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Table 3 Number of knockouts for the biomass reaction in selected networks

From: Double and multiple knockout simulations for genome-scale metabolic network reconstructions

Model   Single knockouts Double knockouts
reaction id cl. size classes reactions cl. pairs reac. pairs
E. coli iJO1366      
Ec_biomass_iJO1366_WT_53p95M 20 101 343 130 339
Ec_biomass_iJO1366_core_53p95M 1 80 288 90 268
S. cerevisiae iND750      
biomass_SC4_bal 26 54 156 60 142
M. tuberculosis iNJ661      
biomass_Mtb_9_60atp 160 64 154 48 83
S. aureus iSB619      
SA_biomass_1a 8 25 63 59 157
SA_biomass_5a 1 58 215 54 100
H. pylori iIT341      
BiomassHP_published 189 36 76 41 81
  1. class size: Number of reactions in the same coupling class as the biomass reaction, i.e., number of reactions that carry flux if and only if the biomass reaction carries flux.
  2. Single Knockouts: Number of different single knockouts (classes and reactions) that block the biomass reaction. Only reactions that are not partially coupled to the biomass (from a different reaction class) are counted.
  3. Double Knockouts: Number of different double knockouts (class pairs and reaction pairs) that block the biomass reaction when combined. Only reactions that are not directionally coupled to the biomass are counted.