Announcement: Module mode of global matabolic pathway map New!
The global metabolic pathway map can now be viewed as consisting of KEGG modules in the module mode. This mode is implemented in the Reconstruct Pathway tool of KEGG Mapper.
Posted on June 1, 2020
The global metabolic pathway map can now be viewed as consisting of KEGG modules in the module mode. This mode is implemented in the Reconstruct Pathway tool of KEGG Mapper.
Posted on June 1, 2020
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.
Query data must be prepared differently for different tools as shown 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 forground 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
- 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
- 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: June 1, 2020