and Common Folds in 20 Genomes

We carried out a structural-genomics analysis of the folds in the first 20 completely sequenced genomes, focusing on the patterns of fold usage. We assigned folds to sequences using PSI-blast, run with a systematic protocol to reduce the amount of computational overhead. On average, folds could be assigned to about a fourth of the ORFs in the genomes and about a fifth of the amino acids in the proteomes. More than 80 % of all the folds in the scop structural classification were identified in one of the 20 organisms, with worm and E. coli having the largest number of distinct folds. Folds are particularly effective at comprehensively measuring levels of gene duplication, as they group together even very remote homologues. Using folds, we find the average level of duplication varies depending on the complexity of the organism, ranging from 2.4 in M. genitalium to 32 for the worm-- values significantly higher than those observed based purely on sequence similarity. We rank the common folds in the 20 organisms, finding that the top three folds are the P-loop NTP hydrolase, the ferrodoxin fold, and the TIM-barrel. We also discuss in detail the many factors that affect and bias these rankings. From the overall patterns of shared folds, we were able to group the 20 organisms into a whole-genome tree, which is similar but not identical to the classic ribosomal tree. We also focus on specific patterns of fol