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KEGG Pathway Reference

Free reference guide: KEGG Pathway Reference

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About KEGG Pathway Reference

The KEGG Pathway Reference is a searchable cheat sheet for the Kyoto Encyclopedia of Genes and Genomes, covering pathway ID formats (hsa, map, ko prefixes), species abbreviations (hsa for human, mmu for mouse, eco for E. coli), KEGG Orthology (KO) identifiers, MODULE functional units, and the complete KEGG REST API with endpoints for list, get, find, conv (ID conversion), and link (cross-reference) operations.

Biological pathway sections cover core metabolic pathways (glycolysis/gluconeogenesis hsa00010, TCA cycle hsa00020, oxidative phosphorylation hsa00190, fatty acid synthesis hsa00061, amino acid metabolism), major signaling cascades (MAPK hsa04010, PI3K-Akt hsa04151, Wnt hsa04310, p53 hsa04115, NF-kB hsa04064), disease pathways (cancer, infectious diseases, neurodegenerative diseases), and compound/drug databases with BRITE classification.

Designed for bioinformaticians, molecular biologists, genomics researchers, and life science students who need quick access to KEGG pathway numbers, REST API URL patterns for programmatic data retrieval, key enzyme names in metabolic pathways, signaling cascade components, and disease-associated pathway identifiers.

Key Features

  • KEGG pathway ID formats with species prefixes (hsa, mmu, sce, eco, ath) and reference map numbering
  • Complete KEGG REST API reference for list, get, find, conv (NCBI/UniProt/PubChem conversion), and link endpoints
  • Core metabolic pathways: glycolysis (hsa00010), TCA cycle (hsa00020), oxidative phosphorylation (hsa00190)
  • Major signaling cascades: MAPK, PI3K-Akt-mTOR, Wnt/beta-catenin, p53 tumor suppressor, NF-kB inflammation
  • Disease pathway IDs for cancer (hsa05200-series), infectious diseases (COVID-19, HIV), and neurodegeneration (Alzheimer, Parkinson)
  • KEGG Compound IDs for key metabolites (glucose C00031, pyruvate C00022, ATP C00002, NAD+ C00003)
  • KEGG Drug database lookup and BRITE biological classification hierarchy system
  • KO (KEGG Orthology) identifiers for cross-species ortholog group mapping

Frequently Asked Questions

What KEGG topics does this reference cover?

It covers six categories: Pathway IDs (format, species prefixes, KO identifiers, MODULE), REST API (list, get, find, conv, link, image download), Metabolic Pathways (glycolysis, TCA cycle, oxidative phosphorylation, fatty acid synthesis, amino acid metabolism), Signaling (MAPK, PI3K-Akt, Wnt, p53, NF-kB), Disease Pathways (cancer, infectious, neurodegenerative), and Compounds/Drugs (compound IDs, drug database, BRITE classification).

How do KEGG pathway IDs work?

KEGG pathway IDs consist of a 3-4 letter species prefix followed by a 5-digit number. For example, hsa00010 is human glycolysis, mmu00010 is mouse glycolysis, and map00010 is the species-independent reference pathway. The prefix hsa stands for Homo sapiens, mmu for Mus musculus, eco for E. coli, and so on.

What KEGG REST API endpoints are covered?

The reference covers all major endpoints: /list for database entry listing, /get for detailed entry retrieval, /find for keyword search, /conv for ID conversion between KEGG and external databases (NCBI Gene ID, UniProt, PubChem), /link for cross-referencing between KEGG databases, and /get/{id}/image for pathway map PNG download.

Which metabolic pathways are included?

Core metabolic pathways include glycolysis/gluconeogenesis (hsa00010) with key enzymes HK, PFK, PK, the TCA cycle (hsa00020) with citrate synthase, IDH, and alpha-KGDH, oxidative phosphorylation (hsa00190) with Complex I-V producing 30-32 ATP per glucose, fatty acid synthesis (hsa00061) via ACC and FAS, and an overview of major amino acid metabolism pathways.

What signaling pathways are covered?

Five major signaling cascades are included: MAPK (RTK-Ras-Raf-MEK-ERK with RAS mutations in ~30% of cancers), PI3K-Akt-mTOR (with PTEN as negative regulator), Wnt/beta-catenin (linked to APC mutations in colorectal cancer), p53 tumor suppressor (ATM/ATR-p53-p21/BAX with MDM2 regulation), and NF-kB inflammation pathway (TNF/IL-1 signaling through IKK).

Does the reference include disease pathways?

Yes. Cancer pathways include the general cancer pathway (hsa05200), colorectal (hsa05210), lung (hsa05223), breast (hsa05224), and liver cancer (hsa05225). Infectious disease pathways cover COVID-19 (hsa05171), HIV (hsa05170), and bacterial infections. Neurodegenerative pathways include Alzheimer (hsa05010), Parkinson (hsa05012), ALS (hsa05014), and Huntington disease (hsa05016).

How can I convert between KEGG IDs and other databases?

Use the KEGG REST API conv endpoint. For example, https://rest.kegg.jp/conv/ncbi-geneid/hsa converts human KEGG gene IDs to NCBI Gene IDs, /conv/hsa/uniprot maps UniProt to KEGG, and /conv/compound/pubchem converts PubChem compound IDs to KEGG compound IDs. This is essential for integrating KEGG data with other bioinformatics databases.

Is this KEGG pathway reference free to use?

Yes, it is completely free with no registration required. All content runs in your browser with no data sent to servers. It is part of liminfo.com's collection of free bioinformatics and life science reference tools.