ReviewBiochemistry2017
Genomic Enzymology: Web Tools for Leveraging Protein Family Sequence-Function Space and Genome Context to Discover Novel Functions.
Review in Biochemistry, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 93 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Who cites it
93 citing papers in PubMed, 192 citations in OpenAlex.
- Synthesis of Six Natural Products Enabled by Selective Hydroxylation of Orcinaldehyde-Like Substrates With an Enzyme Library.Angewandte Chemie (International ed. in English) · 2026Article
- Iterative acylation on mature lasso peptides by widespread acetyltransferases.Nature chemical biology · 2026Article
- Broad Substrate Specificity and High Catalytic Activity ofACS omega · 2025Article
- Sequence and taxonomic feature evaluation facilitated the discovery of alcohol oxidases.Synthetic and systems biotechnology · 2025Article
- Peptide surfactants with post-translational C-methylations that promote bacterial development.Nature chemical biology · 2025Article
- Comparison of a Nonheme Iron Cyclopropanase with a Homologous Hydroxylase Reveals Mechanistic Features Associated with Distinct Reaction Outcomes.Journal of the American Chemical Society · 2025Article
- Trojan horse peptide conjugates remodel the activity spectrum of clinical antibiotics.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Substrate-Multiplexed Assessment of Aromatic Prenyltransferase Activity.Chembiochem : a European journal of chemical biology · 2025Article
- Engineering the Reaction Pathway of a Non-heme Iron Oxygenase Using Ancestral Sequence Reconstruction.Journal of the American Chemical Society · 2024Article
- Periplasmic binding proteins Bug69 and Bug27 from Bordetella pertussis are in vitro high-affinity quinolinate binders with a potential role in NAD biosynthesis.FEBS open bio · 2024Article
- Genome mining of sulfonated lanthipeptides reveals unique cyclic peptide sulfotransferases.Acta pharmaceutica Sinica. B · 2024Article
- The structure of the SufS-SufE complex reveals interactions driving protected persulfide transfer in iron-sulfur cluster biogenesis.bioRxiv : the preprint server for biology · 2024Article
- N-Cα Bond Cleavage Catalyzed by a Multinuclear Iron Oxygenase from a Divergent Methanobactin-like RiPP Gene Cluster.Journal of the American Chemical Society · 2024Article
- Microbial sensor variation across biogeochemical conditions in the terrestrial deep subsurface.mSystems · 2024Article
- EFI-EST, EFI-GNT, and EFI-CGFP: Enzyme Function Initiative (EFI) Web Resource for Genomic Enzymology Tools.Journal of molecular biology · 2023Article
- Metatranscriptomic analysis uncovers prevalent viral ORFs compatible with mitochondrial translation.mSystems · 2023Article
- Leveraging a Structural Blueprint to Rationally Engineer the Rieske Oxygenase TsaM.Biochemistry · 2023Article
- Physiological insight into the conserved properties of Caenorhabditis elegans acid-sensing degenerin/epithelial sodium channels.The Journal of physiology · 2023Article
- Article
- Mechanistic Studies of Aziridine Formation Catalyzed by Mononuclear Non-Heme Iron Enzymes.Journal of the American Chemical Society · 2023Article
33 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
1 author at 1 institution in 1 country.
Funding
Abstract
The exponentially increasing number of protein and nucleic acid sequences provides opportunities to discover novel enzymes, metabolic pathways, and metabolites/natural products, thereby adding to our knowledge of biochemistry and biology. The challenge has evolved from generating sequence information to mining the databases to integrating and leveraging the available information, i.e., the availability of "genomic enzymology" web tools. Web tools that allow identification of biosynthetic gene clusters are widely used by the natural products/synthetic biology community, thereby facilitating the discovery of novel natural products and the enzymes responsible for their biosynthesis. However, many novel enzymes with interesting mechanisms participate in uncharacterized small-molecule metabolic pathways; their discovery and functional characterization also can be accomplished by leveraging information in protein and nucleic acid databases. This Perspective focuses on two genomic enzymology web tools that assist the discovery novel metabolic pathways: (1) Enzyme Function Initiative-Enzyme Similarity Tool (EFI-EST) for generating sequence similarity networks to visualize and analyze sequence-function space in protein families and (2) Enzyme Function Initiative-Genome Neighborhood Tool (EFI-GNT) for generating genome neighborhood networks to visualize and analyze the genome context in microbial and fungal genomes. Both tools have been adapted to other applications to facilitate target selection for enzyme discovery and functional characterization. As the natural products community has demonstrated, the enzymology community needs to embrace the essential role of web tools that allow the protein and genome sequence databases to be leveraged for novel insights into enzymological problems.
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Registered trials
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.