Gene3D and Understanding Proteome Evolution

Gene3D is a database of protein sequence families. The families have been created through clustering the proteome sequences of over 200 species, including more than 15 eukaryotes, and totalling over 750,000 proteins (as derived from UniProt [1]). Each family is then further subclustered on the basis of sequence similarity. Using remote homologue detection methods, we have been able to assign structures – based on the CATH [2] and Pfam [3] databases – to a majority of these sequences. This allows a high resolution view of the functions and evolution of specific protein families, as well as the evolution of a species' gene content.