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fix: couple flavoenzyme dehydrogenases to ubiquinone, not FAD #1060

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d715bcb
fix: couple flavoenzyme dehydrogenases to ubiquinone, not FAD
edkerk Jul 15, 2026
9c63978
chore: update model QC results [skip ci]
edkerk Jul 15, 2026
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6 changes: 3 additions & 3 deletions data/testResults/README.md
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Expand Up @@ -4,9 +4,9 @@ The file here contains results from the [MACAW](https://github.com/Devlin-Moyer/

The test results shown here were obtained by the GitHub Actions run in:

- **PR #1027** (model QC checks)
- **PR #1027** (MEMOTE)
- **PR #1027** (MACAW and mass/charge balance)
- **PR #1060** (model QC checks)
- **PR #1060** (MEMOTE)
- **PR #1060** (MACAW and mass/charge balance)
- **PR #1027** (gene essentiality)

The results will be updated by any subsequent pull request. Summary results are shown as a comment in the corresponding pull request.
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6 changes: 3 additions & 3 deletions data/testResults/macaw_results.csv
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Expand Up @@ -632,7 +632,7 @@ MAR08607,MAM01016c + MAM01975c + 2 MAM02039c --> MAM01974c + MAM02471c,ok,ok,ok,
MAR08608,MAM01742c + MAM02630c --> MAM00558c + MAM02039c + MAM02041c,MAM00558c,ok,ok,ok,N/A
MAR08609,MAM00559m + 2 MAM02039m + MAM02555m --> MAM02554m + MAM02770m,ok,ok,ok,ok,N/A
MAR08610,MAM01802c + MAM02770c --> MAM00559c + MAM01803c + MAM02039c,ok,ok,ok,ok,N/A
MAR08611,MAM01802m + MAM02770m --> MAM00559m + MAM01803m + MAM02039m,ok,ok,ok,ok,N/A
MAR08611,MAM02770m + MAM03103m --> MAM00559m + MAM02039m + MAM03102m,ok,ok,ok,ok,N/A
MAR04285,MAM02040m + MAM02552m + MAM02942m --> 2 MAM02039m + MAM02553m + MAM02943m,ok,ok,ok,ok,N/A
MAR00457,MAM01371c + MAM01982c --> MAM00913c + MAM01285c + MAM02039c,ok,ok,ok,ok,N/A
MAR00460,MAM01371m + MAM01982m --> MAM00913m + MAM01285m + MAM02039m,ok,ok,ok,ok,N/A
Expand Down Expand Up @@ -2474,7 +2474,7 @@ MAR00001,MAM01570e --> MAM01569e + 77243 MAM02956e,ok,ok,ok,ok,N/A
MAR00002,MAM02040e + MAM02956e --> MAM00234e + MAM01807e,ok,ok,ok,ok,N/A
MAR00003,MAM00234e + MAM02040e --> MAM00503e + MAM01807e,ok,ok,ok,ok,N/A
MAR00005,MAM00503c + MAM02040c --> MAM01807c + MAM01983c,ok,ok,ok,ok,N/A
MAR00449,MAM01802m + MAM02914m --> MAM01690m + MAM01803m,ok,ok,ok,ok,N/A
MAR00449,MAM02914m + MAM03103m --> MAM01690m + MAM03102m,ok,ok,ok,ok,N/A
MAR00604,MAM00240c + MAM01371c --> MAM01285c + MAM02039c + MAM02733c,ok,ok,ok,ok,N/A
MAR00605,MAM00240c + MAM10007c --> MAM01597c + MAM02958c,ok,ok,ok,ok,N/A
MAR00665,MAM02040c + MAM02958c --> MAM00240c + MAM02039c + MAM10005c,ok,ok,ok,ok,N/A
Expand Down Expand Up @@ -8198,7 +8198,7 @@ MAR01078,MAM03578g <=> MAM03578c,only when going backwards,ok,ok,ok,N/A
MAR01083,2 MAM01950g + MAM03584g --> MAM01856g + 2 MAM01948g + 2 MAM02039g,ok,ok,ok,ok,N/A
MAR01118,MAM01950g + MAM03092g --> MAM01948g + MAM02039g + MAM03578g,ok,ok,ok,ok,N/A
MAR01141,MAM01950g + MAM03095g --> MAM01948g + MAM02039g + MAM03577g,ok,ok,ok,ok,N/A
MAR01169,MAM01802m + MAM02914c --> MAM01690c + MAM01803m,ok,ok,ok,ok,N/A
MAR01169,MAM02914c + MAM03103m --> MAM01690c + MAM03102m,ok,ok,ok,ok,N/A
MAR01314,MAM00970c + MAM01371c + MAM02040c --> MAM00970e + MAM01285c + MAM02039c + MAM02751c,ok,ok,ok,MAR07738,N/A
MAR01340,MAM01915g <=> MAM01884c,ok,ok,ok,ok,N/A
MAR01348,MAM03586c <=> MAM03586g,only when going backwards,ok,ok,ok,N/A
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12 changes: 6 additions & 6 deletions data/testResults/model_qc_summary.md
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Expand Up @@ -23,17 +23,17 @@ _Duplicate keys (model unloadable) and no growth block the merge; the other rows
| Unused metabolites | 0 | 0 | :white_check_mark: |
| Unused genes | 0 | 0 | :white_check_mark: |
| Malformed cross-references | 0 | 0 | :white_check_mark: |
| Cross-refs inconsistent across compartments | [3](https://github.com/SysBioChalmers/Human-GEM/blob/worktree-matlab-to-python-workflows/data/testResults/qc_annotation_issues.csv) | 0 | :warning: |
| Cross-refs inconsistent across compartments | [3](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-redo/data/testResults/qc_annotation_issues.csv) | 0 | :warning: |

### MACAW and mass/charge balance

| Check | Result | &Delta; vs `develop` | |
| --- | ---: | ---: | :---: |
| Reactions flagged by MACAW dead-end test | [2510](https://github.com/SysBioChalmers/Human-GEM/blob/worktree-matlab-to-python-workflows/data/testResults/macaw_results.csv) | 0 | :warning: |
| Reactions flagged as MACAW duplicates | [377](https://github.com/SysBioChalmers/Human-GEM/blob/worktree-matlab-to-python-workflows/data/testResults/macaw_results.csv) | 0 | :warning: |
| Mass-imbalanced reactions | [87](https://github.com/SysBioChalmers/Human-GEM/blob/worktree-matlab-to-python-workflows/data/testResults/balance_results.csv) | 0 | :warning: |
| Charge-imbalanced reactions | [234](https://github.com/SysBioChalmers/Human-GEM/blob/worktree-matlab-to-python-workflows/data/testResults/balance_results.csv) | 0 | :warning: |
| Structure vs formula/charge inconsistencies | [397](https://github.com/SysBioChalmers/Human-GEM/blob/worktree-matlab-to-python-workflows/data/testResults/qc_structure_consistency.csv) | 0 | :warning: |
| Reactions flagged by MACAW dead-end test | [2510](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-redo/data/testResults/macaw_results.csv) | 0 | :warning: |
| Reactions flagged as MACAW duplicates | [377](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-redo/data/testResults/macaw_results.csv) | 0 | :warning: |
| Mass-imbalanced reactions | [87](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-redo/data/testResults/balance_results.csv) | 0 | :warning: |
| Charge-imbalanced reactions | [234](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-redo/data/testResults/balance_results.csv) | 0 | :warning: |
| Structure vs formula/charge inconsistencies | [397](https://github.com/SysBioChalmers/Human-GEM/blob/fix/etf-ubiquinone-redo/data/testResults/qc_structure_consistency.csv) | 0 | :warning: |

### Model file and metabolic tasks

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18 changes: 9 additions & 9 deletions model/Human-GEM.yml
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Expand Up @@ -70454,13 +70454,13 @@
- confidence_score: 0
- !!omap
- id: "MAR08611"
- name: "L-proline:(acceptor) oxidoreductase"
- name: "L-proline:ubiquinone oxidoreductase"
- metabolites: !!omap
- MAM00559m: 1
- MAM01802m: -1
- MAM01803m: 1
- MAM02039m: 1
- MAM02770m: -1
- MAM03102m: 1
- MAM03103m: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000100033 or ENSG00000250799"
Expand Down Expand Up @@ -101769,12 +101769,12 @@
- confidence_score: 0
- !!omap
- id: "MAR00449"
- name: "sn-Glycerol-3-phosphate:(acceptor) 2-oxidoreductase"
- name: "sn-glycerol-3-phosphate:ubiquinone oxidoreductase"
- metabolites: !!omap
- MAM01690m: 1
- MAM01802m: -1
- MAM01803m: 1
- MAM02914m: -1
- MAM03102m: 1
- MAM03103m: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000115159"
Expand Down Expand Up @@ -187814,12 +187814,12 @@
- confidence_score: 0
- !!omap
- id: "MAR01169"
- name: "Glycerol-3-Phosphate Dehydrogenase (FAD), Mitochondrial"
- name: "Glycerol-3-Phosphate Dehydrogenase (ubiquinone), Mitochondrial"
- metabolites: !!omap
- MAM01690c: 1
- MAM01802m: -1
- MAM01803m: 1
- MAM02914c: -1
- MAM03102m: 1
- MAM03103m: -1
- lower_bound: 0
- upper_bound: 1000
- gene_reaction_rule: "ENSG00000115159"
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