ArticlePloS one2009
The evolutionary history of protein domains viewed by species phylogeny.
Article in PloS one, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 44 papers.
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Who cites it
44 citing papers in PubMed.
- Consequences of Genetic Recombination on Protein Folding Stability.Journal of molecular evolution · 2023Article
- Intraspecies characterization of bacteria via evolutionary modeling of protein domains.Scientific reports · 2022Article
- Promiscuous Domains in Eukaryotes and HAT Proteins in FUNGI Have Followed Different Evolutionary Paths.Journal of molecular evolution · 2022Article
- An evolutionary and physiological perspective on cell-substrate adhesion machinery for cell migration.Frontiers in cell and developmental biology · 2022Review
- Assessment of domain interactions in the fourteenth round of the Critical Assessment of Structure Prediction (CASP14).Proteins · 2021Article
- In Silico Analysis of Fatty Acid Desaturases Structures inInternational journal of molecular sciences · 2021Article
- StAR-Related Lipid Transfer (START) Domains Across the Rice Pangenome Reveal How Ontogeny Recapitulated Selection Pressures During Rice Domestication.Frontiers in genetics · 2021Article
- A horizontally acquired expansin gene increases virulence of the emerging plant pathogen Erwinia tracheiphila.Scientific reports · 2020Article
- Hypothesis: Unifying model of domain architecture for conventional and novel protein kinase C isozymes.IUBMB life · 2020Article
- AnnoTree: visualization and exploration of a functionally annotated microbial tree of life.Nucleic acids research · 2019Article
- Article
- Domain-based Comparative Analysis of Bacterial Proteomes: Uniqueness, Interactions, and the Dark Matter.Current genomics · 2019Article
- Functional and Structural Diversity of Acyl-coA Binding Proteins in Oil Crops.Frontiers in genetics · 2018Review
- Review
- Classification and function of small open reading frames.Nature reviews. Molecular cell biology · 2017Article
- Evolution and structural diversification of Nictaba-like lectin genes in food crops with a focus on soybean (Glycine max).Annals of botany · 2017Article
- The natural history of molecular functions inferred from an extensive phylogenomic analysis of gene ontology data.PloS one · 2017Article
- Resurrecting the Dead (Molecules).Computational and structural biotechnology journal · 2017Review
- Improvement in Protein Domain Identification Is Reached by Breaking Consensus, with the Agreement of Many Profiles and Domain Co-occurrence.PLoS computational biology · 2016Article
- Analyses of Old "Prokaryotic" Proteins Indicate Functional Diversification in Arabidopsis and Oryza sativa.Frontiers in plant science · 2016Article
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2 authors.
Funding
Abstract
backgroundProtein structural domains are evolutionary units whose relationships can be detected over long evolutionary distances. The evolutionary history of protein domains, including the origin of protein domains, the identification of domain loss, transfer, duplication and combination with other domains to form new proteins, and the formation of the entire protein domain repertoire, are of great interest. METHODOLOGY/PRINCIPAL
findingsA methodology is presented for providing a parsimonious domain history based on gain, loss, vertical and horizontal transfer derived from the complete genomic domain assignments of 1015 organisms across the tree of life. When mapped to species trees the evolutionary history of domains and domain combinations is revealed, and the general evolutionary trend of domain and combination is analyzed. CONCLUSIONS/SIGNIFICANCE: We show that this approach provides a powerful tool to study how new proteins and functions emerged and to study such processes as horizontal gene transfer among more distant species.
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