KEGG as a reference resource for gene and protein annotation
Open accessAbstract
KEGG (http://www.kegg.jp/ or http://www.genome.jp/kegg/) is an integrated database resource for biological interpretation of genome sequences and other high-throughput data. Molecular functions of genes and proteins are associated with ortholog groups and stored in the KEGG Orthology (KO) database. The KEGG pathway maps, BRITE hierarchies and KEGG modules are developed as networks of KO nodes, representing high-level functions of the cell and the organism. Currently, more than 4000 complete genomes are annotated with KOs in the KEGG GENES database, which can be used as a reference data set for KO assignment and subsequent reconstruction of KEGG pathways and other molecular networks. As an annotation resource, the following improvements have been made. First, each KO record is re-examined and associated with protein sequence data used in experiments of functional characterization. Second, the GENES database now includes viruses, plasmids, and the addendum category for functionally characterized proteins that are not represented in complete genomes. Third, new automatic annotation servers, BlastKOALA and GhostKOALA, are made available utilizing the non-redundant pangenome data set generated from the GENES database. As a resource for translational bioinformatics, various data sets are created for antimicrobial resistance and drug interaction networks.
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Two important precursors for clavulanic acid are arginine (C5 precursor) and glutaraldehyde-3-phosphate (C3 precursor).
“These efforts then resulted in the identification of two important precursors for clavulanic acid—arginine (C5 precursor) and glutaraldehyde-3-phosphate (C3 precursor) (Romero et al., 1986; Kanehisa and Goto, 2000; Kanehisa et al., 2016).”
From Fermentation Conditions that Affect Clavulanic Acid Production in Streptomyces clavuligerus: A Systematic Review (2016) · cites this paper as Kanehisa et al., 2016
The Overview of KEGG describes databases of chemical compounds and reactions, and the antimicrobial-resistance section mentions antibiotic-biosynthesis pathway maps, but neither identifies clavulanic acid precursors. Searches for clavulanic acid, arginine, and the claimed C3 and C5 precursors found no passage addressing the claim. (LLM, conf=0.76)
Experimental — accuracy not yet measuredMGnify's latest update v5.0, released September 2019, extends analyses further, substantially increasing the scope of functional annotations through the addition of KEGG orthologue predictions for reads and assembled contigs, and KEGG pathways and Genome Properties annotations for assembled contigs.
“The latest update (v5.0), released September 2019, extends the analyses further, substantially increasing the scope of functional annotations through the addition of KEGG (23) orthologue predictions for reads and assembled contigs, and KEGG pathways and Genome Properties (24) annotations for assembled contigs.”
From MGnify: the microbiome analysis resource in 2020 (2019) · cites this paper as [23]
Additional functional analyses are provided in the form of KEGG orthologue annotations, calculated using HMMER and the KOfam library on predicted protein sequences.
“Additional functional analyses are also provided in the form of KEGG orthologue (KO) (23) annotations, which are calculated using HMMER (40) and the KOfam library (using a slightly modified form of the profile hidden Markov model (HMM) database of KEGG orthologues (41)) on the predicted protein sequences.”
From MGnify: the microbiome analysis resource in 2020 (2019) · cites this paper as [23]
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- Authors
- Kanehisa, M., Sato, Y., Kawashima, M., Furumichi, M., & Tanabe, M.
- Affiliations
- Kyoto University (JP)
- Fujitsu (Japan) (JP)
- Corresponding author
- Kanehisa, Minoru
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2015-10-17
- Volume
- 44
- Issue
- D1
- Pages
- D457-D462
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC4702792
- OpenAlex
- W2110256992
- Cited by
- 7,387
- References
- 14
- Citations by year
- 2026: 608 · 2025: 846 · 2024: 766 · 2023: 726 · 2022: 819 · 2021: 811 · 2020: 636 · 2019: 621 · 2018: 638 · 2017: 581 · 2016: 320 · 2015: 6 · 2013: 1 · 2012: 2
- FWCI
- 224.75
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Nucleic Acids Research (publishedVersion, cc-by-nc)
- Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
- PubMed Central (publishedVersion, cc-by-nc)
- PubMed (publishedVersion)
- Institutional Repositories DataBase (IRDB) (submittedVersion, other-oa)
- HighWire Press Open Archive (submittedVersion)
- Kyoto University Research Information Repository (Kyoto University) (submittedVersion, cc-by-nc)
- Funders
- Japan Science and Technology Agency
- Institute for Chemical Research, Kyoto University
- National Bioscience Database Center
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Bioinformatics and Genomic Networks
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Microbial Metabolic Engineering and Bioproduction
- Keywords
- KEGG, KEGG Orthology, genome annotation, KEGG pathways, KEGG modules, orthogroups, pan-genome, drug interaction networks
- MeSH terms
- Amino Acid Sequence, Drug Resistance, Microbial, Genes, Plasmids, Proteins, Viruses, Genome, Databases, Genetic, Metabolic Networks and Pathways, Molecular Sequence Annotation
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