Oxidative phosphorylation (OXPHOS) module

A taxon-neutral decomposition of oxidative phosphorylation: the coupled process by which a respiratory electron transport chain (ETC) oxidizes reduced cofactors and uses the released free energy to pump protons across a coupling membrane, and an F1Fo-ATP synthase uses the resulting proton-motive force to phosphorylate ADP. The module is deliberately phrased in terms of functional modules, protein complexes, and pathway segments rather than a fixed gene list, so it can represent the mitochondrial inner-membrane chain of eukaryotes and the plasma-membrane respiratory chains of aerobic bacteria. Design intent for complexes (the central modelling question): each respiratory complex is represented as a single PROTEIN_COMPLEX node whose emergent, complex-level catalytic activity is carried by ONE complex-level annoton (the redox half-reaction it performs), with its functionally important subunits exposed as `active_units` on the complex descriptor rather than as separate per-subunit annotons. This mirrors the GO `contributes_to` philosophy: an individual subunit contributes to but does not independently enable the complex activity. Large, internally modular complexes (Complex I; the F1Fo-ATP synthase) are additionally decomposed with `parts` into their functional sub-modules (the N/Q/proton-pumping arms of Complex I; the F1 catalytic head and Fo proton turbine of ATP synthase) — this recursive decomposition is the payoff of the module representation over a flat subunit list. Lineage- and chemistry-specific alternatives that bypass the proton-pumping complexes (type-II NADH dehydrogenase, the alternative oxidase, bacterial bd-type oxidases) are captured as `variant_sets` along explicit axes, so OXPHOS reads as one conserved energy-conservation plan with multiple implementations. Complex assembly/biogenesis is treated as a distinct process from chain operation and kept as an optional sub-module.

Identifiers are grounded only where verified against the local validated OXPHOS gene reviews, the OXPHOS project page, or the sibling photosynthesis module; descriptors without a `term` are deliberate (no confident identifier yet, or no exact GO term exists for the abstraction) rather than oversights. Subunit `active_units` are named by their conserved subunit/homolog families (human gene-symbol families given as orienting names) to keep the module taxon-neutral; a concrete organism module can later specialize these with specific UniProt gene products, stoichiometries, and compartments without the generic module enumerating every protein. Complex II is intentionally modelled here as a respiratory-chain electron-entry complex; its succinate->fumarate half-reaction simultaneously belongs to the TCA cycle and is the canonical dual-pathway node. The plasma membrane substitutes for the mitochondrial inner membrane as the coupling membrane in respiring bacteria. Scope boundaries: the biosynthesis of the quinone pool (e.g. the ubiquinone/CoQ COQ pathway) and of the redox cofactors (heme a/b/c, Fe-S clusters, FAD/FMN, copper centres), as well as the pro-apoptotic role of cytochrome c once released to the cytosol, are upstream or downstream of OXPHOS operation and are intentionally out of scope here; they belong to their own pathways/gene reviews, and this module treats the carriers and cofactors as supplied inputs. Per-complex assembly factors are given by example in the biogenesis sub-module rather than broken out as structured per-complex annotons; a concrete organism-specific specialization can add that detail. Yeast alignment (YeastPathways PWY3O-188): S. cerevisiae and S. pombe have no Complex I. They oxidise NADH only through type-II NADH dehydrogenases: matrix-facing NDI1/ndi1 and intermembrane-space-facing NDE1/NDE2 (nde1 in S. pombe). These now ground the type_II_ndh_variant. Subunit exemplars for Complexes II-V are deliberately not duplicated here; they belong to the mitochondrial_complex_* modules. GO-CAM notes: the SGD conversion places every activity in the cytosol and links only NDI1 -> complex II causally. The PomBase model (663d668500000596) includes ndi1 and nde1 without causal links to complex III. It also models ETF/ETF-QO (etf1, etf2, cir2), coq10, erv1 and the IF1 inhibitor (inh1), which correspond to the auxiliary-dehydrogenase, quinone-pool, biogenesis and inhibitor parts here.