KEGG Pathway Map

Identifier The KEGG PATHWAY database is a collection of manually drawn graphical diagrams, called KEGG pathway maps, for metabolic pathways, signaling pathways, pathways involved in various cellular processes and organismal systems, and perturbed pathways associated with human diseases. The pathway map identifier takes the form of:
<prefix><five-digit number>
where the number is uniquely assigned to each pathway map and the prefix is for a different version of the same pathway map, such as "map" for the manually drawn reference pathway and the three- or four-letter organism code for a computationally generated organism specific pathway. The "Pathway menu" at the top is for changing the five-digit map number and the "Change pathway type" button is for changing the prefix.
Side panel The pathway map viewer now comes with a side panel for various operations, which may be expanded or collapsed with a triangular button.
Option
scale slider in all maps
module link mode in global (01100s) and overview (01200s) metabolic pathways
Search
search box in all maps for searching map objects by IDs or aliase
Module
module list in selected metabolic pathways
Reaction module
reaction module list in overview (01200s) metabolic pathways
Network
network list in selected reference and human pathways linking to network variation maps of the KEGG NETWORK database
Notation Except for special metabolic pathway maps called global maps (01100s) and overview maps (01200s), which are drawn with lines and circles representing enzymes and metabolites, respectively, all maps are drawn with the notation shown below. symbol notation
Color
coding
The pathway map without coloring is the original version that is manually drawn by in-house software called KegSketch. The other pathway maps with coloring are all computationally generated as summarized below.
  • Reference pathway: this is the original version; white boxes are hyperlinked to KO, ENZYME, and REACTION entries in metabolic pathways; they are hyperlinked to KO entries in non-metabolic pathways.
  • Reference pathway (KO): blue boxes are hyperlinked to KO entries that are selected from the original version.
  • Reference pathway (EC): blue boxes are hyperlinked to ENZYME entries that are selected from the original version.
  • Reference pathway (Reaction): blue boxes are hyperlinked to REACTION entries that are selected from the original version.
  • Organism-specific pathway: green boxes are hyperlinked to GENES entries by converting K numbers (KO identifiers) to gene identifiers in the reference pathway, indicating the presence of genes in the genome and also the completeness of the pathway.