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 | |||||||