= Protein sequence motif
A \b[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.<PROSITE user manual>[Patterns and pattern 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 admits
$$
1\times20^2\times2=800
$$
strings 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.<EF-hand calcium-binding domain signature and profile in PROSITE>[Description, coordinating positions and atypical/nonbinding relatives]{ref}
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