The Helicobacter pylori genome: From sequence analysis to structural and functional predictions

Fold assignments for proteins from the Helicobacter pylori genome are carri ed out using BASIC, a profile-profile alignment algorithm recently tested o n the Mycoplasma genitalium and Escherichia coli genomes, The fold assignme nts are followed by automated function evaluation, based on the multilevel description of functional sites in proteins. Over 40% of the proteins encod ed in the H, pylori genome can be recognized as belonging to a protein fami ly with known structure. Previous estimates suggested that only 10-15% of g enome proteins could be characterized this way This dramatic increase in th e number of recognized homologies between H. pylori proteins and structural ly characterized protein families is partly due to the rapid increase of th e database of known protein structures, but mostly it is due to the signifi cant improvement in prediction algorithms. Knowledge of a protein fold adds a nem dimension to our understanding of its function and, similarly struct ure prediction can also add to understanding, verification, and/or predicti on of function for uncharacterized proteins. Several examples analyzed in m ore detail in this article illustrate insights that can be achieved from st ructure and detailed function prediction. Proteins 1999;36:20-30, (C) 1999W iley-Liss, Inc.