Conserved ‘Hypothetical’ Proteins New Hints and New Puzzles.pdfVIP

Comparative and Functional Genomics Comp Funct Genom 2001; 2: 14–18. Conference Paper Conserved ‘hypothetical’ proteins: new hints and new puzzles Michael Y. Galperin* National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA Abstract *Correspondence to: M. Y. Galperin, National Center Conserved hypothetical proteins, i.e. conserved proteins whose functions are still unknown, for Biotechnology Information, pose a challenge not just to functional genomics but also to general biology. For many National Library of Medicine, conserved proteins, computational analysis provides only a general prediction of National Institutes of Health, biochemical function; their exact biological functions have to be established through Bethesda, MD 20894, USA. E-mail: galperin@ direct experimentation. In the few cases when this has been accomplished, the results were remarkable, revealing the deoxyxylulose pathway and a new essential enzyme, the ITP pyrophosphatase. Comparative genome analysis is also instrumental in illuminating unsolved problems in biology, e.g. the mechanism of FtsZ-independent cell division in Chlamydia, Ureaplasma and Aeropyrum or the role of uncharacterized conserved domains in signal transduction. Copyright 2001 John Wiley Sons, Ltd. Keywords: sequence analysis; orthologous proteins; database; phylogenetic pattern; GGDEF domain The availability of more than 30 complete genomes,