Comp2GPR: A Sequence-Driven Framework for Gene.Protein-Reaction Rule Reconstruction

Abstract

Accurate gene-protein-reaction (GPR) associations are essential for the predictive performance of genome-scale metabolic models (GEMs), as they define the mapping between genes, enzymes, and metabolic reactions. However, GPR rules are often incomplete or inconsistent due to limitations in annotation transfer and the ambiguous representation of multi-subunit protein complexes, leading to errors in downstream analyses such as gene essentiality prediction. Here, I introduce Comp2GPR, an automated pipeline for reconstructing GPR rules that integrates curated protein complex information with sequence-level evidence. Protein complexes were sourced from the Complex Portal and subjected to an AI-assisted curation workflow to retain only metabolically relevant assemblies. Comp2GPR combines deterministic sequence similarity mapping with explicit rule construction to generate Boolean GPR expressions that accurately represent obligate subunit relationships and isoenzyme redundancy. I evaluated the impact of the reconstructed GPR rules by integrating them into the Yeast9 metabolic model and comparing gene essentiality predictions with the original model. While global performance metrics remained largely unchanged, the updated model achieved a net improvement in prediction accuracy through gene-level corrections. Overall, Comp2GPR demonstrates that combining curated protein complex data with sequence-based validation improves the accuracy, interpretability, and reproducibility of GPR rules. The method provides a robust framework for enhancing metabolic model annotations and supports more reliable simulation-based analyses.