Detailed information of oriT

oriT

The information of the oriT region


oriTDB ID   100036
Name   oriT_pEST4011 in_silico
Organism   Achromobacter denitrificans
Sequence Completeness      intact
NCBI accession of oriT (coordinates [strand])   NC_005793 (74354..74453 [+], 100 nt)
oriT length   100 nt
IRs (inverted repeats)      14..31, 36..53  (GTGAAGATAGATAACCGG..CCGGTTAGCTAACTTCAC)
Location of nic site      61..62
Conserved sequence flanking the
  nic site    		  TATCCTG|C
Note   _

  oriT sequence  


Download         Length: 100 nt

>oriT_pEST4011
GAATAAGGGGATAGTGAAGATAGATAACCGGCTTTCCGGTTAGCTAACTTCACCTATCCTGCCCGCCTTTCGGCGGTATGAACACCAAGGAAAGCATACA

Visualization of oriT structure

  oriT secondary structure

Predicted by RNAfold.

Download structure file

  Reference


[1] Vedler E et al. (2004) The completely sequenced plasmid pEST4011 contains a novel IncP1 backbone and a catabolic transposon harboring tfd genes for 2,4-dichlorophenoxyacetic acid degradation. J Bacteriol. 186(21):7161-74. [PMID:15489427]


Relaxase

ID   35 GenBank   NP_990929
Name   TraI_pEST4011 insolico UniProt ID   Q6QHL4
Length   730 a.a. PDB ID   
Note   relaxase

  Relaxase protein sequence


Download         Length: 730 a.a.        Molecular weight: 80105.51 Da        Isoelectric Point: 10.3299

>NP_990929.1 TraI (plasmid) [Achromobacter denitrificans]
MIAKHVSMKTVQKSDFAGLVKYITDEQAKNERVGYVAVTNCHTDRPEVAITEVLNTQAQNTRSGADKTYH
LIVSFRPGEQPDDATLKAIEARICEGLGFGEHQRVSAVHHDTDNLHIHIAINKIHPTRYTILEPFNAYHT
LGQLCEKLEREYSLERDNHQGNKLVSEGRAQDMERHASVESLQGWVKRECAADMQAAQSWDALHQVMRDN
GLELRERGNGFVIQAADGLDVKASSIGREFSKAKLEERLGTFEPSAEHLERAAQKPRKQYDKKPVRSRVN
TVELHAKYKADQLTISGSRTAEWEKARAKKDRLIEAAKRSGRLKRSTIKLISGAGVGKKLMYSATSKTMK
SEIEKINKQYLKERQEIHEKYQRRAWADWLRAKAAEGDQEALGALRARDAAQGLKGNTVAGTGPLRPQAA
AAEQDSVTKKGTIIYRVGPTAVRDDGDRLKVSRGADQDGMQAALRMAMDRYGDRISVGGTPAFKEQIAQA
AAASKLPITFDDDALERRRQELLTQATTKENDHDRTDRGRAAGGGISGSGPAIAAIPGAARAGQPRAAAA
GRTTKPNVGRVGRKPPPQSQNRLRRLSQLGVVQLASGSEVLLPRHVPGDVEQQGAKPVDGLRRDIFGPGR
LSPQVAAAADKYIAEREGKRLKGFDIPKHSRYTDGQDGAATFAGIRQVEGQSLALLTRGEEVMVLPVDEP
TARRLKRLAVGDAITVTPQGSIKTTKGRSR

  Protein domains


Predicted by InterproScan.

Large polyvalent protein-associated domain 7 (LPD7)

(424-512)

Relaxase/Mobilisation nuclease domain (Relaxase)

(13-250)


  Protein structure


Source ID Structure
AlphaFold DB Q6QHL4

  Reference


[1] Vedler E et al. (2004) The completely sequenced plasmid pEST4011 contains a novel IncP1 backbone and a catabolic transposon harboring tfd genes for 2,4-dichlorophenoxyacetic acid degradation. J Bacteriol. 186(21):7161-74. [PMID:15489427]


Auxiliary protein

ID   53 GenBank   NP_990930
Name   TraH_pEST4011 insolico UniProt ID   Q6QHL3
Length   108 a.a. PDB ID   _
Note   relaxosome stabilization

  Auxiliary protein sequence


Download         Length: 108 a.a.        Molecular weight: 11836.18 Da        Isoelectric Point: 3.8732

>NP_990930.1 TraH (plasmid) [Achromobacter denitrificans]
MTEPTEDELLEAALAAVDQPLPQSPEPPEPDSHEPPQPDGPPSPTLAALDESRRPKAKTVCEDCPNSVWF
SSPAEVKCYCRVMFLVTWSNKEPNQLTACDGIFLGQED

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB Q6QHL3

  Reference


[1] Vedler E et al. (2004) The completely sequenced plasmid pEST4011 contains a novel IncP1 backbone and a catabolic transposon harboring tfd genes for 2,4-dichlorophenoxyacetic acid degradation. J Bacteriol. 186(21):7161-74. [PMID:15489427]

ID   54 GenBank   NP_990932
Name   TraJ_pEST4011 insolico UniProt ID   Q6QHL1
Length   129 a.a. PDB ID   _
Note   oriT recognizing protein; required for relaxase activity

  Auxiliary protein sequence


Download         Length: 129 a.a.        Molecular weight: 14479.81 Da        Isoelectric Point: 10.3612

>NP_990932.1 TraJ (plasmid) [Achromobacter denitrificans]
MAKTRNSDDPRMPTRKAGRHLRVPVLPDEEAEIKRLAASVGLPVAAYLRNVGLGYQVPGILDNKRVEELA
RINGDLGRLGGLLKLWLTDDVRTLQFGETTILALLSRIESTQDRMHEVMQEVVTPRVKR

  Protein domains



No domain identified.



  Protein structure


Source ID Structure
AlphaFold DB Q6QHL1

  Reference


[1] Vedler E et al. (2004) The completely sequenced plasmid pEST4011 contains a novel IncP1 backbone and a catabolic transposon harboring tfd genes for 2,4-dichlorophenoxyacetic acid degradation. J Bacteriol. 186(21):7161-74. [PMID:15489427]

ID   55 GenBank   NP_990933
Name   TraK_pEST4011 insolico UniProt ID   Q6QHL0
Length   132 a.a. PDB ID   _
Note   oriT-binding protein; constitutes a part of relaxosome, necessary for nicking at oriT

  Auxiliary protein sequence


Download         Length: 132 a.a.        Molecular weight: 14780.98 Da        Isoelectric Point: 10.4315

>NP_990933.1 TraK (plasmid) [Achromobacter denitrificans]
MPKSYPEELAEWVKKREATRPRQDKNVVAFLALKSDVQDAIAAGYSLLTIWEHLHEKGKIPYRYETFLKH
VRRHIKGRPPAVVDGQPSTPPDPPRPPAAGKTAAPRPQQPTKSAPAPAGFKFDSQPKKEDLL

  Protein domains


Predicted by InterproScan.

Family of unknown function (DUF5338) (DUF5338)

(7-74)


  Protein structure


Source ID Structure
AlphaFold DB Q6QHL0

  Reference


[1] Vedler E et al. (2004) The completely sequenced plasmid pEST4011 contains a novel IncP1 backbone and a catabolic transposon harboring tfd genes for 2,4-dichlorophenoxyacetic acid degradation. J Bacteriol. 186(21):7161-74. [PMID:15489427]


T4CP

ID   35 GenBank   NP_990928
Name   TraG_pEST4011 insolico UniProt ID   Q6QHL5
Length   637 a.a. PDB ID   _
Note   DNA transport during conjugation; connects relaxosome and Mpf complex

  T4CP protein sequence


Download         Length: 637 a.a.        Molecular weight: 69663.89 Da        Isoelectric Point: 9.0430

>NP_990928.1 TraG (plasmid) [Achromobacter denitrificans]
MTKDRFNNAVGPQVRAEKEGPGKVIPALAVLSLGGGLQAATQFFAHDFKYQAALGAHINHIYPPWGIVQW
AGKWYGQYPDAFMRAGSIGVTITGVGLISLVVAKMVLANSSKVNEYLHGSARWANVRDIQAAGLIPRARS
FWQTITGKDAAASSGVYVGAWIDKKGKQHYLRHNGPEHVLCYAPTRSGKGVGLVVPTLLSWGHSAVITDL
KGELWALTAGWRQKHAKNKVLRFEPATASGSVCWNPLDEIRLGTENEVGDVQNLATLIVDPDGKGLESHW
QKTSQALLVGVILHALYKAKAEGTPATLPGVDAMLADPNRDIGELWMEMTTYSHVDGQVHPVVGSAARDM
MDRPDEEAGSVLSTAKSYLALYRDPIVARNVSKSEFKIKDLMHHDNAVSLYIVTQANDKARLRPLVRVMV
NMIVRLLADKMDFENGRPVAHYKHRMLMMLDEFPSLGKLEIMQESLAFVAGYGIKCYLICQDINQLKSRE
TGYGHDESITSNCHVQNAYPPNRVETAEHLSKLTGQTTVAKEQITTSGRRTSALLGQVSRTIQEVQRPLL
TPDECLRMPGPVKTEGGDIAKAGDMVVYVAGYPAIYGKQPLYFQDPTFQARAAIPAPKNSDKLRNSFVAP
AGEGITI

  Protein domains


Predicted by InterproScan.

Type IV secretory system Conjugative DNA transfer (T4SS-DNA_transf)

(122-620)

  Protein structure


Source ID Structure
AlphaFold DB Q6QHL5

  Reference


[1] Vedler E et al. (2004) The completely sequenced plasmid pEST4011 contains a novel IncP1 backbone and a catabolic transposon harboring tfd genes for 2,4-dichlorophenoxyacetic acid degradation. J Bacteriol. 186(21):7161-74. [PMID:15489427]


Host bacterium

ID   35 GenBank   NC_005793
Plasmid name   pEST4011 Incompatibility group   IncP1
Plasmid size   76958 bp Coordinate of oriT [Strand]   74354..74453 [+]
Host baterium   Achromobacter denitrificans

Cargo genes

Drug resistance gene   _
Virulence gene   _
Metal resistance gene   _
Degradation gene   linF
Symbiosis gene   -
Anti-CRISPR   AcrIF24, AcrIIA9