TraR - UniProtKB: P54294 regulon and binding site collection of Agrobacterium fabrum str. C58


Sites are listed as curated.

ACGTGCAGATTTGCACCT
TTGTGCAGATCTGCACTT
TTGTGCAGATCTGCACTT
ATGTGCAGATCTGCACGT

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

ACGTGCAGATTTGCACCT
AAGTGCAGATCTGCACAA
AAGTGCAGATCTGCACAA
ACGTGCAGATCTGCACAT

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_003065.3 P54294 dimer ACGTGCAGATTTGCACCT +[51927:51944] Experimental technique details Beta-gal reporter assay - Experimental technique details EMSA (ECO:0001807) - Experimental technique details Site directed mutagenesis (ECO:0005667) traI (Atu6042) , trbB (Atu6041) , trbC (Atu6040) , trbD (Atu6039) , trbE (Atu6038) , trbJ (Atu6037) , trbK (Atu6036) , trbL (Atu6035) , trbF (Atu6034) , trbG (Atu6033) , trbH (Atu6032) , trbI (Atu6031) , Atu6030 , repA (Atu6043) , repB (Atu6044)
    ... ... traI trbB trbC trbD trbE trbJ trbK trbL trbF trbG trbH trbI Atu6030 repA repB
    955 17376086
    NC_003065.3 P54294 dimer TTGTGCAGATCTGCACTT +[52018:52035] Experimental technique details Beta-gal reporter assay - Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) repA (Atu6043) , repB (Atu6044) , traI (Atu6042) , trbB (Atu6041) , trbC (Atu6040) , trbD (Atu6039) , trbE (Atu6038) , trbJ (Atu6037) , trbK (Atu6036) , trbL (Atu6035) , trbF (Atu6034) , trbG (Atu6033) , trbH (Atu6032) , trbI (Atu6031) , Atu6030
    ... ... repA repB traI trbB trbC trbD trbE trbJ trbK trbL trbF trbG trbH trbI Atu6030
    1032 12753196
    NC_003065.3 P54294 dimer TTGTGCAGATCTGCACTT +[52018:52035] 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) repA (Atu6043) , repB (Atu6044) , traI (Atu6042) , trbB (Atu6041) , trbC (Atu6040) , trbD (Atu6039) , trbE (Atu6038) , trbJ (Atu6037) , trbK (Atu6036) , trbL (Atu6035) , trbF (Atu6034) , trbG (Atu6033) , trbH (Atu6032) , trbI (Atu6031) , Atu6030
    ... ... repA repB traI trbB trbC trbD trbE trbJ trbK trbL trbF trbG trbH trbI Atu6030
    1032 12753196
    NC_003065.3 P54294 not specified ATGTGCAGATCTGCACGT +[143802:143819] Experimental technique details DNAse footprinting (ECO:0005631) - Experimental technique details EMSA (ECO:0001807) - Experimental technique details In-vitro transcription (ECO:0001204) traC (Atu6126) , traD (Atu6125) , traG (Atu6124) , Atu6123 , traA (Atu6127) , traF (Atu6128) , traB (Atu6129) , traH (Atu6130)
    ... ... traC traD traG Atu6123 traA traF traB traH
    1033 10220379

    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.

    ACGTGCAGATTTGCACCT
    TTGTGCAGATCTGCACTT
    TTGTGCAGATCTGCACTT
    ATGTGCAGATCTGCACGT

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

    ACGTGCAGATTTGCACCT
    AAGTGCAGATCTGCACAA
    AAGTGCAGATCTGCACAA
    ACGTGCAGATCTGCACAT
    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.