Recent improvements to the SMART domain-based sequence annotation resource

Abstract

SMART (Simple Modular Architecture Research Tool, http://smart.embl-heidelberg.de) is a web-based resource used for the annotation of protein domains and the analysis of domain architectures, with particular emphasis on mobile eukaryotic domains. Extensive annotation for each domain family is available, providing information relating to function, subcellular localization, phyletic distribution and tertiary structure. The January 2002 release has added more than 200 hand-curated domain models. This brings the total to over 600 domain families that are widely represented among nuclear, signalling and extracellular proteins. Annotation now includes links to the Online Mendelian Inheritance in Man (OMIM) database in cases where a human disease is associated with one or more mutations in a particular domain. We have implemented new analysis methods and updated others. New advanced queries provide direct access to the SMART relational database using SQL. This database now contains information on intrinsic sequence features such as transmembrane regions, coiled-coils, signal peptides and internal repeats. SMART output can now be easily included in users' documents. A SMART mirror has been created at http://smart.ox.ac.uk.

Figure 1

Using intrinsic features in Architecture SMART queries. The SMART database was queried for all proteins containing a tyrosine kinase domain and a transmembrane region (TyrKc and TRANS). 387 proteins were found, including the five displayed here. Note that the text colour of domain names has been designed to correlate both with its subcellular localisation (blue, secreted; black, intracellular) and its catalytic activity (red, catalytic activity).