This paper presents SMART, a Web-based tool for identifying and annotating signaling domains in proteins. The tool was developed to address the need for accurate annotation of signaling domains in genes and genomes, as current databases like SwissProt and Pfam fail to annotate a significant portion of known domains. SMART uses multiple sequence alignments of 86 signaling domains to detect homologues and predict functional annotations. It was applied to the yeast genome, revealing that at least 6.7% of its genes contain signaling domains, a figure higher than previously annotated. SMART also identified novel domains, such as band 4.1-homologous domains in focal adhesion kinases and a citron-homology domain. It predicted functions for domain families, such as the ubiquitin-binding role of ubiquitin-associated domains (UBA). Additionally, SMART detected signaling domains in disease-related genes, including SPRY domains in Marenostrin/Pyrin and Midline 1. The tool also identified domains in unexpected phylogenetic contexts, such as diacylglycerol kinase homologues in yeast and bacteria. SMART's ability to detect domain boundaries and predict protein function is enhanced by its use of gapped alignments and multiple search methods. The tool is designed to be updated easily and provides a user-friendly interface for automatic sequence annotation. The results demonstrate that SMART improves upon existing tools and databases in the field of signaling domain annotation. The study highlights the importance of domain-based annotation in understanding protein function and signaling pathways, and emphasizes the need for integrating sequence databases with literature knowledge to facilitate research in this area.This paper presents SMART, a Web-based tool for identifying and annotating signaling domains in proteins. The tool was developed to address the need for accurate annotation of signaling domains in genes and genomes, as current databases like SwissProt and Pfam fail to annotate a significant portion of known domains. SMART uses multiple sequence alignments of 86 signaling domains to detect homologues and predict functional annotations. It was applied to the yeast genome, revealing that at least 6.7% of its genes contain signaling domains, a figure higher than previously annotated. SMART also identified novel domains, such as band 4.1-homologous domains in focal adhesion kinases and a citron-homology domain. It predicted functions for domain families, such as the ubiquitin-binding role of ubiquitin-associated domains (UBA). Additionally, SMART detected signaling domains in disease-related genes, including SPRY domains in Marenostrin/Pyrin and Midline 1. The tool also identified domains in unexpected phylogenetic contexts, such as diacylglycerol kinase homologues in yeast and bacteria. SMART's ability to detect domain boundaries and predict protein function is enhanced by its use of gapped alignments and multiple search methods. The tool is designed to be updated easily and provides a user-friendly interface for automatic sequence annotation. The results demonstrate that SMART improves upon existing tools and databases in the field of signaling domain annotation. The study highlights the importance of domain-based annotation in understanding protein function and signaling pathways, and emphasizes the need for integrating sequence databases with literature knowledge to facilitate research in this area.