The GTOP database in 2009: updated content and novel features to expand and deepen insights into protein structures and functions

Abstract

The Genomes TO Protein Structures and Functions (GTOP) database (http://spock.genes.nig.ac.jp/~genome/gtop.html) freely provides an extensive collection of information on protein structures and functions obtained by application of various computational tools to the amino acid sequences of entirely sequenced genomes. GTOP contains annotations of 3D structures, protein families, functions, and other useful data of a protein of interest in user-friendly ways to give a deep insight into the protein structure. From the initial 1999 version, GTOP has been continually updated to reap the fruits of genome projects and augmented to supply novel information, in particular intrinsically disordered regions. As intrinsically disordered regions constitute a considerable fraction of proteins and often play crucial roles especially in eukaryotes, their assignments give important additional clues to the functionality of proteins. Additionally, we have incorporated the following features into GTOP: a platform independent structural viewer, results of HMM searches against SCOP and Pfam, secondary structure predictions, color display of exon boundaries in eukaryotic proteins, assignments of gene ontology terms, search tools, and master files.

Figure 1.

The time courses of the number of genomes included and the fraction of the sequences with homologs in the PDB. The line graphs represent the ratios of the sequences with homologs in the PDB, while the column graph stands for the number of genomes in GTOP. The scales for the fraction and the number of genomes are shown at the right and left ends, respectively. The blue, green, and red lines correspond to fruit fly, E. coli, and the overall average, respectively. The solid and dotted lines respectively show the ratios obtained using reverse PSI-BLAST, and those using BLAST. The exact numbers of genomes are displayed near the top of the rectangles.

Figure 2.

GTOP view examples. (A) The domain assignments of the human androgen receptor are presented in color bars to facilitate intuitive grasp of molecular architecture of the protein. This is a typical protein with long ID regions: the N-terminal half of the protein consists mainly of ID regions (18,22), consistent with the ID regions predicted by DISOPRED2 (gray bars on the line marked by DISOPRED). (B) A structurally aligned region of the same protein is shown in the exon view. This page can be obtained by clicking on the characters ‘1t7rA’ circled in Figure 2A, and by clicking on the EXON Display and 3D (Jmol-applet) buttons in the top section of the pop-up screen. The 3D structure is shown in five colors. By the 3D viewer, the sequence alignment is displayed with the exons represented in the same colors.