About KEGG Mapper

KEGG Mapper is a collection of tools for KEGG mapping: most popular KEGG pathway mapping, as well as BRITE mapping and MODULE mapping. In this new release, fourteen existing tools were reorganized into just five tools. Three of them, "Reconstruct Pathway", "Search Pathway" and "Search&Color Pathway" allow multiple mapping operations to be done at the same time. The result is shown in multiple tabs in the result page. The other two are specialized tools, "Color Pathway" and "Join Brite", for mapping against a single pathway map or a single brite hierarchy/table file.

Reference: Kanehisa, M. and Sato, Y. (2020) KEGG Mapper for inferring cellular functions from protein sequences. Protein Sci. 29, 28-35. [pubmed] [pdf]

General mapping tools against multiple databases

There are three general mapping tools with the name of "Pathway" but applicable to other target databases as well (see table below).

Reconstruct Pathway is the basic mapping tool used for processing of KO annotation (K number assignment) data both internally for KEGG GENES and in the outside services of BlastKOALA and other annotation servers.

Search Pathway and Search&Color Pathway are traditional tools present from the beginning of the KEGG project, although the target databases have been expanded. These tools match objects as they appear in both reference and organism-specific pathways, etc. Mapped objects are marked in red in Search Pathway, while they can be marked in any background and foreground colors in Search&Color Pathway.

Tool Search mode Target database Query data
(KEGG identifier)
Reconstruct Pathway Reference Pathway
Brite hierarchy/table
Module		 K number
Search Pathway Reference Pathway
Brite hierarchy/table
Module		 K/R/EC number
C/G/D/E number
Human-
specific		 Pathway
Brite hierarchy
Module
Network
Disease		 Human gene identifier
C/G/D number
Other
organism-
specific		 Pathway
Brite hierarchy
Module		 Gene identifier
K/R/RC/EC number
C/G/D number
Search&Color Pathway Reference Pathway
Brite hierarchy
Module		 K/R/EC number
C/G/D/E number
Organism-
specific		 Pathway
Brite hierarchy
Module		 Gene identifier
K/R/RC/EC number
C/G/D number
Outside gene identifier

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

Tool Data format Remark
Reconstruct Pathway 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 Pathway Free format - KEGG identifiers separated by whitespace characters (space, tab, newline) Filter
option
available
Search&Color Pathway KEGG identifier in the first column of each line
Optional color specification in the second column
(background color and foreground color)

Specialized tools for Pathway and Brite

Color Pathway - tool to color selected pathway map
  • One selected pathway map is colored in multiple ways
  • Each object is specified in one line together with color attributes, i.e., multiple background and foreground colors in multiple columns
  • Result shown as multiple snapshots of image maps
  • When numerical values are given as attributes, they are displayed by color gradation or 3D bar graph
Join Brite - tool to combine selected brite file and binary relation data
  • One selected brite hierarchy or table file is combined with a binary relation file, which contains object-attributes relations
  • Result shown in an additional column of the hierarchy or table file

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
Annotate Sequence - KO annotation 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 result linked to Reconstruct Pathway

Last updated: October 1, 2020
Version 4.3