gapseq reconstruction for 36 human gut bacterial strains with known amino acid auxotrophy status
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The data set contains genome-scale metabolic network reconstructions for 36 bacterial genomes, for which the auxotrophy/prototrophy status for amino acids has been reported in scientific literature based on laboratory experiments. Auxotrophy/Prototrophy information and the respective PubMed-IDs (PMID) are summarized in "Validation_models_Metadata.csv". Network reconstructions were made using gapseq (development version: 1.2 commit 2dfa8c80 ; 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 -c "cpd00007:0" # 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>
