ArticleNucleic acids research2006
Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space.
Article in Nucleic acids research, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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24 citing papers in PubMed, 62 citations in OpenAlex.
- β-Strand-mediated interactions of protein domains.Proteins · 2020Article
- Building protein-protein interaction networks for Leishmania species through protein structural information.BMC bioinformatics · 2018Article
- The value of protein structure classification information-Surveying the scientific literature.Proteins · 2015Article
- The QQS orphan gene of Arabidopsis modulates carbon and nitrogen allocation in soybean.Plant biotechnology journal · 2015Article
- Structural Symmetry in Membrane Proteins.Annual review of biophysics · 2015Review
- High-throughput protein purification and quality assessment for crystallization.Methods (San Diego, Calif.) · 2011Review
- The evolutionary origin of orphan genes.Nature reviews. Genetics · 2011Review
- 1,000 structures and more from the MCSG.BMC structural biology · 2011Article
- Article
- Quantitative global studies of reactomes and metabolomes using a vectorial representation of reactions and chemical compounds.BMC systems biology · 2010Article
- A galaxy of folds.Protein science : a publication of the Protein Society · 2010Article
- The CATH hierarchy revisited-structural divergence in domain superfamilies and the continuity of fold space.Structure (London, England : 1993) · 2009Article
- FLORA: a novel method to predict protein function from structure in diverse superfamilies.PLoS computational biology · 2009Article
- 7TMRmine: a Web server for hierarchical mining of 7TMR proteins.BMC genomics · 2009Article
- PSI-2: structural genomics to cover protein domain family space.Structure (London, England : 1993) · 2009Review
- ExDom: an integrated database for comparative analysis of the exon-intron structures of protein domains in eukaryotes.Nucleic acids research · 2009Article
- Exploring the structure and function paradigm.Current opinion in structural biology · 2008Review
- The impact of extremophiles on structural genomics (and vice versa).Extremophiles : life under extreme conditions · 2008Review
- Towards completion of the Earth's proteome.EMBO reports · 2007Article
- Structural genomics: keeping up with expanding knowledge of the protein universe.Current opinion in structural biology · 2007Review
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5 authors at 1 institution in 1 country.
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Abstract
We present an analysis of 203 completed genomes in the Gene3D resource (including 17 eukaryotes), which demonstrates that the number of protein families is continually expanding over time and that singleton-sequences appear to be an intrinsic part of the genomes. A significant proportion of the proteomes can be assigned to fewer than 6000 well-characterized domain families with the remaining domain-like regions belonging to a much larger number of small uncharacterized families that are largely species specific. Our comprehensive domain annotation of 203 genomes enables us to provide more accurate estimates of the number of multi-domain proteins found in the three kingdoms of life than previous calculations. We find that 67% of eukaryotic sequences are multi-domain compared with 56% of sequences in prokaryotes. By measuring the domain coverage of genome sequences, we show that the structural genomics initiatives should aim to provide structures for less than a thousand structurally uncharacterized Pfam families to achieve reasonable structural annotation of the genomes. However, in large families, additional structures should be determined as these would reveal more about the evolution of the family and enable a greater understanding of how function evolves.
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