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Zero out unmeasured isoenzymes with a measured sibling, and report coverage #7
Description
Copied from SysBioChalmers/GECKO#480, opened by edkerk on 2026-09-10.
Why
An isoenzyme left undetected next to a measured sibling is a different case from an isoenzyme for which no proteomics data exists at all for that reaction. Leaving the undetected one pool-limited lets the model route flux through it as though it were present, and there is no way to see how many isoenzyme groups in a model carry this kind of partial coverage.
Current situation
getKcatAcrossIsozymes.m groups model.ec.rxns by base reaction (stripping _EXP_n) to fill in missing kcats from isozymes. No equivalent grouping exists for model.ec.concs. When reaction R has isoenzymes E1 and E2 and only E1 has a proteomics measurement, constrainEnzConcs.m caps E1's usage reaction at its measured value and leaves E2's usage reaction pool-limited.
What should change
Add logic that, for a reaction with a mix of measured and NaN isoenzyme concentrations, sets the unmeasured isoenzymes' usage-reaction bounds to zero instead of leaving them pool-limited. Add a separate model-overview function that reports isoenzyme groups with partial proteomics coverage.
Activity
edkerk commentedon Oct 16, 2026
edkerk commented on 2026-09-10 in SysBioChalmers/GECKO#480:
@fma91Does this address what we discussed this morning? A new function could apply this logic of "disable isoenzyme if ec.concs is NaN, while alternative isozyme has ec.concs >0"edkerk commentedon Oct 16, 2026
fma91 commented on 2026-09-11 in SysBioChalmers/GECKO#480:
I think that the isoenzymes groups will help to implemet logics to solve this. I was thinking in disabling them or setting a roof with a maximum not higher than the less detected enzymes. It is also artificial, but I have to test them.
edkerk commentedon Nov 3, 2026
Implemented in CompMetEng/GECKO#30 (geckopy: CompMetEng/geckopy#86).
getIsozymeCoveragereports the isozyme groups with a measured and an unmeasured entry.zeroUnmeasuredIsozymesis a separate function that is called afterconstrainEnzConcs:method'zero'sets the usage bound of the unmeasured isozyme to 0, and'detectionLimit'sets it to the smallest measured concentration or to a given limit, since a protein that was not detected can be below the detection limit and not absent. An enzyme that also catalyses a reaction without a measured sibling is left unchanged.ec.concsis not modified.