Protein sequence modules.

E Aharonovsky; E N Trifonov

doi:10.1080/07391102.2005.10507062

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PubMed · 16218751

Protein sequence modules.

E Aharonovsky·E N Trifonov

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Abstract

Conserved protein sequence segments are commonly believed to correspond to functional sites in the protein sequence. A novel approach is proposed to profile the changing degree of conservation along the protein sequence, by evaluating the occurrence frequencies of all short oligopeptides of the given sequence in a large proteome database. Thus, a protein sequence conservation profile can be plotted for every protein. The profile indicates where along the sequences the potential functional (conserved) sites are located. The corresponding oligopeptides belonging to the sites are very frequent across many prokaryotic species. Analysis of a representative set of such profiles reveals a common feature of all examined proteins: they consist of sequence modules represented by the peaks of conservation. Typical size of the modules (peak-to-peak distance) is 25-30 amino acid residues.

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Amino Acid Sequence Base Sequence Conserved Sequence Databases, Protein Evolution, Molecular Molecular Sequence Data Proteins Proteome Sequence Alignment Sequence Analysis Journal Article Research Support, Non-U.S. Gov't

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E Aharonovsky, E N Trifonov. 2005. Protein sequence modules.. https://doi.org/10.1080/07391102.2005.10507062

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