KpSC-pan-v2.0.3

Sink reactions associated with DNA methylation (originally inherited from iYL1228) have been removed from the KpSC pan reference model as they enabled the model to simulate growth without any resources (see Thiele et al 2010 Nat Protoc for explanation on how this can occur). All catalytic reactions, genes and metabolites associated with methylation were removed to prevent this issue from occurring again.

Specifically, the following were removed:

• Reactions: SK_dna_c, SK_dna5mtc_c, DNAMTn2r & CYTOM
• Metabolites: dna_c & dna5mtc_c
• Genes: KPN_04707, KPN_02428 & Klebsiella_variicola_INF345_05559

The following predicted growth phenotypes have changed based on the 507 isolates described in Cooper et al 2024 Mgen.

• EX_met__L_e sulfur utilisation in aerobic and anerobic conditions: Core growth to no growth across all isolates.
• EX_mmet_e sulfur utilisation in aerobic and anerobic conditions: Core growth to no growth across all isolates.

KpSC-pan-v2.0.2

Minor update to the KpSC pan metabolic model:

• Fixed typo in the gene-reaction-rule for reaction "ACACCT".

KpSC-pan-v2.0.1

Minor updates to the KpSC pan metabolic model:

• Correcting the model ID in KpSC_pan_metabolic_model_v2.xml so that it SBML compliant.
• Restored the file contents in Version-1/KpSC_pan-metabolic_model_v1.xml.

KpSC-pan-v2.0

Updated KpSC pan metabolic model including:

• 1138 additional genes as compared to KpSC pan v1
• 1231 additional reactions, including 57 additional exchange reactions (enable substrate usage simulations) as compared to KpSC pan v1
• updated biomass objective function to remove requirement for strain-specific capsule sugars

For full details and information about phenotypic validation, see https://doi.org/10.1101/2023.12.20.572682.