HdiR - UniProtKB: Q5M4N8 regulon and binding site collection of Streptococcus thermophilus LMD-9


Sites are listed as curated.

GTTAGTTTATAAACTAAC
GTTAGTTTATAAACAAAC
GTTAGTTTATAAGCTAAC
GTAAGTTAATAAACTAAC

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

GTTAGTTTATAAACTAAC
GTTAGTTTATAAACAAAC
GTTAGTTTATAAGCTAAC
GTTAGTTTATTAACTTAC

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_008532.1 Q5M4N8 dimer GTTAGTTTATAAACTAAC +[490619:490636] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) STER_0543 , STER_0544
    ... ... STER_0543 STER_0544
    587 23204467
    NC_008532.1 Q5M4N8 dimer GTTAGTTTATAAACAAAC +[63309:63326] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) STER_0076 , recA (STER_0077)
    ... ... STER_0076 recA
    587 23204467
    NC_008532.1 Q5M4N8 dimer GTTAGTTTATAAGCTAAC +[1247295:1247312] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) STER_1339 , STER_1338
    ... ... STER_1339 STER_1338
    587 23204467
    NC_008532.1 Q5M4N8 dimer GTAAGTTAATAAACTAAC -[848145:848162] Experimental technique details Consensus search (ECO:0005624) - Experimental technique details DNA-array expression analysis (ECO:0005525) STER_0918 , rbgA (STER_0919) , rnhB (STER_0920) , STER_0921 , STER_0922
    ... ... STER_0918 rbgA rnhB STER_0921 STER_0922
    587 23204467

    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.

    GTTAGTTTATAAACTAAC
    GTTAGTTTATAAACAAAC
    GTTAGTTTATAAGCTAAC
    GTAAGTTAATAAACTAAC

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

    GTTAGTTTATAAACTAAC
    GTTAGTTTATAAACAAAC
    GTTAGTTTATAAGCTAAC
    GTTAGTTTATTAACTTAC
    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.