Files describing the model and figures described in the initial submission to PLOS

Model, data and analysis code for A self-consistent autotrophic metabolic model for a hypothetical ancient ancestor (Sturgis), as revised for PLOS Computational Biology. This version matches the revised manuscript (model frozen at repository tag v0.8; bundle exported at commit e2704bd).LUCA_model.xml: the model in SBML (434 reactions, 415 metabolites), with gene–reaction rules.LUCA_model_reactions.tsv: the reactions, with genes, EC numbers, ΔG°′, cofactors and bounds.LUCA_model_compounds.tsv: the metabolites.2026-09-29_PLOSCompBiol_R1.tar.xz: everything needed to reproduce the analyses, figures and manuscript. Unpack it and run makeChanges since v0.7: ferredoxin-coupled ΔG°′ recomputed on a single basis at E°′(Fd) = −420 mV; CO dehydrogenase reversible and acetyl-CoA synthase irreversible; the gene and cofactor annotations reviewed and corrected. No flux result of the original submission changes. Each change is recorded in <code>docs/decisions.md</code> (D23–D25) in the tarball.Licensing: data, model and results are CC BY 4.0; the code (tools/, figures/src/) is MIT.The model is also deposited in BioModels as MODEL2607090001.