Use of homology domains in sequence similarity detection

Periodicity and sequence degeneration in eggcase precursors (vitelline proteins) from Fasciola hepatica

Studies of two 3,4-dihydroxyphenylalanine (dopa) containing eggcase precursor proteins (vitelline proteins vpB1 and 2) from the trematode Fasciola hepatica recently concluded that although oligopeptide motifs occurred in the amino acid sequence, the overall structure (in contrast to dopa proteins from other phyla) was highly degenerate and irregular. An analysis of the distribution of individual amino acids and of oligopeptide motifs by two independent probabilistic pattern analysis methods, however, has now shown that despite superficial amino acid variability, an overall periodic structure exists. Moderately conserved hexadic domains account for almost 70% of the secreted protein, and characteristically contain glycine in position 5 of the hexad (76% of all glycine residues), and tyrosine, dopa or phenylalanine in positions 1 and 4 (88% of all aromatic residues).