HdiR regulon and binding site collection in Streptococcus thermophilus LMD-9

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

Motif structure	Inverted repeat
GC-content	23.61%
Regulatory mode	Activation	Repression	Dual	Not specified
Regulatory mode	0%	100%	0%	0%
TF conformation	Monomer	Dimer	Tetramer	Other	Not specified
TF conformation	0%	100%	0%	0%	0%
Binding site type	Motif-associated	Variable-motif-associated	Non-motif-associated
Binding site type	4	0	0

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) Consensus search - ECO:0005624 This is a weak form of in-silico search, in which the consensus sequence for the motif is compared to genomic positions and the number of mismatches (between candidate site and consensus) is used as a measure of site-quality. - Experimental technique details DNA-array expression analysis (ECO:0005525) DNA-array expression analysis - ECO:0005525 DNA-arrays (or DNA-chips or microarrays) are flat slabs of glass, silicon or plastic onto which thousands of multiple short single-stranded (ss) DNA sequences (corresponding to small regions of a genome) have been attached. After performing a mRNA extraction in induced and non-induced cells, the mRNA is again reverse transcribed, but here the reaction is tweaked, so that the emerging cDNA contains nucleotides marked with different fluorophores for controls and experiment. Targets will hybridize by base-pairing with those probes that resemble them the most. The array can then be stimulated by a laser and scanned for fluorescence at two different wavelengths (control and induced). The ratio or log-ratio between the two fluorescence intensities corresponds to the induction level.	STER_0543 , STER_0544	587	23204467
NC_008532.1	Q5M4N8	dimer	GTTAGTTTATAAACAAAC	+[63309:63326]	Experimental technique details Consensus search (ECO:0005624) Consensus search - ECO:0005624 This is a weak form of in-silico search, in which the consensus sequence for the motif is compared to genomic positions and the number of mismatches (between candidate site and consensus) is used as a measure of site-quality. - Experimental technique details DNA-array expression analysis (ECO:0005525) DNA-array expression analysis - ECO:0005525 DNA-arrays (or DNA-chips or microarrays) are flat slabs of glass, silicon or plastic onto which thousands of multiple short single-stranded (ss) DNA sequences (corresponding to small regions of a genome) have been attached. After performing a mRNA extraction in induced and non-induced cells, the mRNA is again reverse transcribed, but here the reaction is tweaked, so that the emerging cDNA contains nucleotides marked with different fluorophores for controls and experiment. Targets will hybridize by base-pairing with those probes that resemble them the most. The array can then be stimulated by a laser and scanned for fluorescence at two different wavelengths (control and induced). The ratio or log-ratio between the two fluorescence intensities corresponds to the induction level.	STER_0076 , recA (STER_0077)	587	23204467
NC_008532.1	Q5M4N8	dimer	GTTAGTTTATAAGCTAAC	+[1247295:1247312]	Experimental technique details Consensus search (ECO:0005624) Consensus search - ECO:0005624 This is a weak form of in-silico search, in which the consensus sequence for the motif is compared to genomic positions and the number of mismatches (between candidate site and consensus) is used as a measure of site-quality. - Experimental technique details DNA-array expression analysis (ECO:0005525) DNA-array expression analysis - ECO:0005525 DNA-arrays (or DNA-chips or microarrays) are flat slabs of glass, silicon or plastic onto which thousands of multiple short single-stranded (ss) DNA sequences (corresponding to small regions of a genome) have been attached. After performing a mRNA extraction in induced and non-induced cells, the mRNA is again reverse transcribed, but here the reaction is tweaked, so that the emerging cDNA contains nucleotides marked with different fluorophores for controls and experiment. Targets will hybridize by base-pairing with those probes that resemble them the most. The array can then be stimulated by a laser and scanned for fluorescence at two different wavelengths (control and induced). The ratio or log-ratio between the two fluorescence intensities corresponds to the induction level.	STER_1339 , STER_1338	587	23204467
NC_008532.1	Q5M4N8	dimer	GTAAGTTAATAAACTAAC	-[848145:848162]	Experimental technique details Consensus search (ECO:0005624) Consensus search - ECO:0005624 This is a weak form of in-silico search, in which the consensus sequence for the motif is compared to genomic positions and the number of mismatches (between candidate site and consensus) is used as a measure of site-quality. - Experimental technique details DNA-array expression analysis (ECO:0005525) DNA-array expression analysis - ECO:0005525 DNA-arrays (or DNA-chips or microarrays) are flat slabs of glass, silicon or plastic onto which thousands of multiple short single-stranded (ss) DNA sequences (corresponding to small regions of a genome) have been attached. After performing a mRNA extraction in induced and non-induced cells, the mRNA is again reverse transcribed, but here the reaction is tweaked, so that the emerging cDNA contains nucleotides marked with different fluorophores for controls and experiment. Targets will hybridize by base-pairing with those probes that resemble them the most. The array can then be stimulated by a laser and scanned for fluorescence at two different wavelengths (control and induced). The ratio or log-ratio between the two fluorescence intensities corresponds to the induction level.	STER_0918 , rbgA (STER_0919) , rnhB (STER_0920) , 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

To generate the weblogo, aligned binding sites are used.

	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.