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A protein motif is a small section of a protein that has a known function, is folded independently of the rest if the protein, or functions as a docking site.

The metabolism is catalyzed by proteins. A protein's ability to catalyze is determined by the surface it presents to compounds in the cell. After a protein is built from a ProteinEncodingGene, it is folded into a compact shape filled with pockets that serve as docking sites for the compounds to be metabolized. A motif is a small part of the protein's amino acid sequence that plays an important role in the functioning of the pocket.

Because of the folding, the useful parts of a motif can be discontinuous. As a result, when searching for a protein motif, you generally want to specify several small runs of amino acids separated by a certain number of positions whose contents are immaterial. The protein scan function of the tool search allows you to specify a search pattern in which the X letter is used to represent a wild card. An example of using the tool search to find a small motif can be found at FindingADegeneratePeptideMotifInSelectedOrganisms.