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SysBioChalmers / Yarrowia_lipolytica_W29-GEM

Genome-scale model of Yarrowia lipolytica.
http://www.nature.com/articles/npjsba20165
Creative Commons Attribution 4.0 International
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bug: Yarrowia lipolytica should have complex I for respiratory chain #15

Open feiranl opened 4 years ago

feiranl commented 4 years ago

Yarrowia lipolytica should have complex I for respiratory chain, not the alternative internal NADH:ubiquinone oxidoreductase(NDI1 in S. cervesiae )

Reaction : y000773 NADH:ubiquinone oxidoreductase H+[m] + NADH[m] + ubiquinone-6[m] => NAD[m] + ubiquinol-6[m] 1.6.5.9 YALI0F25135g should pump proton.

edkerk commented 4 years ago

It also has complex I: y300029 NADH dehydrogenase (complex I) 5 H+[m] + NADH[m] + ubiquinone-6[m] => 4 H+[c] + NAD[m] + ubiquinol-6[m] although I notice that this reaction has no gene association, probably because it's a mitochondrial gene? But y000773 seems correct?

feiranl commented 4 years ago

I am so sorry for not noticing this one, but then y000773 may can be deleted? since it is reported in Y. lipolytica, it should only contains the complex I not the alternative internal NADH:ubiquinone oxidoreductase. according to "...Other yeasts and fungi, such as Yarrowia lipolytica (19), exclusively utilize Complex I for respiratory oxidation of mitochondrial NADH..."ref. The one in y000773 can only accept NADH in cytosol?

edkerk commented 4 years ago

If you then follow ref. 19 from that paper, they find that Yarrowia lipolytica has an external-facing NADH:ubiquinone oxidoreductase. y000773 should indeed be deleted, y000770 is the correct reaction.