaCTX-M-55
Virulence gene   -
Metal resistance gene   -
Degradation gene   -
Symbiosis gene   -
Anti-CRISPR   -