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Table 5 Environmental Conditions of Models. Table detailing the models used for estimation formulation, along with their environmental conditions.

From: Estimation of the number of extreme pathways for metabolic networks

  Core Metabolites Core Metabolites Specification
Organisms Name Type Inputs Outputs   Free  
H. pylori co2 Free Ac ac mal-L   Single Input along with core metabolite, allowing all outputs (unless specified as input only)
  fe2 Free acac akg orn   
  fe3 Free ad asp-L phe-L   
  h2o Free ade acald pro-L   
  h Free akg etoh pyr   
  nh4 Free etoh fum ser-L   
  pi Free fum glu-L succ   
  so4 Free gsn gsn thr-L   
  o2 Free lac gua trp-L   
    mal h2co3 tyr-L   
    pyr hxan urea   
    succ lac-L    
    urea lys-L    
Mitochondria co2 Free arachd atp glu-L   Single Input along with core metabolite, allowing all outputs (unless specified as input only)
  h Free bhb pheme gly   
  h2o Free crvnc phs-L glyc   
  fe2 Input glc-D 12dgr_m glyc3p   
  o2 Input glu-L acac hdca   
  pi Input hdca arachd lac-L   
  urea Output lac-L bhb ocdca   
    ocdc All coa ocdcea   
    ocdca crvnc ocdcya   
    ocdcea cys-L pheme   
    ocdcya glc-D ps_m   
Mitochondria co2, h, h20 fe2, fe3, o2 urea Free acac atp   12dgr_m (1) Single K/O of: CYOOm3, SUCD3-u10m
   Input arachd lac-L   coa  
   Output Bhb pheme   cys-L  
    crvnc phs-L   glu-L (2) Individual Request for: atp, phs-L, pheme
    glc-D    gly  
    glyc    ps_m  
    glyc3p     
    hdca     
    ocdca     
    ocdcea     
    ocdcya     
E. coli Core co2 Free ac ac    Single Input along with core metabolite, allowing all outputs (unless specified as input only)
  h Free akg akg    
  h2o Free etoh etoh    
  o2 Input for for    
  pi Input fum fum    
    glc-D lac-D    
    lac-D pyr    
    pyr succ    
    succ     
RBC adp, atp, co2, h, h2o, nad, nadh nadp, nadph, nh3, pi Free ade 23dpg ino   (1) Single Input along with core metabolite, allowing all outputs (unless specified as input only)
   Free ado ade lac   
   Free glc ado pyr   
    hx glc    
    ino hx    
    lac     
    pyr     
    glc 23dpg   ade (2) Multiple Inputs
     hx   ado  
       ino  
       pyr  
       ino  
Central E. coli adp, atp, coa, co2, h, h2o, nad, nadh, nadp, nadph, pi, ppi Free glycogen 2dmmql8 mqn8   (1) Glycogen as Primary Input
   Free   2dmmq8 mql8   
   Free   3pg oaa   
     akg pep   
     amp pyr   
     e4p q8   
     fad q8h2   
     fadh2 r5p   
    fad 2dmmq8 pyr   (2) A different set of Primary Input
    q8 fadh2 pep   
    2dmmql8 q8h2 e4p   
     amp r5p   
     oaa 3pg   
     akg