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GEM-iPfu, Genome-scale metabolic model of Pyrococcus furiosus

DOI

Files in this repository represent the genome-scale model of Pyrococcus furiosus. The model is first reported in the following publication:

  • Vailionis, J. Zhao, W., Zhang, K., Rodionov, D., Lipscomb, G. L., Tanwee, T. N. N., O'Quinn, H. C., Kelly R. M., Adams, M. W. W., Zhang, Y. 2023. Optimizing strategies for bio- based ethanol production using genome-scale metabolic model of the hyperthermophilic archaeon, Pyrococcus furiosus. Appl. Environ. Microbiol.

This work is licensed under a Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International License.

List of files

Model files

  • model.yaml

    Basic model definition YAML file, configured for the WT model by default

  • model_product.yaml

    alternative model definition YAML file, configured to use the EX_YM_adhf.yaml media file and COM1 model by default, which requires additional files to be loaded

Model definitions

  • WT_model_def.tsv

    list of reactions that make up the WT (DSM 3638) model

  • COM1_model_def.tsv

    list of reactions that make up the COM1 model

  • media_def.tsv

    includes additional components that are required to use the EX_YM_adhf.tsv media

Model components

  • compounds.yaml

    definition of metabolites

  • reactions.yaml

    definition of reactions based on genome annotations of the P. furiosus DSM 3638

  • engineered_reactions.yaml

    definition of reactions related to the simulation of engineering designs in P. furiosus

  • limits.yaml

    defines bounds on specific reactions that can differ from their enzymatic directionality

  • sink.yaml

    definition of compound sink reactions

  • transport.yaml

    definition of transport reactions

  • EX_byproduct.yaml

    exchange file which allows potential byproducts to be released

  • spontaneous.yaml

    definition of spontaneous/non-enzymatic reactions

  • biomass.yaml

    definition of biomass reactions

  • gapfill.yaml

    gap-filling reactions

  • media_compounds.yaml

    additional compounds that are required to use the EX_YM_adhf.tsv media

  • media_conversion_rxns.yaml

    additional reactions that are required to use the EX_YM_adhf.tsv media

Media definitions

  • EX_Kengen_94.tsv

    Media matching experiments from Kengen and Stams 1994 (Growth and energy conservation in batch cultures of Pyrococcus furiosus. FEMS Microbiol Lett 117:305–309.)

  • Adams_media/*

    Media matching various carbon conditions from Adams et al. 2001. (Key Role for Sulfur in Peptide Metabolism and in Regulation of Three Hydrogenases in the Hyperthermophilic Archaeon Pyrococcus furiosus. J Bacteriol 183:716–724.)

    Inlcudes three files:

    • EX_Adams_Peptide-S0.tsv - Peptide medium with sulfur
    • EX_Adams_Malt-Peptide-S0.tsv - Peptide + maltose medium with sulfur
    • EX_Adams_Malt-S0.tsv - Maltose medium with sulfur

  • EX_YM_adhf.tsv

    minimal maltose medium, can be configured to use different concentrations of yeast extract