How to download KEGG database

# download pathway KO genome
wget -c http://rest.kegg.jp/list/pathway
wget -c http://rest.kegg.jp/list/ko
wget -c http://rest.kegg.jp/list/genome

# KO list
mkdir KO_files
cut -f 1 ko | sed 's/ko://' | while read id; do wget -c http://rest.kegg.jp/link/genes/$id -O KO_files/$id; done
cat KO_files/K* | sed 's/ko://' > ko_genes.txt

# gene list
mkdir gene_files
cut -f 2 genome | cut -f 1 -d "," | while read id; do wget -c http://rest.kegg.jp/list/$id -O gene_files/$id; done
cat gene_files/* | cut -f 1 > all_genes.list

# gene fasta
mkdir gene_fasta
cat all_genes.list | while read id; do wget -c http://rest.kegg.jp/get/$id/aaseq -O gene_fasta/$id; done
cat gene_fasta/* > kegg_genes.fasta

Reference

1. download KEGG database