Protein Distribution Analysis by a High-Precision Prediction System for Membrane Proteins

To determine the proportion of membrane proteins in the whole genome, we developed a membrane protein prediction system, SOSUI. This system used only the physical parameters of each amino acid (hydrophobicity index and amphiphilicity index). This allowed us to predict with an accuracy as high as 95%. The unique feature of this system is that it can make highly accurate predictions even for sequences whose function is unknown. Using this system, we analyzed the entire genomes of many organisms and found that the proportion of membrane proteins in any organism is approximately one-fourth of the total. Furthermore, even in multicellular organisms with splicing, the proportion of membrane proteins was nearly constant. This study was the first step in a series of studies discussing the stability of the entire organism.