ArticleGenome research2002
Structural characterization of the human proteome.
Article in Genome research, 2002. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 31 papers.
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Who cites it
31 citing papers in PubMed.
- Impact of GC content on de novo gene birth.Nature communications · 2026Article
- Domain Architecture Based Methods for Comparative Functional Genomics Toward Therapeutic Drug Target Discovery.Journal of molecular evolution · 2023Review
- Identification of two rate-limiting steps in the degradation of partially folded immunoglobulin light chains.Frontiers in cell and developmental biology · 2022Article
- Measuring the Conformational Distance of GPCR-related Proteins Using a Joint-based Descriptor.Scientific reports · 2017Article
- Mutations in TMEM260 Cause a Pediatric Neurodevelopmental, Cardiac, and Renal Syndrome.American journal of human genetics · 2017Article
- Article
- Statistical removal of background signals from high-throughput (1)H NMR line-broadening ligand-affinity screens.Journal of biomolecular NMR · 2015Article
- From local structure to a global framework: recognition of protein folds.Journal of the Royal Society, Interface · 2014Review
- Deep sequencing of large library selections allows computational discovery of diverse sets of zinc fingers that bind common targets.Nucleic acids research · 2014Article
- Global patterns of protein domain gain and loss in superkingdoms.PLoS computational biology · 2014Article
- Emergence of novel domains in proteins.BMC evolutionary biology · 2013Article
- A human skeletal muscle interactome centered on proteins involved in muscular dystrophies: LGMD interactome.Skeletal muscle · 2013Article
- Zinc biochemistry: from a single zinc enzyme to a key element of life.Advances in nutrition (Bethesda, Md.) · 2013Review
- Article
- Stratification of co-evolving genomic groups using ranked phylogenetic profiles.BMC bioinformatics · 2009Article
- Representative transcript sets for evaluating a translational initiation sites predictor.BMC bioinformatics · 2009Article
- Protein domain organisation: adding order.BMC bioinformatics · 2009Article
- Dynamic interaction between Arf GAP and PH domains of ASAP1 in the regulation of GAP activity.Cellular signalling · 2008Article
- Evolution of a new function by degenerative mutation in cephalochordate steroid receptors.PLoS genetics · 2008Article
- Comprehensive analysis of co-occurring domain sets in yeast proteins.BMC genomics · 2007Article
Corrections and comments
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Authors and funding
3 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
This paper reports an analysis of the encoded proteins (the proteome) of the genomes of human, fly, worm, yeast, and representatives of bacteria and archaea in terms of the three-dimensional structures of their globular domains together with a general sequence-based study. We show that 39% of the human proteome can be assigned to known structures. We estimate that for 77% of the proteome, there is some functional annotation, but only 26% of the proteome can be assigned to standard sequence motifs that characterize function. Of the human protein sequences, 13% are transmembrane proteins, but only 3% of the residues in the proteome form membrane-spanning regions. There are substantial differences in the composition of globular domains of transmembrane proteins between the proteomes we have analyzed. Commonly occurring structural superfamilies are identified within the proteome. The frequencies of these superfamilies enable us to estimate that 98% of the human proteome evolved by domain duplication, with four of the 10 most duplicated superfamilies specific for multicellular organisms. The zinc-finger superfamily is massively duplicated in human compared to fly and worm, and occurrence of domains in repeats is more common in metazoa than in single cellular organisms. Structural superfamilies over- and underrepresented in human disease genes have been identified. Data and results can be downloaded and analyzed via web-based applications at http://www.sbg.bio.ic.ac.uk.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.