edkerk
commented
1 year ago The 3-isopropylmalate dehydrogenase reaction (EC1.1.1.85) is split into two half-reactions in the model:
| Identifier | Reaction equation | Genes |
|---|---|---|
| r_0061 | (2R,3S)-3-isopropylmalate[c] + NAD[c] => (2S)-2-isopropyl-3-oxosuccinate[c] + H+[c] + NADH[c] | YCL018W |
| r_0029 | (2S)-2-isopropyl-3-oxosuccinate[c] + H+[c] => 4-methyl-2-oxopentanoate[c] + carbon dioxide[c] | YJR148W |
But the second reaction (r_0029) is wrongly annotated with YJR148W.
- [x] Remove YJR148W from r_0029 and r_0030 (the latter being a mitochondrial variant).
Otherwise, there are no other obvious problems with Lys2 / Leu2 as suggested in OP. Without further direction on what might be problematic, just this error will be fixed.
Description of the issue:
Check Lys2 and Leu2 gene associations, as commented here: https://github.com/SysBioChalmers/GECKO/issues/74.