Genome-wide protein structural annotation database, GTOP and a correction of the proportions of structural annotations in the bacterial genomes

摘要

Large-scale genome projects generate an unprecedented number of protein sequences. Predicting die 3D structures of sequences provides important clues as to their functions. We constructed the Genomes TO Protein structures and functions (GTOP) database, containing protein fold predictions of a huge number of sequences. Predictions are mainly carried out with the homology search program PSI-BLAST, currently the most popular among high-sensitivity profile search methods. Some genomes analyzed m GTOP show die exceptionally tow percentages of structural annotations. Length distributions of amino acid sequences indicated that the annotated genes in these genomes could contain ORFs by chance, which are just open for translation but not real protein-coding sequences. We corrected the total numbers of genes in these genomes by reviewing ORFs without sequence similarity to any known protein, which are referred to as "orphan" genes, leading to the correction of proportions of structural annotations.