Discrepancy between Reaction biochemistry table and reactions upon reconstruction

[ctseto]

A reaction in an SBML in a metabolic reconstruction is annotated as:
<reaction id="rxn00058_c0" name="Ferrocytochrome_c_oxygen_oxidoreductase_c0" reversible="true">
Although this runs counter to:

id abbreviation name reversibility direction
rxn00058 R00081 Ferrocytochrome-c:oxygen oxidoreductase > >

deltag deltagerr compound_ids status is_obsolete linked_reaction
-79.17 1.12 cpd00109;cpd00067;cpd00007;cpd00110;cpd00001 OK 0 rxn33884

My understanding was that reversible="true" would lead to reversibility of "=" and direction of "=". Do reversibility and direction encoded in the biochemistry affect how reversibility is defined during model reconstruction?

[samseaver]

Can you let me know what template the model originated from?

[ctseto]

Generated from the GramNegative template.

[samseaver]

I can confirm that the template itself shows this reaction to be reversible.

The microbial templates were generated a while before we established the ModelSEEDDatabase repository, would you like to do a review and check to see how many cases there are where the estimated thermodynamics run counter to what you observe in the reactions?

[samseaver]

Couple more things:

This is a transport reaction, the estimated thermodynamics currently shown in the ModelSEEDDatabase do not include the thermodynamics of transport (i.e. species concentration and electrochemical differences across compartments).

Having said that, reviewing the molecular biology underlying the reaction itself shows that it probably should be irreversible.