GTOP: a database of protein structures predicted from genome sequences

Abstract

Large-scale genome projects generate an unprecedented number of protein sequences, most of them are experimentally uncharacterized. Predicting the 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. GTOP also includes the results of other analyses, e.g. homology and motif search, detection of transmembrane helices and repetitive sequences. We have completed analyzing the sequences of 41 organisms, with the number of proteins exceeding 120 000 in total. GTOP uses a graphical viewer to present the analytical results of each ORF in one page in a 'color-bar' format. The assigned 3D structures are presented by Chime plug-in or RasMol. The binding sites of ligands are also included, providing functional information. The GTOP server is available at http://spock.genes.nig.ac.jp/~genome/gtop.html.

Figure 1

Fractions of structure-predicted ORFs in GTOP database. The digits in parentheses are the numbers of ORFs in the corresponding organism.

Figure 2

Snapshots of GTOP web pages. (A) The summary page of citA, an ORF in E.coli. Results of various kinds of analysis are shown in colored bar formats. If SCOP structure domains are assigned, small structure icons are shown above the colored bars. The structure icons were prepared for each superfamily of SCOP. The string indicated by ‘OrgPattern’ is the number of homologs of the given protein in the organisms stored in GTOP database. (B) An alignment of citA and the 3D structure of its homolog 1bxdA found by PSI-BLAST. The characters under the alignment (shown in a blue box) indicate the numbers of atomic contacts between a given residue and the ligand, ANP. (C) A Chime plug-in view of the 3D structure of 1bxdA, a homolog of citA. The regions of insertion and deletion are colored blue.