IErLJJL01: a genome-scale metabolic model of Erwinia sp. str. LJJL01 for plastic-waste upcycling and bioproduct synthesis

ABSTRACT: iErLJJL01 is the first genome-scale metabolic model (GEM) of Erwinia sp. str. LJJL01, a non-model Gammaproteobacterium developed as a chassis for upcycling organic waste materials and plastic-derived compounds into value-added products. The model links 3,100 reactions, 1,962 metabolites, and 1,520 genes, and is provided in SBML Level 3 Version 1 with the Flux Balance Constraints (FBC v2) package. The reconstruction was generated with CarveMe from the strain proteome, manually curated for plastic-monomer catabolism, strain-specific biomass, and product pathways, and integrated with transcriptomic data across eight growth conditions. It reproduces 88% of experimental carbon-source growth phenotypes with zero false negatives, and scores 75.9% on MEMOTE with 100% SBO-term coverage and 99.96% of reactions mass-balanced. The source genome is NCBI GenBank CP178576.1 (RefSeq assembly GCF_047300805.1). This archive contains the SBML model, a JSON copy for browser-based exploration in Escher-FBA, the full MEMOTE quality report, a COBRApy usage script, a user guide, and the technical development report. Released under CC-BY-4.0. Developed by Dushmantha Madushanka and Lahiru N. Jayakody, Southern Illinois University Carbondale, with support from the NSF-funded plastic-upcycling project.

SUBMITTER: Dushmantha Madushanka Haramakkara Gedara  

PROVIDER: MODEL2608200001 | BioModels | 2026-09-02

REPOSITORIES: BioModels