CodY regulon and binding site collection in Streptococcus salivarius 57.I

CodY - UniProtKB: A0A074IWI7 regulon and binding site collection of Streptococcus salivarius 57.I

Sites are listed as curated.

AAATTTCTGAAAATT

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

AAATTTCTGAAAATT

Motif structure	Direct repeat
GC-content	13.33%
Regulatory mode	Activation	Repression	Dual	Not specified
Regulatory mode	0%	100%	0%	0%
TF conformation	Monomer	Dimer	Tetramer	Other	Not specified
TF conformation	0%	0%	0%	0%	100%
Binding site type	Motif-associated	Variable-motif-associated	Non-motif-associated
Binding site type	1	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_017594.1	A0A074IWI7	not specified	AAATTTCTGAAAATT	-[1866396:1866410]	Experimental technique details Ad-hoc quantitative phenotype observation (ECO:0005676) Ad-hoc quantitative phenotype observation - ECO:0005676 A quantifiable phenotypic trait (e.g. glucose intake) is assessed in a quantitative manner after induction of the regulatory mechanism and used as a natural reporter.. The observable phenotypic trait should be described in the experimental notes. - Experimental technique details CAT reporter gene assays (ECO:0005617) CAT reporter gene assays - ECO:0005617 A reporter assay based on the fusion of a promoter of interest with the cat gene, which produces chloramphenicol acetyltransferase, capable of being acetylated by acetyl CoA. The amount of acetylated chloramphenicol is directly proportional to the amount of CAT enzyme present. - Experimental technique details ChIP-PCR (ECO:0005620) ChIP-PCR - ECO:0005620 ChIP-chip (and to a lesser degree ChIP-Seq) results are often validated with ChIP-PCR, in which a PCR with specific primers is performed on the pulled-down DNA. As in the case of RNASeq, there are many variations of these main techniques. - 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 EMSA (ECO:0001807) EMSA - ECO:0001807 Electro-mobility shift-assays (or gel retardation assays) are a standard way of assessing TF-binding. A fragment of DNA of interest is amplified and labeled with a fluorophore. The fragment is left to incubate in a solution containing abundant TF and non-specific DNA (e.g. randomly cleaved DNA from salmon sperm, of all things) and then a gel is run with the incubated sample and a control (sample that has not been in contact with the TF). If the TF has bound the sample, the complex will migrate more slowly than unbound DNA through the gel, and this retarded band can be used as evidence of binding. The unspecific DNA ensures that the binding is specific to the fragment of interest and that any non-specific DNA-binding proteins left-over in the TF purification will bind there, instead of on the fragment of interest. EMSAs are typically carried out in a bunch of fragments, shown as multiple double (control+experiment) lanes in a wide picture. Certain additional controls are run in at least one of the fragments to ascertain specificity. In the most basic of these, specific competitor (the fragment of interest or a known positive control, unlabelled) is added to the reaction. This should sequester the TF and hence make the retardation band disappear, proving that the binding is indeed specific	ureI (Ssal_01903) , ureA (Ssal_01902) , ureB (Ssal_01901) , ureC (Ssal_01900) , ureE (Ssal_01898) , ureF (Ssal_01897) , ureG (Ssal_01896) , ureD (Ssal_01895) , ureM (Ssal_01894) , ureQ (Ssal_01892) , ureO (Ssal_01891) , Ssal_01904	837	24951785

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.

AAATTTCTGAAAATT

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

AAATTTCTGAAAATT

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.