Published August 21, 2023
| Version 0.1.0
Dataset
Open
gapseq reconstruction for 36 human gut bacterial strains with known amino acid auxotrophy status
Creators
- 1. Institute of Human Nutrition and Food Science, Nutriinformatics, Kiel University, Kiel, Germany
Description
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.
# 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
Files
Validation_models.zip
Files
(96.1 MB)
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