SMART, A SIMPLE MODULAR ARCHITECTURE RESEARCH TOOL - IDENTIFICATION OF SIGNALING DOMAINS

Accurate multiple alignments of 86 domains that occur in signaling pro teins have been constructed and used to provide a Web based tool (SMAR T: simple modular architecture research tool) that allows rapid identi fication and annotation of signaling domain sequences. The majority of signaling proteins are multidomain in character with a considerable v ariety of domain combinations known. Comparison with established datab ases showed that 25% of our domain set could not be deduced from Swiss Prot and 41% could not be annotated by Pfam, SMART is able to determin e the modular architectures of single sequences or genomes; applicatio n to the entire yeast genome revealed that at least 6.7% of its genes contain one or more signaling domains, approximately 350 greater than previously annotated. The process of constructing SMART predicted (i) novel domain homologues in unexpected locations such as band 4.1-homol ogous domains in focal adhesion kinases; (ii) previously unknown domai n families, including a citron-homology domain; (iii) putative functio ns of domain families after identification of additional family member s, for example, a ubiquitin-binding role for ubiquitin-associated doma ins (UBA); (iv) cellular roles for proteins, such predicted DEATH doma ins in netrin receptors further implicating these molecules in axonal guidance; (v) signaling domains in known disease genes such as SPRY do mains in both marenostrin/pyrin and Midline I; (vi) domains in unexpec ted phylogenetic contexts such as diacylglycerol kinase homologues in yeast and bacteria; and (vii) likely protein misclassifications exempl ified by a predicted pleckstrin homology domain in a Candida albicans protein, previously described as an integrin.