examples/thermodynamic_metabolic_model/notes.txt
No explicit definition of compartments
Missing several columns from metabolite and reaction tables
Use different reaction ids in different workbooks
All metabolites in ecoli457 except 5:
f1p
fru
gal
gal1p
glcn
All reactions in ecoli457 except 12:
EX_fru(e)
EX_gal(e)
EX_glcn(e)
FRUK
FRUpts
G3PD5
GALabc
GALKr
GlcnUpt
GLYK
GNK
UGLT
Reactions have same stoichiometry and directionality except 2:
ACS: (2) pi vs ppi
FUM_SEC: includes proton symport vs no symport
Reactions have same reversibility except 5
ACKr
FUM
FUM_SEC
GlycUpt
PTAr
Reversed direction of some reactions for consistency with Khodayari and Maranas
[e]: <=> glyc
Mapped all but 14 fluxes to specific reactions:
PFK-FBP
Middle_EMP
Low_EMP
PYK-PPS
ED
PPP_ED_branch
Early_PPP
Non-ox_PPP
Early_TCA
Int_TCA
MDH+MQO
ME
Glx_Cycle
Growth_rate
Mapped all ΔG to specific reactions