Protein sequence motif

A protein sequence motif is a characteristic pattern of amino acid residues in a protein sequence. A pattern can specify fixed residues, alternatives and variable-length or wildcard positions. It is a statement about residue order; it need not specify a complete protein structural motif or independently establish biochemical function. PROSITE documents such signatures together with their interpretation and matching syntax.^[ref]

For an original example, use the invented four-residue pattern D-x(2)-[ST]: an initial D, any two residues, then S or T. With 20 possible standard amino acids, it admitsstrings out of $20^4=160000$ possible four-residue strings. Under an explicitly stipulated uniform independent-residue model, a given window therefore matches with probability $1/200$. This is not an empirical background model for real proteins, and the pattern is not asserted to be a real biological signature.

A sequence of length 103 has 100 length-four windows. Under that model the expected value of the number of matches is $100/200=0.5$. Overlapping windows need not be independent for this expectation: summing their indicator expectations is sufficient. Thus finding a short pattern can occur without a demonstrated functional relationship.

A useful annotation combines the pattern with the rest of the sequence, structural context and experimental evidence. In a calcium-binding family, for example, an EF hand depends on the spatial arrangement and chemistry of coordinating groups, not merely on a count of pattern matches.^[ref]