KEGG in Keg

KEGG Mapper

A suite of KEGG mapping tools

[ Reconstruct | Search | Color | Join | MWsearch ]

About KEGG Mapper

KEGG Mapper is a collection of tools for KEGG mapping including popular KEGG pathway mapping, JOIN BRITE operations and MODULE completeness checks. Historically, two basic tools of "Search Pathway" (currently, Search) and "Search&Color Pathway" (currently, Color) were introduced at the beginning of the KEGG project. As the KEGG database contents expanded, so did the mapping tools [1,2].

The current version 5 of KEGG Mapper released in July 2021 consists of four main tools: Reconstruct, Search, Color and Join. Since October 2023 these tools are tightly integrated with KEGG pathway map viewer and Brite hierarchy viewer, so that the final steps of mapping are processed on the client side.

See also: Map coloring GUI and Map coloring URL in KEGG Web Apps.

KEGG Mapper tools

There are five KEGG Mapper tools as summarized below.

Reconstruct is the basic mapping tool used for linking KO annotation (K number assignment) data to KEGG pathway maps, BRITE hierarchies and tables, and KEGG modules.

Search is the traditional tool for searching mapped objects in the user's dataset and mark them in red.

Color is another traditional tool for searching mapped objects in the user's dataset and mark them in any combination of background and foreground colors. This tool now applies only to KEGG pathway maps. Use the Join tool for coloring of Brite hierarchies.

Join is a tool to combine a Brite hierarchy file and a binary relation file, effectively adding a new column to the hierarchy file.

MWsearch is a variant of the Search tool performing conversion of mass spectropy data, either as a set of molecular masses or molecular formulas, to a set of numbers.

Tool Search mode Target database Query data
(KEGG identifier)
Reconstruct Reference Pathway
Brite hierarchy
Brite table
K number
Search Reference Pathway
Brite hierarchy
Brite table
K/R/EC number
C/G/D/H number
KEGG organism code
hsa Pathway (hsa)
Brite hierarchy (hsa)
Module (hsa)
Human gene identifier
C/G/D number
other org1 Pathway (org)
Brite hierarchy (org)
Module (org)
Gene identifier
C/G/D number
Color Reference Pathway K/R/EC number
C/G/D number
org1 Pathway (org) Gene identifier
C/G/D number
Join Reference Brite hierarchy
Brie table
K number
C/G/D/H number
KEGG organism code
MWsearch Formula
Exact mass
C number
Pathway C number
org1 three- or four-letter organism code

Query data must be prepared differently for different tools as shown below.

Tool Data format Remark
Reconstruct K number in the second column of each line
The first column may be used for user's gene ID
Same as BlastKOALA output
Search Free format - KEGG identifiers separated by
whitespace characters (space, tab, newline)
Filter option available
Color KEGG identifier in the first column of each line
Optional color specification in the second column
(background color and foreground color)
Join KEGG identifier in the first column of each line
Any attribute in the second column
MWsearch Free format - Data items separated by whitespace characters

Other tools

Convert ID - Conversion of outside identifiers to KEGG identifiers
  • Accept NCBI-GeneIDs, NCBI-ProteinID and UniProt accession for conversion into KEGG GENES ID
Assign KO - KO assignment of user's sequence data
  • Accept query amino acid sequence data in FASTA format
  • Compare against a small subset of KEGG GENES database using BlastKOALA
  • Annotation (KO assignment) result linked to the Reconstruct tool

Taxonomy mapping tool

The Taxonomy mapping tool is a special purpose mapping tool based on the KEGG Mapper Join function. It is designed to integrate taxonomic distributions of KOs and modules with phenotypic features.

  1. Kanehisa, M. and Sato, Y.; KEGG Mapper for inferring cellular functions from protein sequences. Protein Sci. 29, 28-35 (2020). [pubmed] [pdf]
  2. Kanehisa, M., Sato, Y., and Kawashima, M.; KEGG mapping tools for uncovering hidden features in biological data. Protein Sci. 31, 47-53 (2022). [pubmed] [doi]

Last updated: July 1, 2024
Version 5.2