Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2004 Jan 1;32(Database issue):D196-9.
doi: 10.1093/nar/gkh043.

The Genomic Threading Database: a comprehensive resource for structural annotations of the genomes from key organisms

Liam J McGuffin  1 , Stefano A Street, Kevin Bryson, Søren-Aksel Sørensen, David T Jones
Affiliations

The Genomic Threading Database: a comprehensive resource for structural annotations of the genomes from key organisms

Liam J McGuffin et al. Nucleic Acids Res. .

Abstract

Currently, the Genomic Threading Database (GTD) contains structural assignments for the proteins encoded within the genomes of nine eukaryotes and 101 prokaryotes. Structural annotations are carried out using a modified version of GenTHREADER, a reliable fold recognition method. The Gen THREADER annotation jobs are distributed across multiple clusters of processors using grid technology and the predictions are deposited in a relational database accessible via a web interface at http://bioinf.cs.ucl.ac.uk/GTD. Using this system, up to 84% of proteins encoded within a genome can be confidently assigned to known folds with 72% of the residues aligned. On average in the GTD, 64% of proteins encoded within a genome are confidently assigned to known folds and 58% of the residues are aligned to structures.

PubMed Disclaimer

Figures

Figure 1
Figure 1
The difference in coverage of structural assignments between the PSI-BLAST based annotations from 3D-GENOMICS, and those in the GTD. (a) The coverage of sequences assigned to structures. In the case of the GTD, only GenTHREADER assignments with p < 1% have been counted (see Methods). (b) The coverage of residues aligned to sequences.
Figure 2
Figure 2
The frequency of the different fold categories of proteins encoded within four representative genomes. Each SCOP (13) code relates to the following folding types: a.4, DNA/RNA-binding 3-helical bundle; a.7, spectrin repeat-like; a.29, bromodomain-like; a.118, α-α superhelix; b.1, immunoglobulin-like β-sandwich; b.40, OB-fold; c.1, TIM β/α-barrel; c.2, NAD(p)-binding Rossmann-fold domains; c.10, leucine-rich repeat; c.23, flavodoxin-like; c.26, adenine nucleotide α hydrolase-like; c.37, P-loop-containing nucleotide triphosphate hydrolases; c.55, ribonuclease H-like motif; c.66, S-adenosul-l-methionine-dependent methyltransferases; d.58, ferredoxin-like; d.95, homing endonuclease-like; d.144, protein kinase-like (PK-like); f.2, membrane all-α; g.37, C2H2 and C2HC zinc fingers; g.39, glucocorticoid receptor-like (DNA-binding domain).
See this image and copyright information in PMC

References

    1. Hoersch S., Leroy,C., Brown,N.P. andrade,M.A. and Sander,C. (2000) The GeneQuiz web server: protein functional analysis through the Web. Trends Biochem. Sci., 25, 33–35. - PubMed
    1. Frishman D., Mokrejs,M., Kosykh,D., Kastenmuller,G., Kolesov,G., Zubrzycki,I., Gruber,C., Geier,B., Kaps,A., Albermann,K. et al. (2003) The PEDANT genome database. Nucleic Acids Res., 31, 207–211. - PMC - PubMed
    1. Gaasterland T., Sczyrba,A., Thomas,E., Aytekin-Kurban,G., Gordon,P. and Sensen,C.W. (2000) MAGPIE/EGRET annotation of the 2.9-Mb Drosophila melanogaster Adh region. Genome Res., 10, 502–510. - PMC - PubMed
    1. Bryson K., Luck,M., Joy,M. and Jones,D.T. (2000) Applying agents to bioinformatics in GeneWeaver. Lect. Notes Artif. Int., 1860, 60–71.
    1. Altschul S.F., Madden,T.L., Schaffer,A.A., Zhang,J., Zhang,Z., Miller,W. and Lipman,D.J. (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25, 3389–3402. - PMC - PubMed

Publication types