gapseq reference sequence databases for Bacteria and Archaea

The repository contains the protein sequences used by gapseq to predict the presence of metabolic reactions and to construct metabolic models.

The workflow using gapseq to generate this set of reference protein sequences:

```sh

# delete all "old" datarm dat/seq/Bacteria/rev/*.fastarm dat/seq/Bacteria/unrev/*.fastarm dat/seq/Bacteria/rxn/*.fastarm dat/seq/Archaea/rev/*.fastarm dat/seq/Archaea/unrev/*.fastarm dat/seq/Archaea/rxn/*.fasta

# run gapseq find to re-download everything## the genome is irrelevant as no blasting is performed ('-x')gapseq find -p all -t Bacteria -n -x -U toy/ecoli.faa.gz > bac_update.log 2>&1gapseq find -p all -t Archaea -n -x -U toy/ecoli.faa.gz > ar_update.log 2>&1

# create all sequence .tar.gz archives (rev/unrev/rxn)cd dat/seq/Bacteria/rev/ && tar -czvf sequences.tar.gz ./*.fasta && cd ../../../../cd dat/seq/Bacteria/unrev/ && tar -czvf sequences.tar.gz ./*.fasta && cd ../../../../cd dat/seq/Bacteria/rxn/ && tar -czvf sequences.tar.gz ./*.fasta && cd ../../../../cd dat/seq/Archaea/rev/ && tar -czvf sequences.tar.gz ./*.fasta && cd ../../../../cd dat/seq/Archaea/unrev/ && tar -czvf sequences.tar.gz ./*.fasta && cd ../../../../cd dat/seq/Archaea/rxn/ && tar -czvf sequences.tar.gz ./*.fasta && cd ../../../../

# create md5sum table for all tar.gz archivescd dat/seq/find -mindepth 2 -type f -name "*.tar.gz" -exec md5sum {} \; > md5sums.txt

# create taxon-specific final archive for Zenodo uploadtar -czvf Bacteria.tar.gz Bacteria/*/*.tar.gztar -czvf Archaea.tar.gz Archaea/*/*.tar.gz

# Upload Bacteria.tar.gz, Archaea.tar.gz, and md5sums.txt  to Zenodo via the web-interface

```