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enzyme usage unit #376

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HossFir opened this issue May 9, 2024 · 1 comment
Closed

enzyme usage unit #376

HossFir opened this issue May 9, 2024 · 1 comment
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fixed in develop Has already been addressed in develop branch

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@HossFir
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HossFir commented May 9, 2024

GECKO/src/geckomat/utilities/enzymeUsage.m

Line 5 in afa2334

% 1) absolute usage: the specific enzyme usage in ug/gDCW/h, which can

For consistency with the proteomics data, the absolute usage should be expressed in mg/gDW, as the proteomics data has this unit. The absolute usage is then multiplied by kcat/mw to convert the unit to mmol/gDW/hr!
@edkerk
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edkerk commented May 26, 2024

The enzymeUsage function is directly reporting the flux value from the enzyme usage reactions, so in mg/gDCW. The function documentation is just incorrect, while change that line to mention mg/gDCW instead.

edkerk added a commit that referenced this issue May 26, 2024
@edkerk
fix: enzymeUsage correct mention of output units
3916779 
solves #376
@edkerk edkerk mentioned this issue May 26, 2024
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@edkerk edkerk added the fixed in develop Has already been addressed in develop branch label May 27, 2024
@edkerk edkerk closed this as completed May 27, 2024
edkerk added a commit that referenced this issue May 27, 2024
@edkerk
feat: prot_usage always draws from prot_pool (#379)
cb54747 
* fix: calculateFfactor can take protData input

* feat: constrainEnzConcs keep prot pool draw

addresses #375

* fix: updateProtPool obsolete

* doc: update full_ecModel for prot_usage rxns

* fix: enzymeUsage correct mention of output units

solves #376

* doc: updateGECKOdoc

* doc: update README.md with protocol change

* fix: README.md link
@edkerk edkerk mentioned this issue May 27, 2024
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@edkerk @HossFir