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
. 2018 Jan 4;46(D1):D435-D439.
doi: 10.1093/nar/gkx1069.

Gene3D: Extensive prediction of globular domains in proteins

Tony E Lewis  1 , Ian Sillitoe  1 , Natalie Dawson  1 , Su Datt Lam  1   2 , Tristan Clarke  1 , David Lee  3 , Christine Orengo  1 , Jonathan Lees  1   4
Affiliations

Gene3D: Extensive prediction of globular domains in proteins

Tony E Lewis et al. Nucleic Acids Res. .

Erratum in

Abstract

Gene3D (http://gene3d.biochem.ucl.ac.uk) is a database of globular domain annotations for millions of available protein sequences. Gene3D has previously featured in the Database issue of NAR and here we report a significant update to the Gene3D database. The current release, Gene3D v16, has significantly expanded its domain coverage over the previous version and now contains over 95 million domain assignments. We also report a new method for dealing with complex domain architectures that exist in Gene3D, arising from discontinuous domains. Amongst other updates, we have added visualization tools for exploring domain annotations in the context of other sequence features and in gene families. We also provide web-pages to visualize other domain families that co-occur with a given query domain family.

PubMed Disclaimer

Figures

Figure 1.
Figure 1.
Gene3D domains are now displayed along with other sequence annotations using the ProtVista tool.
Figure 2.
Figure 2.
The Gene3D website displaying protein domain architectures in a gene tree, using the PhyD3 JavaScript library. (A) A query with an elephant P53 gene, zoomed in on the area of recurrent P53 duplication, shows multiple paralogs with similar architectures. P63 genes with altered domain architectures can be seen in the lower half of the figure as part of the same gene tree. (B) A Gene3D search with mouse Trpt1, shows it has a non-significant hit to domain superfamily 3.20.170.30 (light blue rectangles) whilst other members of the gene family have a significant hit to this same domain family (darker blue–green rectangles).
Figure 3.
Figure 3.
(A) The most frequent Domain Architectures that the SH2 domain family is found in amongst the Ensembl Genomes. (B) Gene3D domain family co-occurrence page, showing domain families that co-occur with the SH2 domain family in selected Eukaryotic and Metazoan genomes. The first two columns (surrounded by a blue box) correspond to two Choanoflagellate genomes. Darker red entries indicate a greater number of proteins in which the SH2 domain family co-occurs with a specific genome/domain family pair. The number of domain families displayed has been limited to the most populous 100 domain families for the selected genomes. Mousing over a point in the matrix gives popups with further detailed information.
See this image and copyright information in PMC

References

    1. The UniProt Consortium UniProt: the universal protein knowledgebase. Nucleic Acids Res. 2017; 45:D158–D169. - PMC - PubMed
    1. Sillitoe I., Lewis T.E., Cuff A., Das S., Ashford P., Dawson N.L., Furnham N., Laskowski R.A., Lee D., Lees J.G. et al. . CATH: comprehensive structural and functional annotations for genome sequences. Nucleic Acids Res. 2015; 43:D376–D381. - PMC - PubMed
    1. Lam S.D., Dawson N.L., Das S., Sillitoe I., Ashford P., Lee D., Lehtinen S., Orengo C.A., Lees J.G.. Gene3D: expanding the utility of domain assignments. Nucleic Acids Res. 2016; 44:D404–D409. - PMC - PubMed
    1. Eddy S.R. Accelerated profile HMM searches. PLoS Comput. Biol. 2011; 7:e1002195. - PMC - PubMed
    1. Pearson W.R., Li W., Lopez R.. Query-seeded iterative sequence similarity searching improves selectivity 5-20-fold. Nucleic Acids Res. 2017; 45:e46. - PMC - PubMed

Publication types

LinkOut - more resources