{"database":"BioModels","file_versions":[],"scores":null,"additional":{"submitter":["Dushmantha Madushanka Haramakkara Gedara"],"curationStatus":["Non-curated"],"modellingApproach":["constraint-based model"],"levelVersion":["L3V1"],"full_dataset_link":["https://www.ebi.ac.uk/biomodels/MODEL2608200001"],"isPrivate":["false"],"repository":["BioModels"],"modelFormat":["SBML"],"omics_type":["Models"],"tokenised_name":["iErLJJL01: a genome scale metabolic model of Erwinia sp. str. LJJL01 for plastic waste upcycling and bioproduct synthesis"],"publication_year":["2026"],"submissionId":["MODEL2608200001"],"publication_authors":["Madushanka, Dushmantha, Jayakody, Lahiru N."],"first_author":["Madushanka, Dushmantha"],"publication":["10.5281/ZENODO.22019746,\n                            N/A. N/A, N/A.\n                            N/A"],"submitter_mail":["dushmantha.haramakkara@siu.edu"],"publication_doi":["10.5281/ZENODO.22019746"],"submitter_affiliation":["Southern Illinois University Carbondale"],"additional_accession":[]},"is_claimable":false,"name":"iErLJJL01: a genome-scale metabolic model of Erwinia sp. str. LJJL01 for plastic-waste upcycling and bioproduct synthesis","description":"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.\n\nThe 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.\n\nThe 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.\n\nReleased 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.","dates":{"last_modification":"2026-08-22","publication":"2026-09-02","submission":"2026-08-20"},"accession":"MODEL2608200001","cross_references":{"doi":["10.5281/ZENODO.22019746"]}}