Identifying domains in protein sequences

Abstract

Amino acid sequences are often inferred without information about the structure or function of the protein. Just as unknown proteins may be identified through comparison with other known sequences, so can structural and functional domains be inferred through analogy with other known domain sequences. A database of domain sequences, along with their known properties, would be very helpful in the characterization of a protein sequence in terms of its possible conformation and function. Here we describe the type of information to be included in such a database and discuss the techniques that may be used to determine the characteristic features of domains. Recently identified domains in thyroid peroxidase, chondroitin-sulfate proteoglycan core proteins, an epidermal growth factor precursor homolog, and a bacterial beta-amylase are presented as examples.