ArticleLife (Basel, Switzerland)2016
Functional Annotations of Paralogs: A Blessing and a Curse.
Article in Life (Basel, Switzerland), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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Who cites it
39 citing papers in PubMed.
- A standardized core genome multilocus sequence typing and life identification number barcoding framework for globalMicrobial genomics · 2026Article
- Large Numbers of New Human Paralogs Discovered.bioRxiv : the preprint server for biology · 2025Article
- Limitations of current machine learning models in predicting enzymatic functions for uncharacterized proteins.G3 (Bethesda, Md.) · 2025Article
- Intrinsic Disorder and Other Malleable Arsenals of Evolved Protein Multifunctionality.Journal of molecular evolution · 2024Review
- Development and implementation of a core genome multilocus sequence typing scheme forMicrobial genomics · 2024Article
- Biosynthesis and function of 7-deazaguanine derivatives in bacteria and phages.Microbiology and molecular biology reviews : MMBR · 2024Review
- Beyond blast: enabling microbiologists to better extract literature, taxonomic distributions and gene neighbourhood information for protein families.Microbial genomics · 2024Article
- Beyond Blast: Enabling Microbiologists to Better Extract Literature, Taxonomic Distributions and Gene Neighborhood Information for Protein Families.bioRxiv : the preprint server for biology · 2024Article
- Diversification of Ubiquinone Biosynthesis via Gene Duplications, Transfers, Losses, and Parallel Evolution.Molecular biology and evolution · 2023Article
- Catalytic Site Proximity Profiling for Functional Unification of Sequence-Diverse RadicalACS bio & med chem Au · 2023Article
- Highly contiguous genomes of human clinical isolates ofMicrobial genomics · 2023Article
- Analysis of Huntington's Disease Modifiers Using the Hyperbolic Mapping of the Protein Interaction Network.International journal of molecular sciences · 2022Article
- Protease activities of vaginal Porphyromonas species disrupt coagulation and extracellular matrix in the cervicovaginal niche.NPJ biofilms and microbiomes · 2022Article
- Functional characterization of prokaryotic dark matter: the road so far and what lies ahead.Current research in microbial sciences · 2022Review
- Experimental and computational investigation of enzyme functional annotations uncovers misannotation in the EC 1.1.3.15 enzyme class.PLoS computational biology · 2021Article
- Complete Characterization of Incorrect Orthology Assignments in Best Match Graphs.Journal of mathematical biology · 2021Article
- BSGatlas: a unifiedMicrobial genomics · 2021Article
- Review
- The Cytoplasmic Domains ofFrontiers in microbiology · 2021Article
- Identification and Expression Profiling of Toll-Like Receptors of Brown Trout (International journal of molecular sciences · 2020Article
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Gene duplication followed by mutation is a classic mechanism of neofunctionalization, producing gene families with functional diversity. In some cases, a single point mutation is sufficient to change the substrate specificity and/or the chemistry performed by an enzyme, making it difficult to accurately separate enzymes with identical functions from homologs with different functions. Because sequence similarity is often used as a basis for assigning functional annotations to genes, non-isofunctional gene families pose a great challenge for genome annotation pipelines. Here we describe how integrating evolutionary and functional information such as genome context, phylogeny, metabolic reconstruction and signature motifs may be required to correctly annotate multifunctional families. These integrative analyses can also lead to the discovery of novel gene functions, as hints from specific subgroups can guide the functional characterization of other members of the family. We demonstrate how careful manual curation processes using comparative genomics can disambiguate subgroups within large multifunctional families and discover their functions. We present the COG0720 protein family as a case study. We also discuss strategies to automate this process to improve the accuracy of genome functional annotation pipelines.
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