Source of the PANTHER phylogenetically-inferred (IBA) annotations for NDUFA9. Per NDUFA9-goa.tsv this reference yields exactly three terms: mitochondrion (GO:0005739), ubiquinone biosynthetic process (GO:0006744) and protein-containing complex binding (GO:0044877). Only the mitochondrion call is a sound propagation from characterised orthologues of the 39 kDa Complex I accessory subunit. The mitochondrial inner membrane (GO:0005743) and respiratory chain complex I (GO:0045271) annotations are not IBA products: they come from GO_REF:0000107 Ensembl Compara projection from mouse Q9DC69 plus ComplexPortal/UniProt IDAs. Mitochondrial electron transport, NADH to ubiquinone (GO:0006120) is NAS from PMID:9878551.

The IBA propagation also produced an incorrect ubiquinone biosynthetic process annotation for NDUFA9; Complex I consumes ubiquinone as an electron acceptor rather than synthesising it, so this term is an over-propagation rather than evidence of a biosynthetic role.

The third IBA product, protein-containing complex binding (GO:0044877), is an uninformative molecular function term for a constitutive Complex I subunit: NDUFA9's relationship to the complex is part_of (GO:0045271), not binding of an external complex. It is marked over-annotated in the existing_annotations review.

Basis for the electronic mitochondrial matrix (GO:0005759) localization annotation, derived by mapping the UniProtKB Q16795 subcellular location statement (SUBCELLULAR LOCATION: Mitochondrion matrix) onto GO via UniProtKB-SubCell:SL-0170. This mapping does not support the mitochondrial inner membrane annotation, which comes from GO_REF:0000107 and IDA evidence. Matrix versus inner membrane is a genuinely contested point for this subunit, and the SubCell mapping only propagates the UniProt matrix statement; see the existing_annotations review of GO:0005759 for the assessment.

Basis for orthology-projected annotations transferred to human NDUFA9 from experimentally characterised mammalian orthologues; NDUFA9 is a highly conserved Complex I accessory subunit, so such projection is biologically reasonable but carries no independent experimental weight for the human protein.

Basis for GO terms assigned by inter-ontology logical inference rather than by direct evidence; for NDUFA9 these are downstream consequences of the complex I and electron transport assertions and add no new experimental support.

Monoclonal antibodies against the 39 kDa Complex I subunit (NDUFA9) were used to profile subunit assembly in Complex I deficient patients.

Subunit-level antibody profiling distinguishes catalytic from assembly defects in Complex I disease, the assay context in which NDUFA9 is detected.

NDUFA9 was identified by mass spectrometry as one of the polypeptides of immunopurified human Complex I, supporting its assignment as a bona fide complex I subunit.

Complex I is built stepwise through discrete subcomplexes, the assembly framework in which the NDUFS2/NDUFS3/NDUFA9-containing Q-module intermediate is defined.

High-throughput yeast two-hybrid and pull-down screening for huntingtin-associated proteins; any NDUFA9 hit here is a large-scale interaction dataset entry and does not establish a molecular function for NDUFA9.

hNOA1 was found by immunoprecipitation-mass spectrometry to associate with Complex I, the source of the NDUFA9 physical-interaction annotation.

The functional link between hNOA1 and Complex I was supported by a Complex I-dependent drop in respiration on hNOA1 knockdown, but this reflects complex-level rather than NDUFA9-specific function.

Large-scale catalogue of proteins detected in isolated sperm nuclei; detection of a mitochondrial inner-membrane subunit such as NDUFA9 in this fraction is most parsimoniously explained as residual contamination and does not support a nuclear localization.

GCN5L1 promotes acetylation of respiratory chain proteins, the post-translational context in which NDUFA9 acetylation is reported; this concerns regulation of NDUFA9 rather than an activity of NDUFA9.

Study of KIF14-Radil-Rap1 signalling in breast cancer. The cached full text (full_text_available: true) does not mention NDUFA9 anywhere, so the basis of the MGI IDA drawn from this paper could not be verified here; it presumably rests on supplementary data not present in the cache. The assay type behind the NDUFA9 entry is therefore unknown rather than demonstrably a large-scale by-product.

Systematic knockout of each human Complex I accessory subunit showed that most, including NDUFA9, are strictly required for assembly of a functional complex.

Loss of an accessory subunit destabilises the other subunits of its structural module, the evidence underpinning the structural/assembly role assigned to NDUFA9.

The 14 core subunits shared with bacteria carry catalysis, whereas the 31 human accessory subunits such as NDUFA9 are non-catalytic.

Cryo-EM of the human respiratory megacomplex assigned individual Complex I subunits, placing NDUFA9 within the complex I module of a higher-order supercomplex.

Complex I is present in higher-order assemblies with complexes III and IV, supporting the respirasome/supercomplex localization context for its subunits.

NDUFA9 was identified as an acetylation substrate of CLOCK; this describes a post-translational modification of NDUFA9 by another enzyme and does not assign NDUFA9 a role in circadian or ureagenesis pathways.

Review establishing that OXPHOS supernumerary subunits such as NDUFA9 act in assembly, regulation and stability rather than catalysis.

Complexes I, III and IV associate into respiratory supercomplexes, the higher-order context in which Complex I subunits operate.

Co-fractionation mass spectrometry map of human mitochondrial protein assemblies; NDUFA9 appears as a member of respiratory chain assemblies in this dataset, which supports complex membership rather than a distinct molecular function.

Systematic yeast two-hybrid reference interactome (HuRI); NDUFA9 entries derived from it are binary interaction data points and are not evidence for a specific molecular function of NDUFA9.

Large-scale yeast two-hybrid network centred on neurodegeneration-associated proteins; any NDUFA9 interaction reported here is a high-throughput screen hit without complex I-specific functional follow-up.

NDUFA9 is a member of the stringently defined human mitochondrial high-confidence proteome (MitoCoP), corroborating its mitochondrial localization.

The human cDNA corresponding to the 39 kDa Complex I subunit (NDUFA9) was first isolated here and mapped to chromosome 12p.

Defines the catalytic activity of the complex that NDUFA9 belongs to - electron transfer from NADH to ubiquinone coupled to proton translocation.

Complex I is a large multiprotein assembly of the inner mitochondrial membrane, the compartment in which NDUFA9 resides.

Reactome reaction describing the catalytic output of Complex I - NADH oxidation with ubiquinone reduction coupled to proton pumping. NDUFA9 participates as a structural subunit of the complex catalysing this reaction, not as a catalytic component.

Reactome assembly step in which the hydrophobic protein (HP) fraction containing NDUFA9 joins Intermediate 1, supporting the mitochondrial respiratory chain complex I assembly annotation.

Late Complex I assembly step involving flavoprotein (FP) peripheral arm subunits. NDUFA9 is not one of the subunits added at this step; it is present in the earlier IP/Q-module intermediates.

Assembly step forming the 315 kDa subcomplex around the NDUFS2/NDUFS3 core, the Q-module intermediate to which NDUFA9 belongs and which it helps stabilise.

Final step of Complex I biogenesis in which assembly factors dissociate to leave the mature complex containing NDUFA9.

Distal membrane-arm assembly step requiring DMAC1/DMAC2; downstream of the NDUFA9-containing intermediates and not a step in which NDUFA9 acts directly.

Assembly step joining the NDUFA9-containing 315 kDa subcomplex to the 370 kDa membrane-arm subcomplex.

Reactome step stating explicitly that NDUFS7, NDUFS8 and NDUFA9, together with NDUFS2 and NDUFS3, form an evolutionarily conserved hydrogenase module within the iron-sulfur protein (IP) subcomplex - the structural context of NDUFA9.

Formation of the IP subcomplex in which NDUFA9 associates with NDUFS2, NDUFS3, NDUFS7 and NDUFS8 to build the conserved hydrogenase module, the primary evidence basis for the structural role of NDUFA9.

UniProt states that NDUFA9 is an accessory Complex I subunit believed not to participate in catalysis but required for proper complex I assembly.

UniProt places NDUFA9 in the hydrophobic protein fraction of the 45-subunit Complex I. Note that Reactome assigns NDUFA9 to the IP subcomplex hydrogenase module (R-HSA-6800868, R-HSA-6799203) as well as to the HP fraction (R-HSA-6799178); the two schemes partition the complex differently, so this is a difference in subcomplex nomenclature rather than a contradiction.