Distribution of Protein Superfamilies in the Three Superkingdoms of Life

Abstract

The Superfamily database provides structural assignments to protein sequences. This assignment enable us to analyze the distribution of specific superfamilies within and across the genomes. Here, we focus on the distributions of superfamilies in archaeal, bacterial and eukaryotic genomes. The distribution of the most common superfamilies in archaea and bacteria are very similar (6 of the top 10 superfamilies are the same) but distinct in eukaryotes. But there is only p-loop superfamily in the top 10 superfamilies in the three superkingdoms. When the total number of domains in a genome is larger, duplication of the 6 common superfamilies in archaea and bacteria are more but relative abundant distribution is lower. This phenomenon is more obvious in metazoa. The 6 superfamilies occur almost in all discussial completed genomes, and the structures are lined to <sup xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:xlink="http://www.w3.org/1999/xlink">alpha/beta</sup> structural class, and their functions are mainly enzyme. So these superfamilies are important for more genomes, even eukaryote genome, although these superfamilies are not mainly duplicated in eukaryote genomes.