KEGG annotation of ORFs
======

KEGG is a database of hierarchical biological functions.

 - Website: https://www.genome.jp/kegg/

 - Citation: Kanehisa M, Furumichi M, Sato Y, Ishiguro-Watanabe M, Tanabe M.
   KEGG: integrating viruses and cellular organisms. Nucleic acids research.
   2021 Jan 8;49(D1):D545-51.

KOfam release 2022-03-01 was used as the reference for annotation.

 - Source: https://www.genome.jp/ftp/db/kofam/archives/2022-03-01/

KofamScan v1.3.0 was used to perform annotation. Command:

```
exec_annotation -f detail-tsv --no-report-unannotated -o output.tsv input.faa
```

KEGG release 102.0+ (2022-05-03) was used to construct high-level hierarchies
of functional catalogs.

 - Source: From the KEGG website using the REST API.

Statistics:

 - Total number of matches: 22,571,932
 - Number of annotated ORFs: 21,541,087
 - Number of KOs ("K"): 10,237
 - Number of modules ("M"): 395
 - Number of pathways ("ko"): 408
 - Number of compounds ("C"): 6,363 *
   - Number of drugs ("D"): 109
   - Number of glycans ("G"): 246
 - Number of reactions ("R"): 4,515
 - Number of rclasses ("RC"): 1,552
 - Number of diseases ("H"): 527

 * Note: drugs and glycans are included in the compound mappings.

Database files:

 - orf-to-ko.map: Mapping of ORFs to KEGG orthologies (KOs). KOs are the
   entrance to the KEGG system.

 - For other files refer to "Typical filename patterns" of ../README.

Collapsing order:

```
           compound
               ^
   EC    > reaction > rclass
     \  /      ^
ORF > KO -> module  > class
      | \      v
      |  >  pathway > class
       \       v
        ->  disease
```

Notes:

- Three KOs: K16119, K16120, and K16121 are present in Kofam but obsolete in
  KEGG. They have no mapping.