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m-jahn / genome-scale-models

Genome scale metabolic models in SBML format
GNU General Public License v3.0
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reactions PYR5OXX and PYR5OXM have wrong directionality #3

Closed m-jahn closed 4 years ago

m-jahn commented 4 years ago

Both reactions in pyridoxal-phosphate metabolism are defined as reversible, but thermodynamics should allow only one direction. Reaction name, id, and reaction definition should be updated according to Bigg standard.

m-jahn commented 4 years ago

Similar reactions in Bigg db are also tagged as reversible so this seems not entirely wrong. However, computed estimation of dG = -25.4±1.14 (kcal/mol) points towards irreversible, forward direction at least for PYR5OXX (source: modelSEED). Reaction name, id (PYDXNO) and directionality should be adjusted to Bigg standard.