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helena-bethany
Helena Cooper
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.