Welcome to the Calmodulation database and meta-analysis target site predictor. Calmodulin (CaM) is a ubiquitous intracellular calcium sensor that directly binds to and modulates a wide variety of enzymes, ion channels, and membrane transport proteins. CaM communicates changes in intracellular calcium levels by binding to consensus sites known as CaM-binding motifs in both the presence and absence of calcium. Canonical CaM-binding motifs are defined by the varied spacing of hydrophobic anchors [FILVWY]; thus, identifying the potential sites by sequence gazing is challenging.

This site uses a straightforward script to identify all of the canonical (14 currently) CaM target sites from an entered sequence and predicts CaM binding sites based on the density of canonical CaM binding sites within in a given sequence. A charge discriminator reduces the misidentification of hydrophobic stretches (e.g. transmembrane domains) as potential CaM binding sites...more

Welcome to the Calmodulation database and meta-analysis target site predictor. Calmodulin (CaM) is a ubiquitous intracellular calcium sensor that directly binds to and modulates a wide variety of enzymes, ion channels, and membrane transport proteins. CaM communicates changes in intracellular calcium levels by binding to consensus sites known as CaM-binding motifs in both the presence and absence of calcium. Canonical CaM-binding motifs are defined by the varied spacing of hydrophobic anchors [FILVWY]; thus, identifying the potential sites by sequence gazing is challenging.

This site uses a straightforward script to identify all of the canonical (14 currently) CaM target sites from an entered sequence and predicts CaM binding sites based on the density of canonical CaM binding sites within in a given sequence. A charge discriminator reduces the misidentification of hydrophobic stretches (e.g. transmembrane domains) as potential CaM binding sites.

In addition to entering a sequence {Sequence Search}, the meta-analysis can be performed on a specific PDB file by either entering the RSCB code {PDB Search} or by clicking on any hyperlinked RSCB code. The Calmodulation Database can be searched to find target peptides derived from a specific gene, protein, organism, or type of membrane transport protein. Lastly, the database can be searched to find target peptides that contain a specific CaM binding Motif. This “motif” search only determines whether a motif is present and does not indicate that CaM is binding to these motifs in the structure. A description of the different canonical CaM binding motifs can be found here.

The Sequence Search allows you to enter a protein sequence to find all of the canonical CaM target sites. In addition, it predicts CaM binding sites based on the number of overlapping canonical CaM motifs. A sample output for the CaV1.2 Pre-IQ and IQ regions can be viewed by clicking here. Text files containing the "wiggle file" and list of CaM binding motifs can be downloaded after the search. Below describes each input box or parameter.

Enter Query Sequence: Type or paste the sequence to be searched. Most non-amino acid chacters will be stripped and the sequence concatenated.
Sequence Name: Name of protein sequence (optional)
List Motifs By: Sorts the output list by either the type of motif (e.g. 1-10, 1-12, 1-14, 1-16, IQ, etc.) or by residue number.
Starting Residue: Allows the protein sequence to start at a number other than 1.
 
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