| name | kegg |
| description | KEGG as a reference for gene/protein annotation — KO orthologs, pathways, modules, BRITE (BlastKOALA / GhostKOALA and related assignment). Use when: (1) Mapping genes/MAGs to KEGG Orthology, (2) Reconstructing pathways/modules, (3) Choosing KEGG vs eggNOG / MetaCyc / DRAM distillation, (4) Citing KEGG releases in Methods. Portal: https://www.kegg.jp/. Licensing/access constraints apply for bulk use — verify institutional rights. For eggNOG use eggnog-mapper. For pathway abundance from reads use humann. For routing use public-databases.
|
| license | MIT |
| category | utilities |
| tags | ["database","KEGG","KO","pathway","annotation"] |
| upstream | https://www.kegg.jp/ |
KEGG (Kyoto Encyclopedia of Genes and Genomes)
Portal: https://www.kegg.jp/ · https://www.genome.jp/kegg/
Citation
Kanehisa, M., Sato, Y., Kawashima, M., Furumichi, M. & Tanabe, M. KEGG as a
reference resource for gene and protein annotation. Nucleic Acids Res. 44,
D457–D462 (2016). https://doi.org/10.1093/nar/gkv1070
See also docs/references.md.
Analytical thinking
KEGG links genes to high-level functions via KO (K numbers) → PATHWAY /
MODULE / BRITE networks. In shotgun workflows it appears as:
| Path | Typical tools |
|---|
| Gene → KO assignment | BlastKOALA / GhostKOALA / KofamKOALA; or via eggNOG-mapper KEGG fields |
| Pathway abundance from reads | Often MetaCyc via humann (not raw KEGG API) |
| Distilled metabolism tables | dram (multi-DB including KEGG-related sources) |
Hard rules:
- License / redistributability — KEGG is not a free-for-all dump; confirm
access rights before bulk downloads or redistributing KO databases.
- Pin KEGG / KOALA DB versions next to software versions.
- Pathway presence from incomplete MAGs ≠ organism capability proof.
- Do not merge HUMAnN MetaCyc pathway names with KEGG map IDs unlabeled.
Decision tree
Functional reference need?
├─ KO / KEGG pathway maps with institutional access → kegg
├─ Orthology + multi-DB (COG/KEGG/CAZy fields) → eggnog-mapper
├─ Read-level gene families / MetaCyc pathways → humann + biobakery-databases
├─ Curated MAG metabolism distillate → dram
└─ CAZymes specifically → dbcan
Related skills
public-databases · eggnog-mapper · humann · dram · gapseq ·
progenomes · biobakery-databases
