fix: couple flavoenzyme dehydrogenases to ubiquinone, not FAD

[edkerk]

Redoes the stale #1028 (branch fix/etf-ubiquinone-coupling, originally #1015) cleanly on current develop.

What

Three flavoenzyme dehydrogenases carried FAD/FADH2 as electron acceptor, but their EC numbers are the quinone-coupled forms:

reaction	enzyme	EC	now reduces
MAR08611	proline dehydrogenase	1.5.5.2 (proline DH (quinone))	ubiquinone
MAR00449	glycerol-3-P dehydrogenase	1.1.5.3 (G3P DH (quinone))	ubiquinone
MAR01169	glycerol-3-P dehydrogenase, mito	1.1.5.3	ubiquinone

MAM01802m/MAM01803m (FAD/FADH2) → MAM03103m/MAM03102m (ubiquinone/ubiquinol). Both are 2 e⁻/2 H⁺ carriers, so all three reactions stay mass- and charge-balanced (verified). Reaction names updated to match.

Scope

Limited to this unambiguous chemistry correction (only model/Human-GEM.yml, 3 reactions). The original branch also renamed reactions (MAR08611→MAR03838, MAR00449→MAR00483), merged MAR01169, and rewrote GPRs — those are structural/curation decisions that conflict with develop's current IDs and are left for separate review with the original author.

Supersedes #1028.

[github-actions]

Model quality report

⚠️ 6 pre-existing finding(s), no regressions vs develop. Non-blocking.

Structural checks

Duplicate keys (model unloadable) and no growth block the merge; the other rows are non-blocking.

Check	Result	Δ vs develop
Duplicate !!omap keys	0	0	✅
Reactions with no metabolites	0	0	✅
Model / annotation-table inconsistencies	0	0	✅
Growth (biomass producible)	125	0	✅

Model QC reports

Check	Result	Δ vs develop
Metabolites missing formula	0	0	✅
Metabolites missing charge	0	0	✅
Reaction bound / GPR issues	0	0	✅
Exact-duplicate reaction groups	0	0	✅
Unused metabolites	0	0	✅
Unused genes	0	0	✅
Malformed cross-references	0	0	✅
Cross-refs inconsistent across compartments	3	0	⚠️

MACAW and mass/charge balance

Check	Result	Δ vs develop
Reactions flagged by MACAW dead-end test	2510	0	⚠️
Reactions flagged as MACAW duplicates	377	0	⚠️
Mass-imbalanced reactions	87	0	⚠️
Charge-imbalanced reactions	234	0	⚠️
Structure vs formula/charge inconsistencies	397	0	⚠️

Model file and metabolic tasks

Check	Result
YAML round-trip (cobrapy)	pass	✅
YAML round-trip (RAVEN)	pass	✅
YAML lint	pass	✅
Essential metabolic tasks	57 passed	✅
Verification metabolic tasks	21 passed	✅

MEMOTE

Total score: 20.2% (core subset)   0

Section	Score	Δ vs base
consistency	42.4%	0
annotation_met	25.0%	0
annotation_rxn	25.0%	0
annotation_gene	0.0%	0
annotation_sbo	0.0%	0

Per-test scores

Section	Test	Score
Consistency	Stoichiometric Consistency	100.0%
Consistency	Mass Balance	0.8%
Consistency	Charge Balance	2.1%
Consistency	Metabolite Connectivity	0.0%
Consistency	Unbounded Flux In Default Medium	100.0%
Annotation - Metabolites	Presence of Metabolite Annotation	100.0%
Annotation - Metabolites	Metabolite Annotations Per Database	100.0%
Annotation - Metabolites	Metabolite Annotation Conformity Per Database	100.0%
Annotation - Metabolites	Uniform Metabolite Identifier Namespace	0.0%
Annotation - Reactions	Presence of Reaction Annotation	100.0%
Annotation - Reactions	Reaction Annotations Per Database	100.0%
Annotation - Reactions	Reaction Annotation Conformity Per Database	100.0%
Annotation - Reactions	Uniform Reaction Identifier Namespace	0.0%
Annotation - Genes	Presence of Gene Annotation	100.0%
Annotation - Genes	Gene Annotations Per Database	100.0%
Annotation - Genes	Gene Annotation Conformity Per Database	100.0%
Annotation - SBO Terms	Metabolite General SBO Presence	100.0%
Annotation - SBO Terms	Metabolite SBO:0000247 Presence	100.0%
Annotation - SBO Terms	Reaction General SBO Presence	100.0%
Annotation - SBO Terms	Metabolic Reaction SBO:0000176 Presence	100.0%
Annotation - SBO Terms	Transport Reaction SBO:0000185 Presence	100.0%
Annotation - SBO Terms	Exchange Reaction SBO:0000627 Presence	100.0%
Annotation - SBO Terms	Demand Reaction SBO:0000628 Presence	100.0%
Annotation - SBO Terms	Sink Reactions SBO:0000632 Presence	100.0%
Annotation - SBO Terms	Gene General SBO Presence	100.0%
Annotation - SBO Terms	Gene SBO:0000243 Presence	100.0%
Annotation - SBO Terms	Biomass Reactions SBO:0000629 Presence	100.0%

The score above is the fast core subset. Comment /run memote to run the full suite on this pull request; the score updates here when it finishes.

Gene essentiality (Hart 2015)

Not run automatically (it takes hours). Comment /run gene-essentiality to run it on this pull request; the result posts as its own comment.

❌ = a count rose vs the target branch (regression) · ⚠️ = a pre-existing non-zero finding (non-blocking) · ⏳ = still running. Counts link to the CSV listing the exact entries.

Full workflow run · this comment is edited as results come in

[edkerk]

Duplicate of #1028