gapseq reconstructions for 124 prototrophic genotypes

The data set contains genome-scale metabolic network reconstructions for 124 bacterial genomes, that are phototrophic for all 20 proteinogenic amino acids (doi: 10.1038/s41559-022-01936-3). Reconstructions were made using gapseq (development version: 1.2, commit 13d88a68; Sequence DB md5sum: bf8ba98 (2023-02-15, Bacteria).

The models were reconstructed using the following workflow.

# Reaction & Pathway prediction
./gapseq find -b 200 -v 1 -p all -k -t Bacteria <genomeID>.fna.gz

# Transporter prediction
./gapseq find-transport -b 200 -k <genomeID>.fna.gz

# Draft network reconstruction
./gapseq draft -r <genomeID>-all-Reactions.tbl -t <genomeID>-Transporter.tbl -b Bacteria -c <genomeID>.fna.gz -p <genomeID>-all-Pathways.tbl -u 200 -l 100

# gapfill/growth medium prediction
./gapseq medium -m <genomeID>-draft.RDS -p <genomeID>-all-Pathways.tbl

# Gap-filling
# (If H2 is part of the medium)
./gapseq fill -m <genomeID>-draft.RDS -n <genomeID>-medium.csv -c <genomeID>-rxnWeights.RDS -g <genomeID>-rxnXgenes.RDS -b 100 -e highH2
# (If H2 is not part of the medium)
./gapseq fill -m <genomeID>-draft.RDS -n <genomeID>-medium.csv -c <genomeID>-rxnWeights.RDS -g <genomeID>-rxnXgenes.RDS -b 100

Please note that the model collection is missing three genomes because they were not available (suppressed) on NCBI (GCF_000014265.1, GCF_000020545.1, GCF_9001188395.1).