Proportion of membrane proteins in proteomes of 15 single-cell organisms analyzed by the SOSUI prediction system

A software system, SOSUI, was previously developed for discriminating betwe en soluble and membrane proteins and predicting transmembrane regions (Hiro kawa et al., Bioinformatics, 14 (1998) 378-379). The performance of the sys tem was 99% for the discrimination between two types of proteins and 96% fo r the prediction of transmembrane helices. When all of the amino acid seque nces from 15 single-cell organisms were analyzed by SOSUI, the proportion o f predicted polytopic membrane proteins showed an almost constant value of 15-20%, irrespective of the total genome size. However, single-cell organis ms appeared to be categorized in terms of the preference of the number of t ransmembrane segments: species with small genomes were characterized by a s ignificant peak at a helix number of approximately six or seven; species wi th large genomes showed a peak at 10 or 11 helices; and species with interm ediate genome sizes showed a monotonous decrease of the population of membr ane proteins against the number of transmembrane helices. (C) 1999 Elsevier Science B.V. All rights reserved.