AphB - UniProtKB: Q9KT56 regulon and binding site collection of Vibrio cholerae O1 biovar El Tor str. N16961


Sites are listed as curated.

TGTAACTAACTGTTTCA
AACAACCTAAGTTTGCA
AGCAAAATAAACTTACT
TGGAAATCAATATTTCA
TAGAATCTTATATTCCG

Sites are listed after the alignment process. For alignment of variable-length binding sites, LASAGNA is used.

TGTAACTAACTGTTTCA
AACAACCTAAGTTTGCA
AGTAAGTTTATTTTGCT
TGGAAATCAATATTTCA
TAGAATCTTATATTCCG

For the selected transcription factor and species, the list of curated binding sites in the database are displayed below. Gene regulation diagrams show binding sites, positively-regulated genes, negatively-regulated genes, both positively and negatively regulated genes, genes with unspecified type of regulation.

    Genome TF TF conformation Site sequence Site location Experimental techniques Gene regulation Curations PMIDs
    NC_002505.1 Q9KT56 dimer TGTAACTAACTGTTTCA +[825165:825181] Experimental technique details Beta-gal reporter assay - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) VC0770 , VC0769
    ... ... VC0770 VC0769
    56 20562308
    NC_002505.1 Q9KT56 dimer AACAACCTAAGTTTGCA +[283246:283262] Experimental technique details Beta-gal reporter assay - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) VC0278 , zntR (VC0277)
    ... ... VC0278 zntR
    56 20562308
    NC_002505.1 Q9KT56 dimer AGCAAAATAAACTTACT +[2049158:2049174] Experimental technique details Beta-gal reporter assay - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) nhaB (VC1901) , VC1900
    ... ... nhaB VC1900
    56 20562308
    NC_002506.1 Q9KT56 dimer TGGAAATCAATATTTCA -[460986:461002] Experimental technique details Beta-gal reporter assay - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) VCA0526 , VCA0527
    ... ... VCA0526 VCA0527
    57 20562308
    NC_002506.1 Q9KT56 dimer TAGAATCTTATATTCCG +[291157:291173] Experimental technique details Beta-gal reporter assay - Experimental technique details DNA-array expression analysis (ECO:0005525) - Experimental technique details EMSA (ECO:0001807) VCA0274 , VCA0272 , VCA0273
    ... ... VCA0274 VCA0272 VCA0273
    57 20562308

    AphB - UniProtKB: Q9KT56 regulon and binding site collection of Vibrio cholerae O395


    Sites are listed as curated.

    TGCAAAATTAGATTGCA
    TGCAAAATTAGATTGCA
    TGCAACATAATGTGTCA
    TGCAAAATTAGATTGCA

    Sites are listed after the alignment process. For alignment of variable-length binding sites, LASAGNA is used.

    TGCAAAATTAGATTGCA
    TGCAAAATTAGATTGCA
    TGACACATTATGTTGCA
    TGCAAAATTAGATTGCA

    For the selected transcription factor and species, the list of curated binding sites in the database are displayed below. Gene regulation diagrams show binding sites, positively-regulated genes, negatively-regulated genes, both positively and negatively regulated genes, genes with unspecified type of regulation.

      Genome TF TF conformation Site sequence Site location Experimental techniques Gene regulation Curations PMIDs
      NC_009457.1 Q9KT56 dimer TGCAAAATTAGATTGCA +[379498:379514] Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) tcpP (VC0395_A0351) , tcpI (VC0395_A0350) , tcpH (VC0395_A0352)
      ... ... tcpP tcpI tcpH
      44 11489126
      NC_009457.1 Q9KT56 dimer TGCAAAATTAGATTGCA +[379498:379514] Experimental technique details EMSA (ECO:0001807) tcpP (VC0395_A0351) , tcpI (VC0395_A0350) , tcpH (VC0395_A0352)
      ... ... tcpP tcpI tcpH
      51 15225309
      NC_009457.1 Q9KT56 dimer TGCAACATAATGTGTCA -[610686:610702] Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Site directed mutagenesis (ECO:0005667) VC0395_A0567 , VC0395_A0568 , VC0395_A0566
      ... ... VC0395_A0567 VC0395_A0568 VC0395_A0566
      54 11972789
      NC_009457.1 Q9KT56 dimer TGCAAAATTAGATTGCA +[379498:379514] Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Site directed mutagenesis (ECO:0005667) tcpP (VC0395_A0351) , tcpI (VC0395_A0350) , tcpH (VC0395_A0352)
      ... ... tcpP tcpI tcpH
      55 11972789

      All binding sites in split view are combined and a sequence logo is generated. Note that it may contain binding site sequences from different transcription factors and different species. To see individiual sequence logos and curation details go to split view.


      Sites are listed as curated.

      TGCAAAATTAGATTGCA
      TGCAAAATTAGATTGCA
      TGTAACTAACTGTTTCA
      AACAACCTAAGTTTGCA
      AGCAAAATAAACTTACT
      TGCAACATAATGTGTCA
      TGCAAAATTAGATTGCA
      TGGAAATCAATATTTCA
      TAGAATCTTATATTCCG

      Sites are listed after the alignment process. For alignment of variable-length binding sites, LASAGNA is used.

      TGCAAAATTAGATTGCA
      TGCAAAATTAGATTGCA
      TGAAACAGTTAGTTACA
      TGCAAACTTAGGTTGTT
      AGCAAAATAAACTTACT
      TGACACATTATGTTGCA
      TGCAAAATTAGATTGCA
      TGAAATATTGATTTCCA
      CGGAATATAAGATTCTA
      Download data in FASTA format.
      Download data in TSV (tab-separated-value) format. For each binding site, all sources of evidence (i.e. experimental techniques and publication information) are combined into one record.
      Download raw data in TSV format. All reported sites are exported individually.
      Download data in Attribute-Relation File Format (ARFF).
      Download Position-Specific-Frequency-Matrix of the motif in TRANSFAC format.
      Download Position-Specific-Frequency-Matrix of the motif in JASPAR format.
      Download Position-Specific-Frequency-Matrix of the motif in raw FASTA format. The matrix consists of four columns in the order A C G T.