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

Fold assignments for proteins from the Helicobacter pylori genome are carried out using BASIC, a profile-profile alignment algorithm recently tested on the Mycoplasma genitalium and Escherichia coli genomes. The fold assignments are followed by automated function evaluation, based on the multilevel description of functional sites in proteins. Over 40% of the proteins encoded in the H. pylori genome can be recognized as belonging to a protein family with known structure. Previous estimates suggested that only 10-15% of genome proteins could be characterized this way. This dramatic increase in the number of recognized homologies between H. pylori proteins and structurally characterized protein families is partly due to the rapid increase of the database of known protein structures, but mostly it is due to the significant improvement in prediction algorithms. Knowledge of a protein fold adds a new dimension to our understanding of its function and, similarly, structure prediction can also add to understanding, verification, and/or prediction of function for uncharacterized proteins. Several examples analyzed in more detail in this article illustrate insights that can be achieved from structure and detailed function prediction.