For KEGG you should put in the raw fasta file to create the database. I know they have a reduced set of proteins as well as a full set. There is a kegg.reduced.fasta.tar.bz2 or fasta.tar.bz2. Both of these work with the pipeline, they just have to be unzipped and placed in the blastDB folder and put in the parameter file (e.g., template_param.txt) before running.
For KEGG you should put in the raw fasta file to create the database. I know they have a reduced set of proteins as well as a full set. There is a kegg.reduced.fasta.tar.bz2 or fasta.tar.bz2. Both of these work with the pipeline, they just have to be unzipped and placed in the blastDB folder and put in the parameter file (e.g., template_param.txt) before running.
Hope this helps.
Niels