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fix: couple non-ETF flavoenzymes directly to ubiquinone #1028

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2210b03
fix: couple non-ETF flavoenzymes to ubiquinone instead of the ETF pat…
edkerk Jul 11, 2026
0f267d8
chore: update model QC results [skip ci]
edkerk Jul 15, 2026
6e04417
Merge remote-tracking branch 'origin/develop' into fix/etf-ubiquinone…
edkerk Jul 18, 2026
26dfd53
chore: update model QC results [skip ci]
edkerk Jul 18, 2026
3d6583b
fix: remove orphaned mitochondrial DHAP node after GPD2 recoupling
edkerk Jul 18, 2026
72a8523
chore: update model QC results [skip ci]
edkerk Jul 18, 2026
a819744
chore: add gene essentiality test result [skip ci]
edkerk Jul 19, 2026
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1 change: 1 addition & 0 deletions data/deprecatedIdentifiers/deprecatedMetabolites.tsv
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Original file line number Diff line number Diff line change
Expand Up @@ -2272,3 +2272,4 @@ MAM00208c MAM00208 C16832 M00208 MNXM21289 m00208c m00208c
MAM00209c MAM00209 C16237 M00209 MNXM96070 m00209c m00209c
MAM00210c MAM00210 C16236 M00210 MNXM4090 m00210c m00210c
MAM01622x MAM01622 b2coa C00877 CHEBI:15473 5280381 HC00572 b2coa MNXM214 m01622p m01622p
MAM01690m MAM01690 dhap C00111 CHEBI:16108 668 HC00109 dhap MNXM77 m01690m m01690m
7 changes: 5 additions & 2 deletions data/deprecatedIdentifiers/deprecatedReactions.tsv
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Expand Up @@ -108,13 +108,11 @@ MAR03751 R02660 R02660M r0560 r0560 HMR_3751 RCR14421 0 HMR_3751
MAR03783 R03172 R03172M r0603 r0603 MNXR108000 HMR_3783 RCR14424 0 HMR_3783
MAR04242 R02487 R02487M r0541 r0541 MNXR100293 HMR_4242 RCR14356 0 RHEA:30847 HMR_4242
MAR03769 R04095 R04095M r0655 r0655 MNXR95318 HMR_3769 RCR14423 0 HMR_3769
MAR03838 r1453 HMR_3838 RCR14286 0 HMR_3838
MAR02366 r1446 r1446 0 r1446
MAR02367 r1447 r1447 0 r1447
MAR02370 r1449 r1449 0 r1449
MAR02372 r1450 r1450 0 r1450
MAR02373 r1451 r1451 0 r1451
MAR00483 R00849 r0205 r0205 MNXR106713 HMR_0483 RCR21050 0 RHEA:18977 HMR_0483
MAR08743 R00408 SUCD1m SUCD1m MNXR99636 HMR_8743 RCR11674 0 RHEA:30343 HMR_8743
MAR05294 R00362 R00362C r1109 r1109 MNXR96731 HMR_5294 RCR11670 0 RHEA:10761 RHEA:10760 HMR_5294
MAR11421 CITL CITL MNXR96731 0 RHEA:10761 RHEA:10760 CITL
Expand Down Expand Up @@ -401,3 +399,8 @@ MAR07851 DNDPt62m DNDPt62m MNXR97327 HMR_7851 RCR20193 0 HMR_7851
MAR07852 DNDPt63m DNDPt63m MNXR97676 HMR_7852 RCR20146 0 HMR_7852
MAR07853 DNDPt6m DNDPt6m MNXR97677 HMR_7853 RCR20194 0 HMR_7853
MAR07854 DNDPt7m DNDPt7m MNXR97175 HMR_7854 RCR20122 0 HMR_7854

MAR08611 R10507 PROD2m r1453 PROD2m MNXR103187 HMR_8611;HMR_3838 RCR11294;RCR14286 0 HMR_8611;HMR_3838;MAR03838
MAR00449 R00848;R00849 r0205 R-HSA-188467 GLYC3PFADm;r0205 MNXR99875;MNXR106713 HMR_0449;HMR_0483 RCR12494;RCR21050 0 RHEA:31283;RHEA:18977 HMR_0449;HMR_0483
MAR01169 R00849;R00848 G3PD2m R00848C r0205 G3PD2m;r0205;HMR_0482 MNXR99878;MNXR106713;MNXR192664 HMR_0483;HMR_0482 RCR21050;RCR14578 0 RHEA:18977 G3PD2m;HMR_0483;HMR_0482;MAR00482;MAR00483
MAR08111 DHAPtm DHAPtc MNXR97366 0 DHAPtc
12 changes: 6 additions & 6 deletions data/testResults/README.md
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Expand Up @@ -21,12 +21,12 @@ own files. The pull request in each row is the one whose run last wrote those fi

| Result file(s) | Produced by | Last updated by |
| --- | --- | --- |
| `qc_duplicate_keys.csv`, `qc_empty_reactions.csv`, `qc_annotation_consistency.csv`, `qc_deprecation_completeness.csv`, `qc_metabolite_completeness.csv`, `qc_reaction_sanity.csv`, `qc_duplicate_reactions.csv`, `qc_unused_entities.csv`, `qc_growth_blockers.csv` | `qcModelChecks.py` | **PR #1061** (model QC checks) |
| `qc_annotation_issues.csv` | `annotationTest.py` | **PR #1061** (model QC checks) |
| `qc_status.tsv` (round-trip, YAML lint, metabolic tasks, growth) | `testYamlConversion.py`, `testMetabolicTasks.py`, `action-yamllint`, `qcModelChecks.py` (via `qcStatus.py`) | **PR #1061** (model QC checks) |
| `macaw_results.csv`, `balance_results.csv`, `qc_structure_consistency.csv` | `macawTests.py`, `balanceTest.py`, `structureConsistencyTest.py` | **PR #1061** (MACAW and balance) |
| `memote_score.md` | `memoteSnapshot.py` (fast subset every PR; full suite via `/run memote`) | **PR #1061** (MEMOTE) |
| `gene-essential.csv`, `gene-essential_summary.md` | `geneEssentiality.py` via `/run gene-essentiality` | **PR #1027** (gene essentiality) |
| `qc_duplicate_keys.csv`, `qc_empty_reactions.csv`, `qc_annotation_consistency.csv`, `qc_deprecation_completeness.csv`, `qc_metabolite_completeness.csv`, `qc_reaction_sanity.csv`, `qc_duplicate_reactions.csv`, `qc_unused_entities.csv`, `qc_growth_blockers.csv` | `qcModelChecks.py` | **PR #1028** (model QC checks) |
| `qc_annotation_issues.csv` | `annotationTest.py` | **PR #1028** (model QC checks) |
| `qc_status.tsv` (round-trip, YAML lint, metabolic tasks, growth) | `testYamlConversion.py`, `testMetabolicTasks.py`, `action-yamllint`, `qcModelChecks.py` (via `qcStatus.py`) | **PR #1028** (model QC checks) |
| `macaw_results.csv`, `balance_results.csv`, `qc_structure_consistency.csv` | `macawTests.py`, `balanceTest.py`, `structureConsistencyTest.py` | **PR #1028** (MACAW and balance) |
| `memote_score.md` | `memoteSnapshot.py` (fast subset every PR; full suite via `/run memote`) | **PR #1028** (MEMOTE) |
| `gene-essential.csv`, `gene-essential_summary.md` | `geneEssentiality.py` via `/run gene-essentiality` | **PR #1028** (gene essentiality) |

## 2. What each check means

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