gapseq reconstructions for 124 prototrophic genotypes
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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. <pre><code># 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</code></pre> 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).
