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. 2000 Jan 1;28(1):231-4.
doi: 10.1093/nar/28.1.231.

SMART: A Web-Based Tool for the Study of Genetically Mobile Domains

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Free PMC article

SMART: A Web-Based Tool for the Study of Genetically Mobile Domains

J Schultz et al. Nucleic Acids Res. .
Free PMC article

Abstract

SMART (a Simple Modular Architecture Research Tool) allows the identification and annotation of genetically mobile domains and the analysis of domain architectures (http://SMART.embl-heidelberg.de ). More than 400 domain families found in signalling, extra-cellular and chromatin-associated proteins are detectable. These domains are extensively annotated with respect to phyletic distributions, functional class, tertiary structures and functionally important residues. Each domain found in a non-redundant protein database as well as search parameters and taxonomic information are stored in a relational database system. User interfaces to this database allow searches for proteins containing specific combinations of domains in defined taxa.

Figures

Figure 1
Figure 1
Structure of the relational database underlying SMART. Table names are in bold and lines indicate the relationships between tables in the RDBMS.
Figure 2
Figure 2
Schematic representations, produced using SMART, of the domain architecture of proteins discussed in the text. Green/grey lines indicate predicted coiled coil regions and pink lines show low complexity segments. Regions of proteins without any predicted features are marked with grey bars and can be subjected individually to gapped BLAST searches. (a) Selective SMART. Domain architecture of plant (Arabidopsis thaliana; gi: 2586157) and metazoan (gi:1755049 Bos taurus; gi:1613788 Homo sapiens) proteins with MyTH4 and B41 domains. (b) Finding proteins with similar domain architecture. SMART detects no PH domain in the C.elegans protein K08B12.5 (gi:1938422), though all thus far sequenced proteins with an identical domain architecture show a PH domain between the C1 and the CNH domain (representative gi:2772930 Drosophila melanogaster). (c) Improved representation of results. SMART merges domain prediction and intrinsic features into a single line output. The red line indicates a signal sequence, the blue bar a transmembrane helix.

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