This repository hosts a Klebsiella pneumoniae Species Complex pan-metabolic model (KpSC-pan)
KpSC-pan v2 was constructed using the 507 strain-specific KpSC genome-scale metabolic models described in Cooper et al, 2023, bioRxiv.
This model was designed as a reference model for input into Bactabolize, a pipeline for rapid construction of strain-specific genome scale metabolic models and phenotype prediction.
This repository contains files corresponding to the KpSC-pan metabolic model. As these are not from a single genome, genomic information has been provided in multifasta files (.fna, .faa) instead of a .gbk. BiGG nomenclature is used.
| File | Description |
|---|---|
| KpSC_pan-metabolic_model_v2.xml | KpSC-pan v2 (.xml) |
| KpSC_pan-metabolic_model_v2.json | KpSC-pan v2 (.json) |
| KpSC_pan-metabolic_model_v2_nucl.fna | Coding sequences of gene reaction rules (GPRs) from KpSC-pan v2 (.fna) |
| KpSC_pan-metabolic_model_v2_prots.faa | Protein sequences of gene reaction rules (GPRs) from KpSC-pan v2 (.faa) |
| KpSC_pan_metabolic_model_v2_reaction_metadata.tsv | Metadata and external database IDs for the reactions from KpSC-pan v2 (.tsv) |
| Version-1/ | Directory containing the KpSC-pan v1 model and associated files |
If you make use of the KpSC pan metabolic model v2, please cite A validated pangenome-scale metabolic model for the Klebsiella pneumoniae species complex, (2023), bioRxiv, https://doi.org/10.1101/2023.12.20.572682.
If you make use of the previous version (KpSC pan metabolic model v1), please cite Bactabolize: A tool for high-throughput generation of bacterial strain-specific metabolic models, (2023), eLife, https://doi.org/10.7554/eLife.87406.1.