relation	source	species	gene	tg_term	tg_label	tg_action	other_term	other_label	other_action	tg_reason	other_reason	file
conflicts_with	ARBA	9POAL	NCGR_LOCUS10166	GO:0005829	cytosol	UNDECIDED	GO:0005783	endoplasmic reticulum	UNDECIDED	The sequence includes a plant HDH-like N-terminus and a hydrophobic ARV-like region. Neither predicted organelle targeting nor possible gene-model fusion proves exclusive localization. The exact TreeGrafter source placement and target processing require adjudication.	Arabidopsis ARV localization supports this possibility but does not determine targeting of the complete fusion. Conversely, an HDH-like N-terminus does not prove that ER localization is impossible. Model structure, processing and targeting remain unresolved.	genes/9POAL/NCGR_LOCUS10166/NCGR_LOCUS10166-ai-review.yaml
conflicts_with	ARBA	DORPE	AP180	GO:0006900	vesicle budding from membrane	KEEP_AS_NON_CORE	GO:0006898	receptor-mediated endocytosis	MARK_AS_OVER_ANNOTATED	Vesicle budding from membrane is a valid but very general description of AP180 function. The protein's role is specifically in clathrin-mediated vesicle budding at the synapse. More specific terms (GO:0048268 clathrin coat assembly, GO:0048488 synaptic vesicle endocytosis) capture the core function 	The characterized function of squid AP180 is in synaptic vesicle endocytosis, not receptor-mediated endocytosis. While the clathrin machinery is shared, receptor-mediated endocytosis implies cargo selection via receptor internalization signals, which is not what squid AP180 has been shown to do. The	genes/DORPE/AP180/AP180-ai-review.yaml
conflicts_with	ARBA	PSEPK	PP_2213	GO:0015645	fatty acid ligase activity	ACCEPT	GO:0016405	CoA-ligase activity	KEEP_AS_NON_CORE	This is a specific, biologically appropriate annotation for this gene product.	Retain as a supporting/non-core annotation rather than using it as the main functional summary.	genes/PSEPK/PP_2213/PP_2213-ai-review.yaml
conflicts_with	EC2GO	METEA	mdcD	GO:0003989	acetyl-CoA carboxylase activity	REMOVE	GO:0004658	propionyl-CoA carboxylase activity	REMOVE	The target has the MdcD-specific family assignment and neighboring mdcA/C/E genes. Its inferred reaction is decarboxylation of specialized ACP-bound malonyl substrate; it is not the ATP/biotin-dependent acetyl-CoA-to-malonyl-CoA reaction. Shared carboxyltransferase-fold ancestry does not establish r	The source EC6.4.1.3 mapping conflicts with the MdcD-specific family and malonate-decarboxylase gene neighborhood. The inferred ACP-bound decarboxylation does not carboxylate propionyl-CoA to methylmalonyl-CoA. No source EC field is rewritten.	genes/METEA/mdcD/mdcD-ai-review.yaml
conflicts_with	EC2GO	PSEPK	gabD-II	GO:0004777	succinate-semialdehyde dehydrogenase (NAD+) activity	UNDECIDED	GO:0036243	succinate-semialdehyde dehydrogenase (NADP+) activity	UNDECIDED	No direct Q88EN2 assay establishes either cofactor or substrate. Re-review against the OpenScientist control report: its decisive facts were checked. A BLOSUM62 global alignment gives Q88EN2 50.8% identity to NADP+-specific E. coli GabD (P25526; report 51.7%), 48.4% to human ALDH5A1 and 31.6% to E. 	No direct Q88EN2 assay establishes the annotated EC reaction. Retain the row as unresolved until comparative substrate kinetics or genetics distinguishes SSADH from DoeC-like activity. The blinded OpenScientist control run offered this NADP+ term as its more specific alternative to GO:0004777, on a 	genes/PSEPK/gabD-II/gabD-II-ai-review.yaml
conflicts_with	EC2GO	PSEPK	quiA	GO:0008876	quinoprotein glucose dehydrogenase activity	MARK_AS_OVER_ANNOTATED	GO:0047519	quinate dehydrogenase (quinone) activity	ACCEPT	The specific EC2GO term GO:0047519 quinate dehydrogenase (quinone) activity is present and better matches the protein name, EC assignment, and pathway context. Glucose dehydrogenase specificity is not supported for this gene in the supplied evidence.	This is the core molecular function and is supported by the submitted EC annotation plus PQQ membrane dehydrogenase family evidence.	genes/PSEPK/quiA/quiA-ai-review.yaml
conflicts_with	InterPro2GO	CANLF	Canf2	GO:0005549	odorant binding	ACCEPT	GO:0036094	small molecule binding	MARK_AS_OVER_ANNOTATED	Electronic inference matching the lipocalin odorant-binding function.	Uninformative broad parent; the specific odorant-binding activity is already captured.	genes/CANLF/Canf2/Canf2-ai-review.yaml
conflicts_with	InterPro2GO	CANLF	Canf6	GO:0005549	odorant binding	ACCEPT	GO:0036094	small molecule binding	MARK_AS_OVER_ANNOTATED	Electronic inference matching the lipocalin odorant-binding function.	Uninformative broad parent; the specific odorant-binding activity is already captured.	genes/CANLF/Canf6/Canf6-ai-review.yaml
conflicts_with	InterPro2GO	CAPO3	CoBra	GO:0006357	regulation of transcription by RNA polymerase II	ACCEPT	GO:0045893	positive regulation of DNA-templated transcription	ACCEPT	Follows from the DNA-binding transcription factor activity. The process is generic and holds for every T-box family member, so the transfer from the deep node is appropriate here, unlike the developmental row. The genes CoBra regulates directly in Capsaspora are inferred from motifs and ChIP-qPCR, n	Brachyury-class proteins are transcriptional activators. Activation by CoBra has been shown directly only in the heterologous Xenopus system. The Capsaspora data are correlative: bound sites carry activating marks, but no CoBra knockout or knockdown expression study exists. Accepted, with activation	genes/CAPO3/CoBra/CoBra-ai-review.yaml
conflicts_with	InterPro2GO	COTJA	A0A8C2TBA7	GO:0005576	extracellular region	ACCEPT	GO:0016020	membrane	KEEP_AS_NON_CORE	"PAM exists in both membrane-bound and soluble forms. Soluble PAM forms generated through endoproteolytic processing are secreted into the extracellular space in active form. The deep research confirms ""Soluble PAM forms generated through endoproteolytic processing can be secreted into the extracellu"	The UniProt entry documents a transmembrane helix at residues 734-758 and PAM is annotated as a single-pass membrane protein. The InterPro-based annotation from IPR000720 correctly identifies PAM as membrane-associated. However, GO:0016020 (membrane) is extremely broad. The more specific term GO:003	genes/COTJA/A0A8C2TBA7/A0A8C2TBA7-ai-review.yaml
conflicts_with	InterPro2GO	DOROP	ADAR2	GO:0003726	double-stranded RNA adenosine deaminase activity	ACCEPT	GO:0004000	adenosine deaminase activity	MODIFY	This is the defining catalytic activity of sqADAR2 and the most important molecular function annotation. It has been demonstrated directly using recombinant enzyme on multiple substrates, with quantitative activity data. The term is at exactly the right level of specificity.	GO:0004000 (adenosine deaminase activity) describes the deamination of free adenosine, which is the activity of ADA enzymes, not ADAR enzymes. ADAR2 specifically deaminates adenosine residues within double-stranded RNA. The correct term GO:0003726 is already annotated, so this annotation should be r	genes/DOROP/ADAR2/ADAR2-ai-review.yaml
conflicts_with	InterPro2GO	DORPE	AP180	GO:0000149	SNARE binding	UNDECIDED	GO:0030276	clathrin binding	ACCEPT	No direct evidence for SNARE binding by squid AP180. However, the ANTH domain of AP180/CALM family members binds directly to the SNARE motif of VAMP2/synaptobrevin, and this interaction is conserved from yeast to mammals. AP180-knockout mice show greatly reduced VAMP2 in synaptic vesicles, and yeast	Clathrin binding is a central and well-demonstrated function of squid AP180. The protein directly binds clathrin triskelia via DLL motifs in its C-terminal domain and promotes their assembly into clathrin lattices (PMID:10575017, PMID:11102472).	genes/DORPE/AP180/AP180-ai-review.yaml
conflicts_with	InterPro2GO	FELCA	Feld4	GO:0005549	odorant binding	ACCEPT	GO:0036094	small molecule binding	MARK_AS_OVER_ANNOTATED	Electronic inference matching the documented pheromone/odorant-carrier role.	Overly broad parent term; the specific ligand-binding activity (odorant/pheromone binding) is already captured.	genes/FELCA/Feld4/Feld4-ai-review.yaml
conflicts_with	InterPro2GO	HYPJE	IRE1	GO:0070059	intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress	MARK_AS_OVER_ANNOTATED	GO:0030968	endoplasmic reticulum unfolded protein response	ACCEPT	The focused fungal IRE1 report found no evidence that Trichoderma IRE1 drives the mammalian IRE1-TRAF2-ASK1/JNK apoptotic arm. The direct target paper supports adaptive UPR signaling through kinase autophosphorylation and HAC1 processing, while the apoptotic branch derives from mammalian SF17 IRE1 e	Correct. This is the core biological process of IRE1. Confirmed by functional studies showing UPR target gene upregulation (PMID:15480788).	genes/HYPJE/IRE1/IRE1-ai-review.yaml
conflicts_with	InterPro2GO	METBS	Pks1	GO:0004312	fatty acid synthase activity	REMOVE	GO:0004315	3-oxoacyl-[acyl-carrier-protein] synthase activity	MODIFY			genes/METBS/Pks1/Pks1-ai-review.yaml
conflicts_with	InterPro2GO	OSCPE	TLN	GO:0005178	integrin binding	ACCEPT	GO:0051015	actin filament binding	ACCEPT	TLN retains the FERM head and the talin domain architecture, and sponges are inside the animal clade in which talin-integrin linkage is conserved. No target-specific evidence of loss. Not experimentally tested in sponge.	TLN has the I/LWEQ domain and talin rod; conserved activity, not tested in sponge.	genes/OSCPE/TLN/TLN-ai-review.yaml
conflicts_with	InterPro2GO	PSEPK	PP_2528	GO:0071269	L-homocysteine biosynthetic process	UNDECIDED	GO:0019346	transsulfuration	MARK_AS_OVER_ANNOTATED	O-acetylhomoserine sulfhydrylase chemistry would form homocysteine, but the pathway-level review identifies MetXS plus MetZ as the substrate-matched O-succinylhomoserine route. Keep this process unresolved for PP_2528 until substrate use or mutant phenotypes are available.	The module template separates direct sulfhydrylation by MetY/O-acetylhomoserine sulfhydrylase from the two-step cystathionine trans-sulfuration route. PP_2528 is predicted as the direct O-acetylhomoserine sulfhydrylase route.	genes/PSEPK/PP_2528/PP_2528-ai-review.yaml
conflicts_with	InterPro2GO	PSEPK	PP_3117	GO:0006281	DNA repair	MODIFY	GO:0009432	SOS response	KEEP_AS_NON_CORE	ImuA is an accessory component of the mutagenic DnaE2 damage-tolerance pathway rather than a canonical repair enzyme.	The cassette is experimentally damage inducible; translesion synthesis is the more direct effector process.	genes/PSEPK/PP_3117/PP_3117-ai-review.yaml
conflicts_with	InterPro2GO	PSEPK	alaS	GO:0002161	aminoacyl-tRNA deacylase activity	ACCEPT	GO:0004812	aminoacyl-tRNA ligase activity	MARK_AS_OVER_ANNOTATED	Editing is supported by TreeGrafter and the Thr/Ala-tRNA synthetase editing-domain assignment, but is not directly demonstrated for KT2440 AlaS.	GO:0004813 records the known amino-acid and tRNA specificity and is already present.	genes/PSEPK/alaS/alaS-ai-review.yaml
conflicts_with	InterPro2GO	PSEPK	fruA	GO:0090563	protein-phosphocysteine-sugar phosphotransferase activity	KEEP_AS_NON_CORE	GO:0008982	protein-N(PI)-phosphohistidine-carbohydrate phosphotransferase activity	MARK_AS_OVER_ANNOTATED	This is a genuine mechanistic EIIB sub-step within the single net FruA transport-phosphorylation reaction represented by core term GO:0022877, not a second independent core function.	GO:0022877 is the fructose-specific child term that captures FruA's net transport-coupled phosphotransfer reaction.	genes/PSEPK/fruA/fruA-ai-review.yaml
conflicts_with	InterPro2GO	PSEPK	gcl	GO:0050660	flavin adenine dinucleotide binding	KEEP_AS_NON_CORE	GO:0030976	thiamine pyrophosphate binding	ACCEPT	OpenScientist and family evidence support Gcl as a ThDP/TPP-family enzyme with FAD binding; FAD is retained as cofactor context rather than treated as the core function.	The protein is a TPP-enzyme family member and the catalytic reaction is TPP-dependent.	genes/PSEPK/gcl/gcl-ai-review.yaml
conflicts_with	InterPro2GO	PSEPK	lptC	GO:0017089	glycolipid transfer activity	MARK_AS_OVER_ANNOTATED	GO:0140332	lipopolysaccharide transfer activity	ACCEPT	The broad MF adds no useful information beyond lipopolysaccharide transfer activity.	This specific term best captures the direct molecular function of LptC.	genes/PSEPK/lptC/lptC-ai-review.yaml
conflicts_with	InterPro2GO	PSEPK	mexB	GO:0042910	xenobiotic transmembrane transporter activity	ACCEPT	GO:0015562	efflux transmembrane transporter activity	ACCEPT			genes/PSEPK/mexB/mexB-ai-review.yaml
conflicts_with	InterPro2GO	PSEPK	paaJ	GO:0010124	phenylacetate catabolic process	ACCEPT	GO:0019619	3,4-dihydroxybenzoate catabolic process	MARK_AS_OVER_ANNOTATED	The assigned bifunctional name includes the 3-oxo-5,6-dehydrosuberyl-CoA intermediate of phenylacetate catabolism.	The pathway-level paralog analysis identifies this as a PcaF-derived cross-annotation. PaaJ is the paa-locus thiolase named for the phenylacetate-specific dehydrosuberyl-CoA intermediate; a separate PcaF should carry the beta-ketoadipate pathway role.	genes/PSEPK/paaJ/paaJ-ai-review.yaml
conflicts_with	InterPro2GO	PSEPK	pdxH	GO:0042823	pyridoxal 5'-phosphate biosynthetic process	ACCEPT	GO:0008615	pyridoxine biosynthetic process	REMOVE	This is the immediate product-forming step of PLP biosynthesis.	GO:0008615 names pyridoxine synthesis, whereas PdxH consumes PNP or PMP and forms PLP. Upstream enzymes are conventionally associated with this process because they produce PNP, but PdxH acts downstream of that endpoint. GO:0042823 is already present, so replacement would duplicate the correct PLP-b	genes/PSEPK/pdxH/pdxH-ai-review.yaml
conflicts_with	InterPro2GO	PSEPK	pvdE	GO:0034040	ATPase-coupled lipid transmembrane transporter activity	REMOVE	GO:0140359	ABC-type transporter activity	ACCEPT	"Rejection confirmed on re-review, with an explicit reason added. GO:0034040 names a specific substrate class, transfer of a lipid across a membrane coupled to ATP hydrolysis. UniProt describes PvdE as the ""Pyoverdine ABC export system, fused ATPase and permease components"", and the peptide-directed "		genes/PSEPK/pvdE/pvdE-ai-review.yaml
conflicts_with	InterPro2GO	PSEPK	pvdE	GO:0042626	ATPase-coupled transmembrane transporter activity	KEEP_AS_NON_CORE	GO:0016887	ATP hydrolysis activity	KEEP_AS_NON_CORE			genes/PSEPK/pvdE/pvdE-ai-review.yaml
conflicts_with	InterPro2GO	PSEPK	pyrC	GO:0006221	pyrimidine nucleotide biosynthetic process	MARK_AS_OVER_ANNOTATED	GO:0019856	pyrimidine nucleobase biosynthetic process	MARK_AS_OVER_ANNOTATED	Retain de novo UMP biosynthesis.	Retain GO:0044205.	genes/PSEPK/pyrC/pyrC-ai-review.yaml
conflicts_with	InterPro2GO	PSEPK	pyrG	GO:0019856	pyrimidine nucleobase biosynthetic process	MARK_AS_OVER_ANNOTATED	GO:0006221	pyrimidine nucleotide biosynthetic process	TOO_GENERAL	Rejection confirmed on re-review, with the reason strengthened. GO:0019856 is defined as formation of pyrimidine nucleobases, i.e. the free 1,3-diazine bases, which are made upstream at the orotate/UMP stage. PyrG instead catalyses ATP-dependent amination of the already assembled nucleotide UTP to C	The de novo CTP biosynthetic process annotation is more specific and should be preferred.	genes/PSEPK/pyrG/pyrG-ai-review.yaml
conflicts_with	InterPro2GO	PSEPK	secA	GO:0005829	cytosol	ACCEPT	GO:0016020	membrane	MARK_AS_OVER_ANNOTATED	The specific cytosol term captures the soluble half of the approximately 50:50 distribution reported by UniProt and is retained as a core location.		genes/PSEPK/secA/secA-ai-review.yaml
conflicts_with	InterPro2GO	PSEPK	ttgB	GO:0042910	xenobiotic transmembrane transporter activity	ACCEPT	GO:0015562	efflux transmembrane transporter activity	ACCEPT	This is an excellent annotation from TreeGrafter that captures the core molecular function at the right level of specificity. TtgB specifically transports xenobiotic compounds (antibiotics, plant antimicrobials, bipyridyls) across the inner membrane. The broad substrate specificity spanning multiple	This is the core molecular function of TtgB. It is the substrate-translocating inner membrane component of the TtgABC RND efflux pump. InterPro mapping from IPR004764 is appropriate. Multiple publications confirm efflux transporter function: TtgABC overexpression causes multidrug resistance via effl	genes/PSEPK/ttgB/ttgB-ai-review.yaml
conflicts_with	InterPro2GO	SACEN	eryAI	GO:0004312	fatty acid synthase activity	MODIFY	GO:0004315	3-oxoacyl-[acyl-carrier-protein] synthase activity	MODIFY	Wrong product class. Replace with GO:0016218 (polyketide synthase activity).	Wrong-specific (FAS) term for a polyketide ketosynthase domain. Replace with GO:0016218 (polyketide synthase activity).	genes/SACEN/eryAI/eryAI-ai-review.yaml
conflicts_with	InterPro2GO	SACEN	eryAII	GO:0004312	fatty acid synthase activity	MODIFY	GO:0004315	3-oxoacyl-[acyl-carrier-protein] synthase activity	MODIFY	Wrong product class. Replace with GO:0016218 (polyketide synthase activity).	Wrong-specific (FAS) term for a polyketide ketosynthase domain. Replace with GO:0016218.	genes/SACEN/eryAII/eryAII-ai-review.yaml
conflicts_with	InterPro2GO	SACEN	eryAIII	GO:0004312	fatty acid synthase activity	MODIFY	GO:0004315	3-oxoacyl-[acyl-carrier-protein] synthase activity	MODIFY	The characterized assembly-line product is 6-deoxyerythronolide B, a macrolide polyketide. This supports a polyketide-synthase refinement of the fatty-acid-synthase assignment. Shared acyl-carrier/condensation chemistry is real; absence of DH/ER domains from this particular subunit is not, by itself	The current GO:0004315 definition specifies malonyl-ACP condensation. DEBS modules 5 and 6 use methylmalonyl-derived units during erythronolide assembly, so retain a substrate-aware refinement to polyketide synthase activity. The distinction is the defined reaction, not a rule excluding all PKS doma	genes/SACEN/eryAIII/eryAIII-ai-review.yaml
conflicts_with	InterPro2GO	SALRS	PTSG_05882	GO:0016339	calcium-dependent cell-cell adhesion	MARK_AS_OVER_ANNOTATED	GO:0007156	homophilic cell-cell adhesion	MARK_AS_OVER_ANNOTATED	Calcium-dependent cell-cell adhesion is a general cadherin capability, so it is not impossible for this protein. But it is untested, the donor biology is classical-cadherin adhesion in bilaterian tissues, and the EC-like repeats of F2UD23 lack the canonical calcium-binding motifs. Kept as an over-an	The mapping turns domain membership into a specific adhesive mechanism. Nichols et al. suggest that cadherins of unicellular holozoans may serve other functions, such as prey capture or substrate attachment. A homophilic cell-cell role is untested and not implied by the domain alone.	genes/SALRS/PTSG_05882/PTSG_05882-ai-review.yaml
conflicts_with	InterPro2GO	SALRS	PTSG_05882	GO:0044331	cell-cell adhesion mediated by cadherin	MARK_AS_OVER_ANNOTATED	GO:0007156	homophilic cell-cell adhesion	MARK_AS_OVER_ANNOTATED	The definition fits any cadherin that mediates cell-cell attachment, so the term is not excluded. But it is untested, and the S. rosetta rosette is held together by other means (cytoplasmic bridges, a C-type lectin-containing extracellular matrix). Premetazoan cadherins may well serve non-adhesive o	The mapping turns domain membership into a specific adhesive mechanism. Nichols et al. suggest that cadherins of unicellular holozoans may serve other functions, such as prey capture or substrate attachment. A homophilic cell-cell role is untested and not implied by the domain alone.	genes/SALRS/PTSG_05882/PTSG_05882-ai-review.yaml
conflicts_with	InterPro2GO	SALRS	PTSG_06458	GO:0016339	calcium-dependent cell-cell adhesion	MARK_AS_OVER_ANNOTATED	GO:0007156	homophilic cell-cell adhesion	MARK_AS_OVER_ANNOTATED	Calcium-dependent cell-cell adhesion is a general cadherin capability, and the EC repeats of this protein keep canonical calcium-binding motifs, so the term is not impossible. But it is untested, the donor biology is classical-cadherin adhesion in bilaterian tissues, and S. rosetta rosettes are held	The mapping turns domain membership into a specific adhesive mechanism. Nichols et al. suggest that cadherins of unicellular holozoans may serve other functions, such as prey capture or substrate attachment. A homophilic cell-cell role is untested and not implied by the domain alone.	genes/SALRS/PTSG_06458/PTSG_06458-ai-review.yaml
conflicts_with	InterPro2GO	SALRS	PTSG_06458	GO:0044331	cell-cell adhesion mediated by cadherin	MARK_AS_OVER_ANNOTATED	GO:0007156	homophilic cell-cell adhesion	MARK_AS_OVER_ANNOTATED	The definition fits any cadherin that mediates cell-cell attachment, so the term is not excluded. But it is untested, and the S. rosetta rosette is held together by other means (cytoplasmic bridges, a C-type lectin-containing extracellular matrix). Premetazoan cadherins may well serve non-adhesive o	The mapping turns domain membership into a specific adhesive mechanism. Nichols et al. suggest that cadherins of unicellular holozoans may serve other functions, such as prey capture or substrate attachment. A homophilic cell-cell role is untested and not implied by the domain alone.	genes/SALRS/PTSG_06458/PTSG_06458-ai-review.yaml
conflicts_with	InterPro2GO	SALRS	PTSG_11235	GO:0016339	calcium-dependent cell-cell adhesion	MARK_AS_OVER_ANNOTATED	GO:0007156	homophilic cell-cell adhesion	MARK_AS_OVER_ANNOTATED	Calcium-dependent cell-cell adhesion is a general cadherin capability, and the EC repeats of this protein keep canonical calcium-binding motifs, so the term is not impossible. But it is untested, the donor biology is classical-cadherin adhesion in bilaterian tissues, and S. rosetta rosettes are held	The mapping turns domain membership into a specific adhesive mechanism. Nichols et al. suggest that cadherins of unicellular holozoans may serve other functions, such as prey capture or substrate attachment. A homophilic cell-cell role is untested and not implied by the domain alone.	genes/SALRS/PTSG_11235/PTSG_11235-ai-review.yaml
conflicts_with	InterPro2GO	SALRS	PTSG_11235	GO:0044331	cell-cell adhesion mediated by cadherin	MARK_AS_OVER_ANNOTATED	GO:0007156	homophilic cell-cell adhesion	MARK_AS_OVER_ANNOTATED	The definition fits any cadherin that mediates cell-cell attachment, so the term is not excluded. But it is untested, and the S. rosetta rosette is held together by other means (cytoplasmic bridges, a C-type lectin-containing extracellular matrix). Premetazoan cadherins may well serve non-adhesive o	The mapping turns domain membership into a specific adhesive mechanism. Nichols et al. suggest that cadherins of unicellular holozoans may serve other functions, such as prey capture or substrate attachment. A homophilic cell-cell role is untested and not implied by the domain alone.	genes/SALRS/PTSG_11235/PTSG_11235-ai-review.yaml
conflicts_with	UniProt subcellular location	9POAL	NCGR_LOCUS67308	GO:0005739	mitochondrion	ACCEPT	GO:0009536	plastid	KEEP_AS_NON_CORE	Correct localization for both alternative splice products of this locus.	Plastid SDH exists in plants but the evidence for plastid localization of this specific SDH2 is from automated prediction only. The primary function is mitochondrial.	genes/9POAL/NCGR_LOCUS67308/NCGR_LOCUS67308-ai-review.yaml
conflicts_with	UniProt subcellular location	CAPO3	coITGB2	GO:0009986	cell surface	KEEP_AS_NON_CORE	GO:0016020	membrane	KEEP_AS_NON_CORE	Correct for a type I transmembrane adhesion receptor and indirectly supported by the antibody-blocking experiment. It adds little beyond plasma membrane.	True (one transmembrane helix) but redundant with the more specific plasma membrane annotation.	genes/CAPO3/coITGB2/coITGB2-ai-review.yaml
conflicts_with	UniProt subcellular location	DESRO	K9J287	GO:0005634	nucleus	REMOVE	GO:0005783	endoplasmic reticulum	ACCEPT	UniProt subcellular location indicates endoplasmic reticulum, not nucleus.	Subcellular location indicates ER.	genes/DESRO/K9J287/K9J287-ai-review.yaml
conflicts_with	UniProt subcellular location	DORPE	cpx	GO:0031201	SNARE complex	MARK_AS_OVER_ANNOTATED	GO:0005829	cytosol	ACCEPT	Complexin is not a core subunit of the SNARE complex; it binds to the exterior surface of the assembled SNARE four-helix bundle as an accessory regulatory protein. The part_of qualifier used in the GOA annotation implies complexin is a structural component of the SNARE complex, which is inaccurate. 	Cytosol localization is experimentally confirmed in this species. Complexin is primarily a soluble cytosolic protein that associates with the SNARE complex at the membrane.	genes/DORPE/cpx/cpx-ai-review.yaml
conflicts_with	UniProt subcellular location	OSCPE	TLN	GO:0005886	plasma membrane	ACCEPT	GO:0005938	cell cortex	ACCEPT	Consistent with the conserved FERM head (membrane- and integrin-binding) in TLN. Not tested in sponge.	Talins act at the membrane-cortex interface; general and plausible.	genes/OSCPE/TLN/TLN-ai-review.yaml
conflicts_with	UniRule	9POAL	NCGR_LOCUS10166	GO:0005737	cytoplasm	ACCEPT	GO:0016020	membrane	ACCEPT	Both plastids and the endoplasmic reticulum are cytoplasmic organelles. The previous reasoning wrongly treated cytoplasm as equivalent to cytosol and used unresolved organelle targeting to reject a broad TreeGrafter inference. The UniProt compartment/architecture assignment is electronic supporting 	Broad membrane association is supported by the actual candidate sequence. It is not an over-annotation merely because specific membranes were also predicted; exact ER versus plastid targeting remains unresolved. The UniProt compartment/architecture assignment is electronic supporting evidence, not a	genes/9POAL/NCGR_LOCUS10166/NCGR_LOCUS10166-ai-review.yaml
conflicts_with	UniRule	9POAL	NCGR_LOCUS10166	GO:0005829	cytosol	UNDECIDED	GO:0016020	membrane	ACCEPT	The sequence includes a plant HDH-like N-terminus and a hydrophobic ARV-like region. Neither predicted organelle targeting nor possible gene-model fusion proves exclusive localization. The exact TreeGrafter source placement and target processing require adjudication.	Broad membrane association is supported by the actual candidate sequence. It is not an over-annotation merely because specific membranes were also predicted; exact ER versus plastid targeting remains unresolved. The UniProt compartment/architecture assignment is electronic supporting evidence, not a	genes/9POAL/NCGR_LOCUS10166/NCGR_LOCUS10166-ai-review.yaml
conflicts_with	UniRule	PSEPK	ahcY	GO:0033353	L-methionine cycle	ACCEPT	GO:0071269	L-homocysteine biosynthetic process	ACCEPT	SAH hydrolysis connects SAM-dependent methylation to homocysteine remethylation. This is the direct AhcY implementation of the bacterial methionine cycle.	UniProt assigns the enzyme to the single-step route from SAH to L-homocysteine, so the process annotation is chemically and pathway appropriate even though homocysteine is subsequently remethylated.	genes/PSEPK/ahcY/ahcY-ai-review.yaml
conflicts_with	UniRule	PSEPK	fruA	GO:0090563	protein-phosphocysteine-sugar phosphotransferase activity	KEEP_AS_NON_CORE	GO:0051119	sugar transmembrane transporter activity	MARK_AS_OVER_ANNOTATED	This is a genuine mechanistic EIIB sub-step within the single net FruA transport-phosphorylation reaction represented by core term GO:0022877, not a second independent core function.	GO:0022877 is the informative direct function.	genes/PSEPK/fruA/fruA-ai-review.yaml
conflicts_with	UniRule	PSEPK	mutS	GO:0003690	double-stranded DNA binding	KEEP_AS_NON_CORE	GO:0003684	damaged DNA binding	MARK_AS_OVER_ANNOTATED	GO:0003690 is a direct is_a ancestor of GO:0030983 mismatched DNA binding, which MutS already carries from UniRule/InterPro, and UniProt's mismatch-recognition function statement is consistent with binding duplex DNA. The parent is therefore true; redundancy with the more informative descendant is n	The specific mismatch-sensor terms capture the core activity.	genes/PSEPK/mutS/mutS-ai-review.yaml
conflicts_with	UniRule	PSEPK	nuoH	GO:0003954	NADH dehydrogenase activity	MODIFY	GO:0016655	oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor	MARK_AS_OVER_ANNOTATED	GO:0003954 (NADH + H+ + acceptor = NAD+ + reduced acceptor) is an is_a ancestor of GO:0008137 NADH dehydrogenase (ubiquinone) activity, the reaction catalysed by the assembled 13-subunit NDH-1 complex of which NuoH is an obligate component. NuoH is an 8-TM integral membrane subunit of the membrane s	The complete NADH:quinone oxidoreductase reaction is an emergent activity of assembled complex I; this subunit contributes to it but does not independently enable the full reaction.	genes/PSEPK/nuoH/nuoH-ai-review.yaml
conflicts_with	UniRule	PSEPK	secD	GO:0015031	protein transport	KEEP_AS_NON_CORE	GO:0006605	protein targeting	KEEP_AS_NON_CORE	The over-annotation call is relaxed and the ancestor is retained as non-core. GO:0015031 protein transport is the directed movement of proteins into, out of or within a cell, which secD does as part of the SecDF accessory complex that uses the proton motive force to complete translocation after the 	Protein targeting is compatible pathway context but is not the subunit's direct mechanistic role.	genes/PSEPK/secD/secD-ai-review.yaml
conflicts_with	UniRule	PSEPK	secF	GO:0015031	protein transport	KEEP_AS_NON_CORE	GO:0006605	protein targeting	KEEP_AS_NON_CORE	The over-annotation call is relaxed and the ancestor is retained as non-core. GO:0015031 protein transport is the directed movement of proteins into, out of or within a cell, which secF does as part of the SecDF accessory complex that uses the proton motive force to complete translocation after the 	Protein targeting is compatible pathway context but is not the subunit's direct mechanistic role.	genes/PSEPK/secF/secF-ai-review.yaml
conflicts_with	combined IEA	9POAL	NCGR_LOCUS1270	GO:0006002	fructose 6-phosphate metabolic process	ACCEPT	GO:0030388	fructose 1,6-bisphosphate metabolic process	ACCEPT	GO:0006002 covers chemical reactions involving F6P without requiring a cytosolic location. Chloroplast Calvin-cycle chemistry therefore satisfies the term. The previous review incorrectly treated absent pathway specificity as over-annotation.	This substrate-centered process directly describes the work performed by the enzyme and is core. Calvin-cycle context is complementary; it does not relegate FBP metabolism to a non-core function.	genes/9POAL/NCGR_LOCUS1270/NCGR_LOCUS1270-ai-review.yaml
conflicts_with	combined IEA	9POAL	NCGR_LOCUS1765	GO:0003729	mRNA binding	ACCEPT	GO:0000339	RNA cap binding	ACCEPT			genes/9POAL/NCGR_LOCUS1765/NCGR_LOCUS1765-ai-review.yaml
conflicts_with	combined IEA	CANLF	ALB	GO:0005737	cytoplasm	KEEP_AS_NON_CORE	GO:0005576	extracellular region	ACCEPT	Biosynthetic/transit localization; the functional compartment is extracellular plasma.	Albumin functions in blood plasma (extracellular region).	genes/CANLF/ALB/ALB-ai-review.yaml
conflicts_with	combined IEA	DROVI	B4MAQ2	GO:0006405	RNA export from nucleus	ACCEPT	GO:0006611	protein export from nucleus	REMOVE	RNA nuclear export is the central biological process for Exportin-5 proteins, directly supported by the domain architecture and Drosophila Exportin-5 literature showing export of pre-miRNAs and tRNAs.	Protein nuclear export is the function of CRM1/Exportin-1, not Exportin-5. This protein's Exportin-5_C domain and PANTHER EXPORTIN-5 subfamily assignment indicate it is an RNA transporter, and this annotation appears to be an overgeneralization from the XPO1/5 family.	genes/DROVI/B4MAQ2/B4MAQ2-ai-review.yaml
conflicts_with	combined IEA	FELCA	ALB	GO:0005737	cytoplasm	KEEP_AS_NON_CORE	GO:0005576	extracellular region	ACCEPT	Biosynthetic/transit localization; the functional compartment is extracellular plasma.	Albumin functions in blood plasma (extracellular region).	genes/FELCA/ALB/ALB-ai-review.yaml
conflicts_with	combined IEA	METEA	fumC	GO:0006108	malate metabolic process	ACCEPT	GO:0006106	fumarate metabolic process	ACCEPT			genes/METEA/fumC/fumC-ai-review.yaml
conflicts_with	combined IEA	PSEPK	PP_1084	GO:0033554	cellular response to stress	KEEP_AS_NON_CORE	GO:0006979	response to oxidative stress	KEEP_AS_NON_CORE	GO:0033554 is defined as any process changing the state or activity of a cell as a result of a stimulus indicating the organism is under stress, which is what PpPrx does: UniProt records a thiol-specific peroxidase that plays a role in cell protection against oxidative stress, and the same PANTHER n	The protein protects against oxidative stress through peroxidase activity; the direct detoxification process terms are more specific.	genes/PSEPK/PP_1084/PP_1084-ai-review.yaml
conflicts_with	combined IEA	PSEPK	PP_2528	GO:0004124	cysteine synthase activity	MARK_AS_OVER_ANNOTATED	GO:0003961	O-acetylhomoserine aminocarboxypropyltransferase activity	ACCEPT	Downgraded from removal because the activity cannot be excluded on architectural grounds. GO:0004124 is O3-acetyl-L-serine + hydrogen sulfide = L-cysteine + acetate, differing from the propagated-and-accepted GO:0003961 (O-acetyl-L- homoserine + a thiol) by a single methylene in the substrate, and O	UniProt names PP_2528 as O-acetylhomoserine (thiol)-lyase and the GOA EC-based annotation assigns the corresponding O-acetylhomoserine sulfhydrylase molecular function.	genes/PSEPK/PP_2528/PP_2528-ai-review.yaml
conflicts_with	combined IEA	PSEPK	aceK	GO:0016208	AMP binding	ACCEPT	GO:0005524	ATP binding	ACCEPT	The E. coli AceK structure shows AMP at an interdomain allosteric site controlling the opposing catalytic activities. This provides positive family-level support for the TreeGrafter inference to the conserved P. putida AceK. An unmeasured target-specific binding constant is not sufficient reason to 	The UniProt record explicitly annotates ATP-binding residues, and the characterized AceK structure contains ATP. This functional ligand interaction is real and core; coexistence with kinase activity is not over-annotation.	genes/PSEPK/aceK/aceK-ai-review.yaml
conflicts_with	combined IEA	PSEPK	ahpC	GO:0033554	cellular response to stress	ACCEPT	GO:0006979	response to oxidative stress	ACCEPT	The general stress-response annotation is supported by the direct antioxidant mechanism and OxyR-associated response. Broadness alone does not turn that response into a non-core function.	Direct peroxide reduction performs work in the oxidative-stress response. The more specific detoxification annotation is complementary and does not make this core protective role peripheral.	genes/PSEPK/ahpC/ahpC-ai-review.yaml
conflicts_with	combined IEA	PSEPK	alr	GO:0005829	cytosol	REMOVE	GO:0042597	periplasmic space	ACCEPT	Remove the phylogenetic cytosol transfer because Q88GJ9 has a cleaved N-terminal signal peptide and experimentally detected periplasmic activity. The fractionation study did not exclude all cytoplasmic activity, so this decision is based on the positive targeting evidence.	Retain the specific localization.	genes/PSEPK/alr/alr-ai-review.yaml
conflicts_with	combined IEA	PSEPK	ampD	GO:0009254	peptidoglycan turnover	ACCEPT	GO:0009253	peptidoglycan catabolic process	ACCEPT	The target belongs to the AmpD-specific subfamily, and the P. putida pathway model explicitly includes cytoplasmic AmpD processing.	Hydrolysis of the sugar-peptide bond disassembles an imported peptidoglycan fragment and is therefore a direct catabolic step within peptidoglycan recycling.	genes/PSEPK/ampD/ampD-ai-review.yaml
conflicts_with	combined IEA	PSEPK	clpX	GO:0051301	cell division	KEEP_AS_NON_CORE	GO:0006457	protein folding	MODIFY	Cell division is an indirect, pleiotropic effect of ClpXP-mediated proteolysis of regulators, not the core molecular/biological function of ClpX. Retain as non-core.	ClpX directs proteolytic degradation rather than folding. The biological process is better captured by protein catabolic process; ClpX unfolds substrates for ClpP rather than folding them.	genes/PSEPK/clpX/clpX-ai-review.yaml
conflicts_with	combined IEA	PSEPK	dapE	GO:0008777	acetylornithine deacetylase activity	REMOVE	GO:0009014	succinyl-diaminopimelate desuccinylase activity	ACCEPT	Q88MP5 is assigned to the proteobacterial DapE subfamily and EC 3.5.1.18; no evidence supports acetylornithine as its physiological substrate.	EC 3.5.1.18, HAMAP MF_01690, and NCBIfam:TIGR01246 support the same reaction.	genes/PSEPK/dapE/dapE-ai-review.yaml
conflicts_with	combined IEA	PSEPK	davA	GO:0050126	N-carbamoylputrescine amidase activity	REMOVE	GO:0047588	5-aminopentanamidase activity	ACCEPT	GO:0050126 is defined as hydrolysis of N-carbamoylputrescine to putrescine, CO2 and ammonium, the carbamoyl-amide step of the agmatine route to putrescine. Q88QV2 is the Dav-pathway enzyme that hydrolyses the simple amide 5-aminopentanamide to 5-aminovalerate, the reaction captured by GO:0047588 on 	Purified KT2440 DavA directly converts 5-aminopentanamide to 5-aminovalerate, supporting an experimental evidence upgrade beyond the current IEA row.	genes/PSEPK/davA/davA-ai-review.yaml
conflicts_with	combined IEA	PSEPK	flgE	GO:0005829	cytosol	REMOVE	GO:0009425	bacterial-type flagellum basal body	REMOVE	FlgE is an exported axial subunit. UniProt gives its subcellular location as the bacterial flagellum basal body, and the assembly literature places the protein outside the cytoplasm, travelling through the central channel of the growing structure and polymerizing at the distal end of the rod; its te		genes/PSEPK/flgE/flgE-ai-review.yaml
conflicts_with	combined IEA	PSEPK	flgE	GO:0009424	bacterial-type flagellum hook	ACCEPT	GO:0009425	bacterial-type flagellum basal body	REMOVE			genes/PSEPK/flgE/flgE-ai-review.yaml
conflicts_with	combined IEA	PSEPK	fumC	GO:0006108	malate metabolic process	KEEP_AS_NON_CORE	GO:0006106	fumarate metabolic process	KEEP_AS_NON_CORE	Accurate given malate is directly produced/consumed, but a broad parent process relative to the TCA cycle. Retained as supporting, non-core.	Accurate (the enzyme acts on fumarate) but a broad parent process. The TCA cycle annotation is the more informative core process; this is retained as a supporting, non-core term.	genes/PSEPK/fumC/fumC-ai-review.yaml
conflicts_with	combined IEA	PSEPK	glnA	GO:0016020	membrane	REMOVE	GO:0005737	cytoplasm	ACCEPT	GO:0016020 is defined as a lipid bilayer with the proteins embedded in or attached to it. Q88CY3 has no transmembrane feature and no signal peptide in UniProt, which gives its subcellular location as cytoplasm; the protein is a soluble dodecamer of two stacked hexameric rings with catalytic sites at		genes/PSEPK/glnA/glnA-ai-review.yaml
conflicts_with	combined IEA	PSEPK	hisA	GO:0000162	L-tryptophan biosynthetic process	REMOVE	GO:0000105	L-histidine biosynthetic process	ACCEPT	Q88R42 has the HisA-specific activity and is assigned only to the histidine pathway by the reviewed UniProt record. KT2440 has a distinct reviewed TrpF protein, Q88LE0, that catalyzes the phosphoribosylanthranilate isomerase reaction in L-tryptophan biosynthesis. No evidence supports a PriA-like bif	The reviewed UniProt entry, EC/Rhea chemistry, UniPathway assignment, and HisA-specific family signatures all support L-histidine biosynthesis.	genes/PSEPK/hisA/hisA-ai-review.yaml
conflicts_with	combined IEA	PSEPK	hmgB	GO:0006572	L-tyrosine catabolic process	ACCEPT	GO:0006559	L-phenylalanine catabolic process	ACCEPT	The P. putida pathway study establishes that tyrosine is converted to homogentisate and then catabolized by HmgABC.	The P. putida pathway study establishes that phenylalanine is converted through tyrosine to homogentisate and then catabolized by HmgABC.	genes/PSEPK/hmgB/hmgB-ai-review.yaml
conflicts_with	combined IEA	PSEPK	ilvA-I	GO:0003941	L-serine ammonia-lyase activity	KEEP_AS_NON_CORE	GO:0004794	threonine deaminase activity	ACCEPT	Direct recombinant enzyme studies demonstrate L-serine use by biosynthetic IlvA homologs (PMID:30226377, Mycobacterium smegmatis; PMID:30327426, Salmonella enterica). The target retains the biosynthetic Ser/Thr-dehydratase catalytic architecture, supporting the TreeGrafter molecular-activity inferen	EC 4.3.1.19, RHEA:22108, InterPro:IPR005787, and the full-length ACT-domain architecture support biosynthetic L-threonine deamination.	genes/PSEPK/ilvA-I/ilvA-I-ai-review.yaml
conflicts_with	combined IEA	PSEPK	ilvA-II	GO:0003941	L-serine ammonia-lyase activity	KEEP_AS_NON_CORE	GO:0004794	threonine deaminase activity	ACCEPT	Direct recombinant enzyme studies demonstrate L-serine use by biosynthetic IlvA homologs (PMID:30226377, Mycobacterium smegmatis; PMID:30327426, Salmonella enterica). The target retains the biosynthetic Ser/Thr-dehydratase catalytic architecture, supporting the TreeGrafter molecular-activity inferen	EC 4.3.1.19, RHEA:22108, InterPro:IPR005787, and the full-length ACT-domain architecture support biosynthetic L-threonine deamination.	genes/PSEPK/ilvA-II/ilvA-II-ai-review.yaml
conflicts_with	combined IEA	PSEPK	infC	GO:0016020	membrane	REMOVE	GO:0005737	cytoplasm	KEEP_AS_NON_CORE	The exact target record assigns IF-3 to the cytoplasm and contains no signal peptide, transmembrane segment, or membrane-localization statement; the membrane transfer conflicts with the characterized soluble 30S role. The graft position explains the error: Q88K26's PANTHER family PTHR10938 matches s	GO:0005737 is a correct, directly supported broad location for soluble IF-3. It is retained as non-core because the same GOA set already contains the more specific GO:0005829 cytosol annotation.	genes/PSEPK/infC/infC-ai-review.yaml
conflicts_with	combined IEA	PSEPK	pgm	GO:0008973	phosphopentomutase activity	MARK_AS_OVER_ANNOTATED	GO:0004614	phosphoglucomutase activity	ACCEPT	Rejection confirmed on re-review, with the reason strengthened. GO:0008973 is defined as catalysis of D-ribose 1-phosphate = D-ribose 5-phosphate, a pentose-phosphate substrate, whereas Q88GY7 carries the glucose-specific classifiers NCBIfam TIGR01132 and InterPro IPR005852 PGM_a-D-Glc-sp and is ass	This is a specific, biologically appropriate annotation for this gene product.	genes/PSEPK/pgm/pgm-ai-review.yaml
conflicts_with	combined IEA	PSEPK	prpC	GO:0005975	carbohydrate metabolic process	REMOVE	GO:0006099	tricarboxylic acid cycle	MARK_AS_OVER_ANNOTATED	"Re-review: the rejection stands. PrpC condenses propanoyl-CoA with oxaloacetate (UniProt CATALYTIC ACTIVITY) and UniProt assigns PATHWAY ""Organic acid metabolism; propanoate degradation"", so the carbon handled is an organic acid, not a carbohydrate. GO:0005975 is a wrong-branch propagation from the "	UniProt includes a TCA/citrate-synthase-family mapping, but the pathway-level review identifies prpC as K01659 2-methylcitrate synthase rather than the canonical TCA citrate synthase. GltA is the unambiguous TCA citrate synthase in KT2440, so PrpC should not be used to satisfy the core TCA citrate s	genes/PSEPK/prpC/prpC-ai-review.yaml
conflicts_with	combined IEA	PSEPK	pyrC'	GO:0004038	allantoinase activity	REMOVE	GO:0004151	dihydroorotase activity	REMOVE	The TreeGrafter transfer reflects broad amidohydrolase-family similarity. Direct work on the P. putida complex instead identifies this protein as a catalytically inactive PyrC-like partner of PyrB.	The protein lacks catalytic histidines, does not complement an E. coli pyrC auxotroph, and is distinct from the active P. putida PyrC enzyme.	genes/PSEPK/pyrC'/pyrC'-ai-review.yaml
conflicts_with	combined IEA	PSEPK	rbsD	GO:0016866	intramolecular transferase activity	KEEP_AS_NON_CORE	GO:0016872	intramolecular lyase activity	REMOVE		Q88K33 is assigned EC 5.4.99.62 and GO:0062193; GO:0016872 is not an ancestor of the specific pyranase term and should not be propagated as a catalytic parent.	genes/PSEPK/rbsD/rbsD-ai-review.yaml
conflicts_with	combined IEA	PSEPK	recD	GO:0017116	single-stranded DNA helicase activity	KEEP_AS_NON_CORE	GO:0043139	5'-3' DNA helicase activity	ACCEPT	GO:0017116 is not a parent of the 5-prime-to-3-prime term and is biologically true, but GO:0043139 better captures RecD's defining polarity in the core-function summary.	The target record explicitly assigns 5-prime-to-3-prime helicase activity to this RecD family protein and describes ATP-coupled translocation in that direction.	genes/PSEPK/recD/recD-ai-review.yaml
conflicts_with	combined IEA	PSEPK	tatC-I	GO:0065002	intracellular protein transmembrane transport	ACCEPT	GO:0043953	protein transport by the Tat complex	ACCEPT	This valid parent process records transmembrane movement of intracellular folded-protein substrates; GO:0043953 supplies the Tat-specific context.	This is the defining conserved biological process of TatC-family proteins.	genes/PSEPK/tatC-I/tatC-I-ai-review.yaml
conflicts_with	combined IEA	PSEPK	tatC-II	GO:0065002	intracellular protein transmembrane transport	ACCEPT	GO:0043953	protein transport by the Tat complex	ACCEPT	This valid parent process records transmembrane movement of intracellular folded-protein substrates; GO:0043953 supplies the Tat-specific context.	This is the defining conserved biological process of TatC-family proteins.	genes/PSEPK/tatC-II/tatC-II-ai-review.yaml
conflicts_with	combined IEA	PSEPK	tig	GO:0043335	protein unfolding	KEEP_AS_NON_CORE	GO:0006457	protein folding	MARK_AS_OVER_ANNOTATED	The current PAINT IBD assertion is experimentally seeded by E. coli trigger factor P0A850, and PMID:24812405 directly supports context-dependent unfoldase behavior. Retain the propagated BP for P. putida Tig, but as non-core because free-cytosolic unfoldase activity is weak and ribosome-enhanced unf	True but redundant with the more specific child term 'de novo' cotranslational protein folding (GO:0051083), which better captures the co-translational, exit-tunnel role of trigger factor. Retaining the broad parent alongside the specific child is an over-annotation.	genes/PSEPK/tig/tig-ai-review.yaml
conflicts_with	combined IEA	SACEN	eryAI	GO:0004312	fatty acid synthase activity	MODIFY	GO:0047879	erythronolide synthase activity	ACCEPT	Wrong product class. Replace with GO:0016218 (polyketide synthase activity).	Correct, specific molecular function for the DEBS subunit.	genes/SACEN/eryAI/eryAI-ai-review.yaml
conflicts_with	combined IEA	SACEN	eryAII	GO:0004312	fatty acid synthase activity	MODIFY	GO:0047879	erythronolide synthase activity	ACCEPT	Wrong product class. Replace with GO:0016218 (polyketide synthase activity).	Correct, specific molecular function for the DEBS subunit.	genes/SACEN/eryAII/eryAII-ai-review.yaml
conflicts_with	combined IEA	SACEN	eryAIII	GO:0004312	fatty acid synthase activity	MODIFY	GO:0047879	erythronolide synthase activity	ACCEPT	The characterized assembly-line product is 6-deoxyerythronolide B, a macrolide polyketide. This supports a polyketide-synthase refinement of the fatty-acid-synthase assignment. Shared acyl-carrier/condensation chemistry is real; absence of DH/ER domains from this particular subunit is not, by itself	Correct, specific molecular function for the DEBS subunit.	genes/SACEN/eryAIII/eryAIII-ai-review.yaml
conflicts_with	combined IEA	SPHPI	Q53353	GO:0010436	carotenoid dioxygenase activity	REMOVE	GO:0050054	lignostilbene alpha beta-dioxygenase activity	ACCEPT	LSD-I is an experimentally characterized lignostilbene dioxygenase (EC 1.13.11.43), not a carotenoid enzyme; the correct specific MF (GO:0050054) is already present by IDA. Same substrate-class error as LSD-III, NOV1/NOV2, Rco1, and cao-1.	Core molecular function, corroborated by IDA.	genes/SPHPI/Q53353/Q53353-ai-review.yaml
conflicts_with	combined IEA	SPHPI	lsdB	GO:0010436	carotenoid dioxygenase activity	REMOVE	GO:0050054	lignostilbene alpha beta-dioxygenase activity	ACCEPT	LSD-III is an experimentally characterized lignostilbene dioxygenase (EC 1.13.11.43), not a carotenoid enzyme; the correct specific MF (GO:0050054) is already present by IDA. Same substrate-class error as cao-1 (IBA) and NOV1 (IEA/TreeGrafter).	Core molecular function - the exact activity of LSD-III - corroborated by the IDA annotation of the same term.	genes/SPHPI/lsdB/lsdB-ai-review.yaml
deeper_than	ARBA	9AVES	TAS1R1	GO:0050917	sensory perception of umami taste	KEEP_AS_NON_CORE	GO:0050909	sensory perception of taste	KEEP_AS_NON_CORE	"GO:0050917 is defined as perception of ""the savory taste of meats and other foods that are rich in glutamates"" - i.e. amino-acid/glutamate detection. That is the correct, ancestral TAS1R1-TAS1R3 function, and it is retained in non-hummingbird birds: ""cells expressing chicken or swift T1R1-T1R3 faile"	"Uncontroversial at this level of generality; both the ancestral umami-sensing role of TAS1R1-TAS1R3 and the hummingbird-specific sweet-sensing repurposing are instances of ""sensory perception of taste."" Retained as a valid but non-core parent term, since the more specific process calls below already"	genes/9AVES/TAS1R1/TAS1R1-ai-review.yaml
deeper_than	ARBA	9AVES	TAS1R3	GO:0050916	sensory perception of sweet taste	ACCEPT	GO:0050909	sensory perception of taste	KEEP_AS_NON_CORE	This is the headline, well-supported functional claim for the TAS1R1-TAS1R3 heterodimer in the hummingbird lineage generally, directly paralleling and supporting the ACCEPT decision for GO:0033041. Treated as a core, not merely peripheral, biological process for this gene, with the caveat (noted in 	"Correct broad parent term; both sweet-taste and umami-taste perception are children of ""sensory perception of taste,"" so this generic annotation is consistent with either or both of the more specific annotations being correct, but it is uninformative given that the more specific GO:0050916 (below) i"	genes/9AVES/TAS1R3/TAS1R3-ai-review.yaml
deeper_than	ARBA	9AVES	TAS1R3	GO:0050917	sensory perception of umami taste	KEEP_AS_NON_CORE	GO:0050909	sensory perception of taste	KEEP_AS_NON_CORE	The PANTHER/TreeGrafter node correctly reflects that umami/amino-acid detection is the ancestral, family-wide function of the TAS1R1-TAS1R3 heterodimer (and remains the primary function in most other birds, which retain only this dimer). However, for the hummingbird lineage specifically, PMID:251462	"Correct broad parent term; both sweet-taste and umami-taste perception are children of ""sensory perception of taste,"" so this generic annotation is consistent with either or both of the more specific annotations being correct, but it is uninformative given that the more specific GO:0050916 (below) i"	genes/9AVES/TAS1R3/TAS1R3-ai-review.yaml
deeper_than	ARBA	9POAL	NCGR_LOCUS1270	GO:0005986	sucrose biosynthetic process	UNDECIDED	GO:0005985	sucrose metabolic process	UNDECIDED	The dominant Calvin-cycle role and separation from cytosolic FBPase are supported, but the previous absolute exclusion and claimed paralog misgraft were not established. Current PTN004269459 is the sorghum A0A1B6QP66 leaf, annotated to chloroplast/Calvin cycle and 96.85% identical across the full gl	Chloroplast FBPase supplies and regulates carbon partitioning, whereas the best-established sucrose-synthesis reactions use the cytosolic paralog. Supplying precursors alone is not sufficient participation, but a different main compartment is not a negative functional assay. The named TreeGrafter re	genes/9POAL/NCGR_LOCUS1270/NCGR_LOCUS1270-ai-review.yaml
deeper_than	ARBA	CAPO3	coWts	GO:0031032	actomyosin structure organization	REMOVE	GO:0007010	cytoskeleton organization	MARK_AS_OVER_ANNOTATED	The term comes from a family-level placement with the Rho-effector kinases, which do organize actomyosin directly; it is not inherited from the Warts/LATS lineage. The Capsaspora data do not rescue it: coWts loss increases a contractile behaviour through coYki-dependent transcription (phenocopied by	coWts influences cytoskeletal behaviour, but indirectly: the phenotypes are attributed to derepressed coYki-dependent transcription, not to coWts acting on cytoskeletal structures. By the participation test, coWts does not do the work of assembling or arranging the cytoskeleton. Process terms descri	genes/CAPO3/coWts/coWts-ai-review.yaml
deeper_than	ARBA	DORPE	AP180	GO:0008021	synaptic vesicle	MODIFY	GO:0012505	endomembrane system	ACCEPT	AP180 is not a component of mature synaptic vesicles. It is a cytosolic adaptor protein that transiently associates with the presynaptic plasma membrane and nascent clathrin-coated pits during endocytosis. A more appropriate localization would be the presynaptic endocytic zone or cytosol.	While very general, this is not incorrect as AP180 does associate with endomembrane compartments (clathrin-coated pits and vesicles). More specific CC terms are already annotated (GO:0005905 clathrin-coated pit, GO:0030136 clathrin-coated vesicle, GO:0098894 presynaptic endocytic zone membrane).	genes/DORPE/AP180/AP180-ai-review.yaml
deeper_than	ARBA	DORPE	AP180	GO:0016185	synaptic vesicle budding from presynaptic endocytic zone membrane	ACCEPT	GO:0048488	synaptic vesicle endocytosis	ACCEPT	This is an excellent and specific annotation for AP180 function at the squid giant synapse. The experimental evidence from PMID:10575017 directly demonstrates that AP180 is required for synaptic vesicle budding from the presynaptic membrane: blocking AP180 function caused depletion of synaptic vesic	Synaptic vesicle endocytosis is a well-established core function of squid AP180, supported by IMP evidence from PMID:10575017. The ARBA prediction is correct.	genes/DORPE/AP180/AP180-ai-review.yaml
deeper_than	ARBA	DORPE	AP180	GO:0098894	extrinsic component of presynaptic endocytic zone membrane	ACCEPT	GO:0016020	membrane	ACCEPT	Highly appropriate and specific CC annotation. AP180 is not a transmembrane protein but rather an extrinsic membrane-associated adaptor that is recruited to the presynaptic membrane via PtdIns(4,5)P2 binding. The experimental work was performed at the squid giant presynaptic terminal, placing AP180 	While extremely general, membrane association is not incorrect. AP180 binds PtdIns(4,5)P2 at membranes as part of its function. More specific CC terms are already present. This broad IEA annotation does not misrepresent the protein.	genes/DORPE/AP180/AP180-ai-review.yaml
deeper_than	ARBA	GADMO	A0A8C5FPT8	GO:0031267	small GTPase binding	ACCEPT	GO:0019899	enzyme binding	MARK_AS_OVER_ANNOTATED	RAB11 binding is the best-characterized molecular function of TBC1D14. The protein binds GTP-RAB11 as an effector and also associates with RAB1B. Small GTPase binding accurately captures this core activity.	While TBC1D14 does bind enzymes (RAB11 GTPase, ULK1 kinase), this is already captured more informatively by the small GTPase binding annotation. The generic enzyme binding term adds no biological insight.	genes/GADMO/A0A8C5FPT8/A0A8C5FPT8-ai-review.yaml
deeper_than	ARBA	NICAT	NaUGT1_candidate_UGT85A2_0	GO:0080043	quercetin 3-O-glucosyltransferase activity	UNDECIDED	GO:0035251	UDP-glucosyltransferase activity	MODIFY	Primary 2026 data support nicotinate N-glucosylation at the mapped g26396 locus, with a documented construct-boundary caveat. They do not assay every alternative acceptor. Neither the positive nicotine function nor sequence-family distance establishes that quercetin or 7-deoxyloganetic acid cannot a	GO:0050139 already exists for this exact reaction. The Cell 2026 NaUGT1 assay/perturbation primers map to the g26396 locus, and its primer-compatible extended ORF contains the complete A0A2H4GSI3 sequence. Independent tobacco UGT1 supplements explicitly map the assayed N-glucosyltransferase to a clo	genes/NICAT/NaUGT1_candidate_UGT85A2_0/NaUGT1_candidate_UGT85A2_0-ai-review.yaml
deeper_than	ARBA	NICAT	NaUGT1_candidate_UGT85A2_0	GO:0080044	quercetin 7-O-glucosyltransferase activity	UNDECIDED	GO:0035251	UDP-glucosyltransferase activity	MODIFY	Primary 2026 data support nicotinate N-glucosylation at the mapped g26396 locus, with a documented construct-boundary caveat. They do not assay every alternative acceptor. Neither the positive nicotine function nor sequence-family distance establishes that quercetin or 7-deoxyloganetic acid cannot a	GO:0050139 already exists for this exact reaction. The Cell 2026 NaUGT1 assay/perturbation primers map to the g26396 locus, and its primer-compatible extended ORF contains the complete A0A2H4GSI3 sequence. Independent tobacco UGT1 supplements explicitly map the assayed N-glucosyltransferase to a clo	genes/NICAT/NaUGT1_candidate_UGT85A2_0/NaUGT1_candidate_UGT85A2_0-ai-review.yaml
deeper_than	ARBA	PSEPK	PP_0581	GO:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	ACCEPT	GO:0016491	oxidoreductase activity	MARK_AS_OVER_ANNOTATED	The SDR domains and convergent family assignments support NAD(H)-dependent 3-oxoacyl reduction, but no target-specific experiment distinguishes an ACP-linked substrate from a CoA-linked substrate.	UniProt's submitted name and PANTHER subfamily both assign an NADH-dependent 3-oxoacyl reductase; the closer mechanistic annotation below captures the supported reaction class without asserting an experimentally unresolved ACP-versus-CoA substrate.	genes/PSEPK/PP_0581/PP_0581-ai-review.yaml
deeper_than	ARBA	PSEPK	PP_0892	GO:0008808	cardiolipin synthase activity	UNDECIDED	GO:0030572	phosphatidyltransferase activity	ACCEPT	TreeGrafter and PANTHER place PP_0892 in a ClsB-like node, but the current UniProt record remains generic and supplies no reaction or experimental substrate evidence.	The two PLD-like regions support phosphatidyltransferase chemistry, while the exact phospholipid substrates remain unresolved.	genes/PSEPK/PP_0892/PP_0892-ai-review.yaml
deeper_than	ARBA	PSEPK	PP_1084	GO:0005829	cytosol	KEEP_AS_NON_CORE	GO:0005737	cytoplasm	ACCEPT	Retain as a non-core location annotation in the bacterial cytoplasm/cytosol context.	The protein is annotated as cytoplasmic and has no evidence for another compartment; a PSORTb prediction independently places PP_1084/PpPrx in the cytoplasm.	genes/PSEPK/PP_1084/PP_1084-ai-review.yaml
deeper_than	ARBA	PSEPK	PP_1084	GO:0008379	thioredoxin peroxidase activity	ACCEPT	GO:0004601	peroxidase activity	ACCEPT	The UniProt entry identifies the protein as a thiol-specific/thioredoxin peroxidase that reduces peroxides, and the directly studied KT2440 protein PpPrx (PP_1084) is experimentally a thioredoxin-dependent peroxidase.	UniProt describes reduction of hydrogen peroxide and organic hydroperoxides, supporting peroxidase activity.	genes/PSEPK/PP_1084/PP_1084-ai-review.yaml
deeper_than	ARBA	PSEPK	PP_1907	GO:0008967	phosphoglycolate phosphatase activity	ACCEPT	GO:0003824	catalytic activity	MARK_AS_OVER_ANNOTATED	TreeGrafter, PANTHER, KEGG, and OpenScientist all converge on 2-phosphoglycolate phosphatase activity; the caveat is paralog ambiguity rather than evidence against the annotation.	UniProt identifies PP_1907 as a HAD-like hydrolase, and the OpenScientist report supports a Mg(2+)-dependent phosphatase mechanism with a more specific phosphoglycolate phosphatase prediction.	genes/PSEPK/PP_1907/PP_1907-ai-review.yaml
deeper_than	ARBA	PSEPK	PP_2320	GO:0018104	peptidoglycan-protein cross-linking	ACCEPT	GO:0000270	peptidoglycan metabolic process	ACCEPT	Its exact PANTHER subfamily matches the experimentally characterized Pseudomonas LdtPae2/ErfK anchoring enzyme.	The L,D-transpeptidase reaction directly remodels the peptide component of peptidoglycan.	genes/PSEPK/PP_2320/PP_2320-ai-review.yaml
deeper_than	ARBA	PSEPK	PP_2320	GO:0071972	peptidoglycan L,D-transpeptidase activity	ACCEPT	GO:0004180	carboxypeptidase activity	REMOVE	The catalytic YkuD domain and exact ErfK-related PANTHER subfamily support this reaction class.	The closely matched ErfK/LdtPae2 subfamily resolves the YkuD reaction as lipoprotein-acceptor L,D-transpeptidation.	genes/PSEPK/PP_2320/PP_2320-ai-review.yaml
deeper_than	ARBA	PSEPK	carB	GO:0006541	L-glutamine metabolic process	MARK_AS_OVER_ANNOTATED	GO:0006520	amino acid metabolic process	MARK_AS_OVER_ANNOTATED	Retain the UMP and arginine biosynthetic processes as the informative pathway assignments.	Retain the specific L-arginine biosynthetic process.	genes/PSEPK/carB/carB-ai-review.yaml
deeper_than	ARBA	PSEPK	ccmH	GO:0005886	plasma membrane	ACCEPT	GO:0016020	membrane	MARK_AS_OVER_ANNOTATED	This specific location is integral to CcmH's role in the membrane-associated maturation machinery.	Redundant, less precise parent of the plasma-membrane annotation.	genes/PSEPK/ccmH/ccmH-ai-review.yaml
deeper_than	ARBA	PSEPK	davD	GO:0004777	succinate-semialdehyde dehydrogenase (NAD+) activity	REMOVE	GO:0016620	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor	MARK_AS_OVER_ANNOTATED	DavD is assigned to oxidation of 5-oxopentanoate in the lysine-derived Dav pathway, whereas GO:0004777 specifies succinate semialdehyde. This substrate mismatch is independent of the unresolved NAD versus NADP preference of Q88RC0.	GO:0102810 captures the physiological substrate and NADP dependence.	genes/PSEPK/davD/davD-ai-review.yaml
deeper_than	ARBA	PSEPK	dinB	GO:0042276	error-prone translesion synthesis	ACCEPT	GO:0006259	DNA metabolic process	MARK_AS_OVER_ANNOTATED	Error-prone translesion synthesis is the most specific and accurate process term for Pol IV, directly matching its error-prone, untargeted-mutagenesis role and lack of proofreading.	DNA metabolic process is a high-level parent of the specific DNA repair and translesion synthesis terms already annotated, so it adds no informative content.	genes/PSEPK/dinB/dinB-ai-review.yaml
deeper_than	ARBA	PSEPK	dnaQ	GO:0008408	3'-5' exonuclease activity	ACCEPT	GO:0004527	exonuclease activity	MARK_AS_OVER_ANNOTATED	The local UniProt record identifies DnaQ as the 3'-to-5' editing exonuclease of polymerase III.	GO:0008408 supplies the biologically relevant 3'-to-5' directionality.	genes/PSEPK/dnaQ/dnaQ-ai-review.yaml
deeper_than	ARBA	PSEPK	folD2	GO:0005829	cytosol	ACCEPT	GO:0005737	cytoplasm	MARK_AS_OVER_ANNOTATED	The localization is computational rather than experimentally measured in KT2440, but it is biologically appropriate and is the least redundant of the two existing compartment annotations.	Mark GO:0005737 as over-annotated because the accepted GO:0005829 child already captures the supported soluble compartment more precisely; the parent location adds no independent localization information.	genes/PSEPK/folD2/folD2-ai-review.yaml
deeper_than	ARBA	PSEPK	gabD-II	GO:0004777	succinate-semialdehyde dehydrogenase (NAD+) activity	UNDECIDED	GO:0016620	oxidoreductase activity, acting on the aldehyde or oxo group of donors, NAD or NADP as acceptor	KEEP_AS_NON_CORE	No direct Q88EN2 assay establishes either cofactor or substrate. Re-review against the OpenScientist control report: its decisive facts were checked. A BLOSUM62 global alignment gives Q88EN2 50.8% identity to NADP+-specific E. coli GabD (P25526; report 51.7%), 48.4% to human ALDH5A1 and 31.6% to E. 	Q88EN2 contains conserved aldehyde-dehydrogenase domains, so the broad enzyme-class annotation is compatible. It is subsumed by the more informative substrate-neutral GO:0004030 core function and does not resolve the physiological aldehyde.	genes/PSEPK/gabD-II/gabD-II-ai-review.yaml
deeper_than	ARBA	PSEPK	gbd	GO:0004022	alcohol dehydrogenase (NAD+) activity	MODIFY	GO:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	MODIFY	Replace this parent with GO:0047577, which captures the submitted 4-hydroxybutyrate substrate and NAD-dependent chemistry. Group III Fe-ADH signatures in Q88JJ9 and characterized bacterial homologs independently support the enzyme class, while the exact substrate assignment remains predictive.	Replace it with GO:0047577, which preserves the independently supported Group III Fe-ADH chemistry while adding the submitted substrate specificity; the latter remains a prediction for Q88JJ9.	genes/PSEPK/gbd/gbd-ai-review.yaml
deeper_than	ARBA	PSEPK	glgP	GO:0005980	glycogen catabolic process	ACCEPT	GO:0005977	glycogen metabolic process	KEEP_AS_NON_CORE	The glycogen-phosphorylase family assignment and EC 2.4.1.1 reaction support a direct role in glycogen catabolism, while the imported claim that this is rate-limiting in KT2440 is not adopted.	Q88CY8 is predicted to mobilize rather than synthesize glycogen, so the child glycogen catabolic process is the core pathway role.	genes/PSEPK/glgP/glgP-ai-review.yaml
deeper_than	ARBA	PSEPK	gshB	GO:0016879	ligase activity, forming carbon-nitrogen bonds	KEEP_AS_NON_CORE	GO:0003824	catalytic activity	MARK_AS_OVER_ANNOTATED	GO:0004363 glutathione synthase activity is_a GO:0016879 in the current ontology, so this term is simply a true parent of the reaction GshB catalyses (gamma-L-glutamyl-L-cysteine + glycine + ATP, ATP-grasp C-N ligase chemistry; EC 6.3.2.3). Redundancy with the more specific term that another row alr	GO:0004363 captures the substrate-specific glutathione-forming reaction.	genes/PSEPK/gshB/gshB-ai-review.yaml
deeper_than	ARBA	PSEPK	hemB	GO:0006783	heme biosynthetic process	ACCEPT	GO:0006779	porphyrin-containing compound biosynthetic process	KEEP_AS_NON_CORE	The reaction is required upstream of hydroxymethylbilane, uroporphyrinogen III, and all subsequent heme-b intermediates.	Porphobilinogen formation supplies the common tetrapyrrole trunk. The annotation is biologically correct, but the catalytic activity and direct tetrapyrrole-biosynthesis role are more informative core claims.	genes/PSEPK/hemB/hemB-ai-review.yaml
deeper_than	ARBA	PSEPK	hemBB	GO:0006783	heme biosynthetic process	ACCEPT	GO:0006779	porphyrin-containing compound biosynthetic process	KEEP_AS_NON_CORE	Its predicted porphobilinogen product feeds the shared reactions leading to uroporphyrinogen III, protoporphyrin IX, and heme b.	Predicted porphobilinogen formation supplies the common tetrapyrrole trunk. The annotation is biologically correct, while the catalytic activity and direct tetrapyrrole role are the more informative core claims.	genes/PSEPK/hemBB/hemBB-ai-review.yaml
deeper_than	ARBA	PSEPK	hemE	GO:0006783	heme biosynthetic process	ACCEPT	GO:0006778	porphyrin-containing compound metabolic process	KEEP_AS_NON_CORE	Coproporphyrinogen III is required for the subsequent HemF/HemN, protoporphyrinogen oxidase, and ferrochelatase reactions.	HemE does participate in porphyrin-containing compound metabolism, but its substrate-specific decarboxylase activity and biosynthetic process assignments describe the role more informatively.	genes/PSEPK/hemE/hemE-ai-review.yaml
deeper_than	ARBA	PSEPK	ilvH	GO:0005829	cytosol	KEEP_AS_NON_CORE	GO:0005737	cytoplasm	MARK_AS_OVER_ANNOTATED	IlvH is a small soluble ACT-domain subunit of the cytoplasmic IlvI-IlvH acetohydroxy-acid synthase, with no membrane-targeting features; cytosol is therefore a plausible propagated location for it. The sibling cytoplasm parent lacks independent record-level support and is treated as redundant; this 	GO:0005829 is the only localization assertion propagated to this record; the UniProt record has no independent SUBCELLULAR LOCATION line for the broader cytoplasm parent. Mark the parent as redundant here and retain the directly supported cytosol child.	genes/PSEPK/ilvH/ilvH-ai-review.yaml
deeper_than	ARBA	PSEPK	metB	GO:0016846	carbon-sulfur lyase activity	MODIFY	GO:0003824	catalytic activity	MODIFY	MetB-family cystathionine gamma-synthase is the specific trans-sulfuration first-step activity represented in the module.	The protein name and pathway context support cystathionine gamma-synthase activity, which is more specific than the ARBA catalytic activity parent.	genes/PSEPK/metB/metB-ai-review.yaml
deeper_than	ARBA	PSEPK	metZ	GO:0016846	carbon-sulfur lyase activity	REMOVE	GO:0003824	catalytic activity	MODIFY	GO:0016846 is defined as catalysis of the elimination of hydrogen sulfide or substituted H2S (EC 4.4.-.-). MetZ does the opposite, consuming sulfide to form the new C-S bond of L-homocysteine (RHEA:27826), and UniProt/HAMAP classify it as a transferase (EC 2.5.1.-). A blinded OpenScientist control r	UniProt assigns the specific O-succinylhomoserine sulfhydrylase reaction (RHEA:27826, EC 2.5.1.-). GO has no term for this reaction, so the replacement is the proposed new term, with the existing transferase parent GO:0016765 as the best available id. The carbon-sulfur lyase term previously proposed	genes/PSEPK/metZ/metZ-ai-review.yaml
deeper_than	ARBA	PSEPK	moeB	GO:0004792	thiosulfate-cyanide sulfurtransferase activity	REMOVE	GO:0003824	catalytic activity	MODIFY	MoeB activates MoaD by ATP-dependent adenylylation; it does not use thiosulfate or cyanide in the assigned reaction. The 251-aa target lacks the C-terminal rhodanese domain found in multifunctional MoeB/MoeZ-family fusions; this is an architecture and reaction mismatch, not merely absence of a targe	Catalysis is central to this enzyme, but GO:0003824 does not identify the reaction. Use the specific molecular function already supported elsewhere in this review; this is a specificity refinement, not a claim that catalysis is peripheral or absent.	genes/PSEPK/moeB/moeB-ai-review.yaml
deeper_than	ARBA	PSEPK	moeB	GO:0008146	sulfotransferase activity	REMOVE	GO:0003824	catalytic activity	MODIFY	MoeB adenylates MoaD; sulfur loading is a separate reaction supplied by a sulfur-donor system. Sulfotransferases transfer sulfate groups; the shared sulfur-pathway context does not confer that chemistry on the MoaD adenylase.	Catalysis is central to this enzyme, but GO:0003824 does not identify the reaction. Use the specific molecular function already supported elsewhere in this review; this is a specificity refinement, not a claim that catalysis is peripheral or absent.	genes/PSEPK/moeB/moeB-ai-review.yaml
deeper_than	ARBA	PSEPK	moeB	GO:0016779	nucleotidyltransferase activity	ACCEPT	GO:0003824	catalytic activity	MODIFY	ATP-dependent transfer of AMP to the terminal carboxylate of MoaD is catalytic nucleotidyl transfer. The specific molybdopterin-synthase adenylyltransferase term is already retained, and its broad catalytic ancestors remain correct. OpenScientist supports the classical MoeB architecture and conserve	Catalysis is central to this enzyme, but GO:0003824 does not identify the reaction. Use the specific molecular function already supported elsewhere in this review; this is a specificity refinement, not a claim that catalysis is peripheral or absent.	genes/PSEPK/moeB/moeB-ai-review.yaml
deeper_than	ARBA	PSEPK	mqo1	GO:0047545	(S)-2-hydroxyglutarate dehydrogenase activity	REMOVE	GO:0016614	oxidoreductase activity, acting on CH-OH group of donors	KEEP_AS_NON_CORE	UniProt's curated catalytic activity for Q88PU7 is malate:quinone oxidoreductase, not (S)-2-hydroxyglutarate dehydrogenase. The protein carries MQO/HAMAP/Pfam evidence and the OpenScientist report supports L-malate oxidation to oxaloacetate with quinone as acceptor. No gene-specific evidence support	The enzyme is an oxidoreductase acting on the CH-OH group of malate, but GO:0008924 captures the specific substrate and quinone acceptor. This parent term is retained only as non-core background.	genes/PSEPK/mqo1/mqo1-ai-review.yaml
deeper_than	ARBA	PSEPK	mqo2	GO:0047545	(S)-2-hydroxyglutarate dehydrogenase activity	REMOVE	GO:0016614	oxidoreductase activity, acting on CH-OH group of donors	KEEP_AS_NON_CORE	UniProt's curated catalytic activity for Q88NF9 is malate:quinone oxidoreductase, not (S)-2-hydroxyglutarate dehydrogenase. The protein carries MQO/HAMAP/Pfam evidence, while the 2-hydroxyglutarate annotation appears to derive from the broad PANTHER family label and has no gene-specific support. The	The enzyme is an oxidoreductase acting on the CH-OH group of malate, but GO:0008924 captures the specific substrate and quinone acceptor.	genes/PSEPK/mqo2/mqo2-ai-review.yaml
deeper_than	ARBA	PSEPK	mqo3	GO:0047545	(S)-2-hydroxyglutarate dehydrogenase activity	REMOVE	GO:0016614	oxidoreductase activity, acting on CH-OH group of donors	KEEP_AS_NON_CORE	UniProt's curated catalytic activity for Q88IS4 is malate:quinone oxidoreductase, not (S)-2-hydroxyglutarate dehydrogenase. The protein carries MQO/HAMAP/Pfam evidence, while the 2-hydroxyglutarate annotation appears to derive from the broad PANTHER family label and has no gene-specific support. The	The enzyme is an oxidoreductase acting on the CH-OH group of malate, but GO:0008924 captures the specific substrate and quinone acceptor.	genes/PSEPK/mqo3/mqo3-ai-review.yaml
deeper_than	ARBA	PSEPK	mupP	GO:0008967	phosphoglycolate phosphatase activity	REMOVE	GO:0016791	phosphatase activity	ACCEPT	The rejection is backed by a direct experimental exclusion of this chemistry, not merely by family-level propagation. The characterizing study explicitly argues that 2-phosphoglycolate is not a MupP substrate, because P. putida encodes a separate, much closer Gph ortholog (PP_0416, 46% identity) whi	Retain the broad phosphatase term and propose a more specific ontology term.	genes/PSEPK/mupP/mupP-ai-review.yaml
deeper_than	ARBA	PSEPK	paaH	GO:0006635	fatty acid beta-oxidation	MARK_AS_OVER_ANNOTATED	GO:0032787	monocarboxylic acid metabolic process	MARK_AS_OVER_ANNOTATED	"The rejection is retained on substrate grounds rather than on the propagation alone. GO:0006635 is defined as the process that ""results in the complete oxidation of a long-chain fatty acid"". The exact target is named 3-hydroxyadipyl-CoA dehydrogenase and sits in the paa locus, acting on the 3-hydrox"	The specific physiological role is phenylacetate catabolism.	genes/PSEPK/paaH/paaH-ai-review.yaml
deeper_than	ARBA	PSEPK	pgsA	GO:0046474	glycerophospholipid biosynthetic process	ACCEPT	GO:0008610	lipid biosynthetic process	MODIFY	PgsA performs a committed phosphatidylglycerol/glycerophospholipid biosynthetic reaction.	Use glycerophospholipid biosynthetic process for this phosphatidylglycerol-branch enzyme.	genes/PSEPK/pgsA/pgsA-ai-review.yaml
deeper_than	ARBA	PSEPK	pgsA	GO:0046474	glycerophospholipid biosynthetic process	ACCEPT	GO:0019637	organophosphate metabolic process	MARK_AS_OVER_ANNOTATED	PgsA performs a committed phosphatidylglycerol/glycerophospholipid biosynthetic reaction.	The useful annotation is glycerophospholipid/phosphatidylglycerol biosynthesis, not a generic organophosphate process.	genes/PSEPK/pgsA/pgsA-ai-review.yaml
deeper_than	ARBA	PSEPK	phnX	GO:0008967	phosphoglycolate phosphatase activity	REMOVE	GO:0003824	catalytic activity	MODIFY	Q88KT1 is assigned the PhnX-specific PANTHER subfamily, HAMAP rule, InterPro signature, and phosphonoacetaldehyde reaction. Those exact classifiers override the broad phosphoglycolate-phosphatase family label.	Q88KT1 has a substrate- and reaction-specific annotation supported by EC 3.11.1.1, RHEA:18905, HAMAP MF_01375, and InterPro IPR006323.	genes/PSEPK/phnX/phnX-ai-review.yaml
deeper_than	ARBA	PSEPK	pssA	GO:0005829	cytosol	KEEP_AS_NON_CORE	GO:0005737	cytoplasm	MARK_AS_OVER_ANNOTATED	Retain the soluble-state location, but do not use it as the core catalytic location because type-I PssA is active at the membrane surface.	GO:0005829 already captures the soluble compartment at useful specificity.	genes/PSEPK/pssA/pssA-ai-review.yaml
deeper_than	ARBA	PSEPK	ptxD	GO:0016618	hydroxypyruvate reductase [NAD(P)H] activity	UNDECIDED	GO:0016491	oxidoreductase activity	MARK_AS_OVER_ANNOTATED	"Re-review: changed from REMOVE to UNDECIDED. The stated ground was only the absence of a target-specific assay, which is not by itself a refutation of a phylogenetic inference. Q88HI1 carries no experimentally determined substrate: UniProt gives only the EMBL-derived SubName ""Phosphonate dehydrogena"	GO:0008114 is the appropriate pathway-grounded molecular function.	genes/PSEPK/ptxD/ptxD-ai-review.yaml
deeper_than	ARBA	PSEPK	ptxD	GO:0030267	glyoxylate reductase (NADPH) activity	UNDECIDED	GO:0016491	oxidoreductase activity	MARK_AS_OVER_ANNOTATED	Re-reviewed against the OpenScientist control report, which recommended retaining GO:0030267 and adding GO:0016618 on the grounds that the nearest characterized homolog is E. coli GhrB (P37666). Verified in this re-review: a BLOSUM62 global alignment gives 53.1% identity of Q88HI1 to GhrB, 40.0% to 	GO:0008114 is the appropriate pathway-grounded molecular function.	genes/PSEPK/ptxD/ptxD-ai-review.yaml
deeper_than	ARBA	PSEPK	pyrC'	GO:0004038	allantoinase activity	REMOVE	GO:0016812	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides	REMOVE	The TreeGrafter transfer reflects broad amidohydrolase-family similarity. Direct work on the P. putida complex instead identifies this protein as a catalytically inactive PyrC-like partner of PyrB.	The direct genetic and sequence evidence establishes loss of dihydroorotase catalysis.	genes/PSEPK/pyrC'/pyrC'-ai-review.yaml
deeper_than	ARBA	PSEPK	sucD	GO:0009361	succinate-CoA ligase complex (ADP-forming)	ACCEPT	GO:0042709	succinate-CoA ligase complex	ACCEPT	SucD is the alpha subunit of the SucC/SucD succinate-CoA ligase complex, described by UniProt as a heterotetramer of two alpha and two beta subunits.	This parent complex term is accurate for the SucC/SucD heterotetramer. The ADP-forming complex term GO:0009361 is more specific, but the generic complex membership is not misleading.	genes/PSEPK/sucD/sucD-ai-review.yaml
deeper_than	ARBA	PSEPK	visC	GO:0019168	2-polyprenylphenol 6-hydroxylase activity	ACCEPT	GO:0004497	monooxygenase activity	MARK_AS_OVER_ANNOTATED	The UbiI/VisC orthology assignment, KEGG K18800 placement, and complete three-hydroxylase pathway support this oxygen-dependent reaction. The assignment is inferred rather than directly assayed in Q88CI4.	GO:0019168 captures the evolved ubiquinone-intermediate hydroxylase function.	genes/PSEPK/visC/visC-ai-review.yaml
deeper_than	InterPro2GO	9POAL	NCGR_LOCUS1270	GO:0005986	sucrose biosynthetic process	UNDECIDED	GO:0005975	carbohydrate metabolic process	MODIFY	The dominant Calvin-cycle role and separation from cytosolic FBPase are supported, but the previous absolute exclusion and claimed paralog misgraft were not established. Current PTN004269459 is the sorghum A0A1B6QP66 leaf, annotated to chloroplast/Calvin cycle and 96.85% identical across the full gl	The chloroplast FBPase itself performs the fructose-1,6-bisphosphate hydrolysis step during Calvin-cycle carbon regeneration, rather than being a substrate or an indirect requirement. The close chloroplast-associated sorghum homolog, conserved catalytic architecture and comparative cpFBPase studies 	genes/9POAL/NCGR_LOCUS1270/NCGR_LOCUS1270-ai-review.yaml
deeper_than	InterPro2GO	9POAL	NCGR_LOCUS1270	GO:0006000	fructose metabolic process	UNDECIDED	GO:0005975	carbohydrate metabolic process	MODIFY	The report correctly separates fructose from its phosphorylated derivatives in the is_a hierarchy, but absence of an ancestor relation does not make pathways disjoint or require direct free-fructose turnover by every enzyme. QuickGO explicitly assigns this term to human FBP1/FBP2 with TAS and Dictyo	The chloroplast FBPase itself performs the fructose-1,6-bisphosphate hydrolysis step during Calvin-cycle carbon regeneration, rather than being a substrate or an indirect requirement. The close chloroplast-associated sorghum homolog, conserved catalytic architecture and comparative cpFBPase studies 	genes/9POAL/NCGR_LOCUS1270/NCGR_LOCUS1270-ai-review.yaml
deeper_than	InterPro2GO	9POAL	NCGR_LOCUS1270	GO:0006094	gluconeogenesis	UNDECIDED	GO:0005975	carbohydrate metabolic process	MODIFY	GO:0006094 describes glucose formation from noncarbohydrate precursors and does not impose the prior asserted cytosolic-only location. Chloroplast targeting and redox regulation distinguish this enzyme from the canonical cytosolic paralog, but neither is a direct demonstration of loss of all glucone	The chloroplast FBPase itself performs the fructose-1,6-bisphosphate hydrolysis step during Calvin-cycle carbon regeneration, rather than being a substrate or an indirect requirement. The close chloroplast-associated sorghum homolog, conserved catalytic architecture and comparative cpFBPase studies 	genes/9POAL/NCGR_LOCUS1270/NCGR_LOCUS1270-ai-review.yaml
deeper_than	InterPro2GO	9POAL	NCGR_LOCUS1765	GO:0000184	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	ACCEPT	GO:0016070	RNA metabolic process	KEEP_AS_NON_CORE		The term is accurate but uninformative. The specific processes annotated (NMD, mRNA export, RNA splicing) provide more precise functional description.	genes/9POAL/NCGR_LOCUS1765/NCGR_LOCUS1765-ai-review.yaml
deeper_than	InterPro2GO	9POAL	NCGR_LOCUS1765	GO:0003729	mRNA binding	ACCEPT	GO:0003723	RNA binding	KEEP_AS_NON_CORE		RNA binding is accurate but very general. The more specific RNA cap binding (GO:0000339) and mRNA binding (GO:0003729) annotations already capture the relevant molecular functions more precisely.	genes/9POAL/NCGR_LOCUS1765/NCGR_LOCUS1765-ai-review.yaml
deeper_than	InterPro2GO	9POAL	NCGR_LOCUS29329	GO:0009067	aspartate family amino acid biosynthetic process	ACCEPT	GO:0006520	amino acid metabolic process	MARK_AS_OVER_ANNOTATED	This is the most appropriate level of specificity for the overall pathway role. The enzyme acts at the branch point of multiple amino acid biosynthetic pathways derived from aspartate. TreeGrafter classification via PANTHER:PTN009166675 supports this annotation.	Redundant with the more specific biological process annotations. The protein is specifically involved in aspartate family amino acid biosynthesis (GO:0009067), threonine biosynthesis (GO:0009088), and homoserine biosynthesis (GO:0009090), all of which are children of this term.	genes/9POAL/NCGR_LOCUS29329/NCGR_LOCUS29329-ai-review.yaml
deeper_than	InterPro2GO	9POAL	NCGR_LOCUS29329	GO:0009067	aspartate family amino acid biosynthetic process	ACCEPT	GO:0008652	amino acid biosynthetic process	MARK_AS_OVER_ANNOTATED	This is the most appropriate level of specificity for the overall pathway role. The enzyme acts at the branch point of multiple amino acid biosynthetic pathways derived from aspartate. TreeGrafter classification via PANTHER:PTN009166675 supports this annotation.	Redundant with GO:0009067 (aspartate family amino acid biosynthetic process), which is a more specific child term that better captures the function.	genes/9POAL/NCGR_LOCUS29329/NCGR_LOCUS29329-ai-review.yaml
deeper_than	InterPro2GO	9POAL	NCGR_LOCUS29329	GO:0009090	L-homoserine biosynthetic process	ACCEPT	GO:0006520	amino acid metabolic process	MARK_AS_OVER_ANNOTATED	Directly catalyzed by the HSD domain. L-homoserine is the direct product of the enzyme's C-terminal catalytic activity and serves as a precursor for both threonine and methionine biosynthesis. TreeGrafter classification supports this annotation.	Redundant with the more specific biological process annotations. The protein is specifically involved in aspartate family amino acid biosynthesis (GO:0009067), threonine biosynthesis (GO:0009088), and homoserine biosynthesis (GO:0009090), all of which are children of this term.	genes/9POAL/NCGR_LOCUS29329/NCGR_LOCUS29329-ai-review.yaml
deeper_than	InterPro2GO	9POAL	NCGR_LOCUS29329	GO:0009090	L-homoserine biosynthetic process	ACCEPT	GO:0008652	amino acid biosynthetic process	MARK_AS_OVER_ANNOTATED	Directly catalyzed by the HSD domain. L-homoserine is the direct product of the enzyme's C-terminal catalytic activity and serves as a precursor for both threonine and methionine biosynthesis. TreeGrafter classification supports this annotation.	Redundant with GO:0009067 (aspartate family amino acid biosynthetic process), which is a more specific child term that better captures the function.	genes/9POAL/NCGR_LOCUS29329/NCGR_LOCUS29329-ai-review.yaml
deeper_than	InterPro2GO	ACET2	celC	GO:0008422	beta-glucosidase activity	REMOVE	GO:0004553	hydrolase activity, hydrolyzing O-glycosyl compounds	ACCEPT	This annotation is incorrect. CelC (EC 3.2.1.4) is an endoglucanase that cleaves internal beta-1,4-glucosidic linkages in cellulose chains. Beta-glucosidase (EC 3.2.1.21) is a distinct enzyme class that removes terminal glucose residues. The TreeGrafter prediction appears to be based on broad sequen	As a GH5 family endoglucanase, CelC hydrolyzes O-glycosyl compounds (specifically beta-1,4-glucosidic bonds). The InterPro-based IEA annotation is accurate. This parent term is retained alongside the more specific cellulase activity term.	genes/ACET2/celC/celC-ai-review.yaml
deeper_than	InterPro2GO	ACET2	celC	GO:0009251	glucan catabolic process	ACCEPT	GO:0005975	carbohydrate metabolic process	ACCEPT	This annotation is accurate. CelC breaks down cellulose, which is a glucan (polymer of glucose). The TreeGrafter annotation correctly infers this biological process from sequence homology to characterized cellulases.	While very general, this annotation is not incorrect. CelC is involved in carbohydrate metabolism via its cellulolytic activity. More specific child terms (cellulose catabolic process) provide better functional resolution. IEA from InterPro is reasonable for this broad term.	genes/ACET2/celC/celC-ai-review.yaml
deeper_than	InterPro2GO	AERER	ermA	GO:0031167	rRNA methylation	ACCEPT	GO:0000154	rRNA modification	ACCEPT	Erm enzymes confer resistance by methylating 23S rRNA; this process annotation is biologically appropriate.	Erm enzymes confer resistance by methylating 23S rRNA; this process annotation is biologically appropriate.	genes/AERER/ermA/ermA-ai-review.yaml
deeper_than	InterPro2GO	AERME	mcr-3	GO:0016776	phosphotransferase activity, phosphate group as acceptor	MODIFY	GO:0016772	transferase activity, transferring phosphorus-containing groups	MODIFY	Replace the broad or over-specific electronic term 'phosphotransferase activity, phosphate group as acceptor' with phosphatidylethanolamine:Kdo2-lipid A phosphoethanolamine transferase activity based on UniProt/CARD determinant identity and the curated ARO->GO mapping.	Replace the broad or over-specific electronic term 'transferase activity, transferring phosphorus-containing groups' with phosphatidylethanolamine:Kdo2-lipid A phosphoethanolamine transferase activity based on UniProt/CARD determinant identity and the curated ARO->GO mapping.	genes/AERME/mcr-3/mcr-3-ai-review.yaml
deeper_than	InterPro2GO	BACAN	ermJ	GO:0031167	rRNA methylation	ACCEPT	GO:0000154	rRNA modification	ACCEPT	Erm enzymes confer resistance by methylating 23S rRNA; this process annotation is biologically appropriate.	Erm enzymes confer resistance by methylating 23S rRNA; this process annotation is biologically appropriate.	genes/BACAN/ermJ/ermJ-ai-review.yaml
deeper_than	InterPro2GO	BACFG	ermF	GO:0031167	rRNA methylation	ACCEPT	GO:0000154	rRNA modification	ACCEPT	Erm enzymes confer resistance by methylating 23S rRNA; this process annotation is biologically appropriate.	Erm enzymes confer resistance by methylating 23S rRNA; this process annotation is biologically appropriate.	genes/BACFG/ermF/ermF-ai-review.yaml
deeper_than	InterPro2GO	BETPN	Betv2	GO:0003785	actin monomer binding	ACCEPT	GO:0003779	actin binding	ACCEPT	Profilins are G-actin (actin monomer) binding proteins.	Defining function of the profilin family.	genes/BETPN/Betv2/Betv2-ai-review.yaml
deeper_than	InterPro2GO	CAPO3	CoBra	GO:0000981	DNA-binding transcription factor activity, RNA polymerase II-specific	ACCEPT	GO:0003700	DNA-binding transcription factor activity	ACCEPT	"This is the core molecular function, consistent with the core function chosen for human TBXT. Binding comes from Capsaspora protein and Capsaspora chromatin. Transcriptional activation has been shown only heterologously, in Xenopus embryos and animal caps, where CoBra acts as a nonselective ""pan-T-b"	The T-box domain is present and functional (sequence-specific binding in vitro and occupancy in Capsaspora), and the protein activates transcription in a heterologous embryo. The term is a correct parent of the core function.	genes/CAPO3/CoBra/CoBra-ai-review.yaml
deeper_than	InterPro2GO	CAPO3	CoBra	GO:0006357	regulation of transcription by RNA polymerase II	ACCEPT	GO:0006355	regulation of DNA-templated transcription	ACCEPT	Follows from the DNA-binding transcription factor activity. The process is generic and holds for every T-box family member, so the transfer from the deep node is appropriate here, unlike the developmental row. The genes CoBra regulates directly in Capsaspora are inferred from motifs and ChIP-qPCR, n	A DNA-binding transcription factor regulates transcription. The term is correct and is a parent of the more specific process rows.	genes/CAPO3/CoBra/CoBra-ai-review.yaml
deeper_than	InterPro2GO	DESRO	K9J287	GO:0004530	deoxyribonuclease I activity	ACCEPT	GO:0003824	catalytic activity	MODIFY	UniProt names this protein deoxyribonuclease-1-like 1, consistent with DNase I activity.	Use the specific deoxyribonuclease I activity term.	genes/DESRO/K9J287/K9J287-ai-review.yaml
deeper_than	InterPro2GO	DESRO	K9J287	GO:0004530	deoxyribonuclease I activity	ACCEPT	GO:0004536	DNA nuclease activity	MODIFY	UniProt names this protein deoxyribonuclease-1-like 1, consistent with DNase I activity.	Use the specific deoxyribonuclease I activity term.	genes/DESRO/K9J287/K9J287-ai-review.yaml
deeper_than	InterPro2GO	DESVH	Q725T9	GO:0005886	plasma membrane	ACCEPT	GO:0016020	membrane	ACCEPT	Plasma membrane localization is consistent with the role of KdpD-like sensors, which function at the membrane interface to sense osmotic/K+ changes. While direct localization evidence for DVU_3336 is lacking, the TreeGrafter annotation based on phylogenetic inference (PANTHER:PTN008137371) supports 	"Membrane localization is consistent with KdpD-like sensors. While more specific than ""plasma membrane"" would be ideal, this general term is acceptable as a broader annotation alongside the more specific plasma membrane annotation. Both annotations capture the membrane association of this sensory pro"	genes/DESVH/Q725T9/Q725T9-ai-review.yaml
deeper_than	InterPro2GO	DOROP	ADAR2	GO:0008251	tRNA-specific adenosine deaminase activity	REMOVE	GO:0004000	adenosine deaminase activity	MODIFY	tRNA-specific adenosine deaminase activity is the function of ADAT enzymes, not ADAR enzymes. sqADAR2 has been tested and shown to be active on dsRNA and mRNA substrates. There is no evidence that sqADAR2 edits tRNAs, and the domain architecture (dsRBDs + ADAR-type deaminase domain) is inconsistent 	GO:0004000 (adenosine deaminase activity) describes the deamination of free adenosine, which is the activity of ADA enzymes, not ADAR enzymes. ADAR2 specifically deaminates adenosine residues within double-stranded RNA. The correct term GO:0003726 is already annotated, so this annotation should be r	genes/DOROP/ADAR2/ADAR2-ai-review.yaml
deeper_than	InterPro2GO	DORPE	AP180	GO:0005546	phosphatidylinositol-4,5-bisphosphate binding	ACCEPT	GO:0005543	phospholipid binding	ACCEPT	Well-supported core molecular function. PtdIns(4,5)P2 binding via the ANTH domain is a conserved and essential function of AP180 family proteins, enabling membrane targeting during clathrin-coated pit formation.	Phospholipid binding is a valid parent term for the ANTH domain activity. While GO:0005546 (PtdIns(4,5)P2 binding) is more specific and also annotated, this broader InterPro-derived annotation is not incorrect and captures general lipid binding capacity of the ANTH domain. The UniProt record notes t	genes/DORPE/AP180/AP180-ai-review.yaml
deeper_than	InterPro2GO	DORPE	AP180	GO:0032050	clathrin heavy chain binding	ACCEPT	GO:0030276	clathrin binding	ACCEPT	Well-supported by experimental evidence from the squid system. AP180 binds the N-terminal domain of clathrin heavy chain, and progressive deletion of DLL motifs caused gradual reduction in clathrin assembly ability (PMID:11102472). This is a more informative and specific term than the broader clathr	Clathrin binding is a central and well-demonstrated function of squid AP180. The protein directly binds clathrin triskelia via DLL motifs in its C-terminal domain and promotes their assembly into clathrin lattices (PMID:10575017, PMID:11102472).	genes/DORPE/AP180/AP180-ai-review.yaml
deeper_than	InterPro2GO	DORPE	cpx	GO:0016079	synaptic vesicle exocytosis	MODIFY	GO:0006836	neurotransmitter transport	MODIFY	While complexin is clearly involved in the synaptic vesicle exocytosis pathway, it functions as a positive regulator rather than a core component of the fusion machinery itself. The term GO:2000302 (positive regulation of synaptic vesicle exocytosis) more accurately captures the regulatory role demo	Neurotransmitter transport implies a direct role in moving neurotransmitter molecules, which is misleading. Complexin regulates exocytosis of neurotransmitter-containing synaptic vesicles at a late prefusion step. The correct process is regulation of neurotransmitter secretion or synaptic vesicle ex	genes/DORPE/cpx/cpx-ai-review.yaml
deeper_than	InterPro2GO	ECOLX	mcr-1	GO:0016776	phosphotransferase activity, phosphate group as acceptor	MODIFY	GO:0016772	transferase activity, transferring phosphorus-containing groups	ACCEPT	Retain MODIFY as a refinement to GO:0043838, not a finding that phosphoethanolamine transfer is false. Existing reports disagree: Falcon treats the phosphate-acceptor wording as applicable, whereas OpenScientist emphasizes EC 2.7.8.43 and the substituted-phosphate branch. Current QuickGO places GO:0	This broad transferase activity is chemically entailed by the established lipid A modification reaction and is a current GO ancestor of GO:0043838. Retain it alongside the more specific function.	genes/ECOLX/mcr-1/mcr-1-ai-review.yaml
deeper_than	InterPro2GO	ECOLX	mcr2	GO:0016776	phosphotransferase activity, phosphate group as acceptor	MODIFY	GO:0016772	transferase activity, transferring phosphorus-containing groups	MODIFY	Replace the broad or over-specific electronic term 'phosphotransferase activity, phosphate group as acceptor' with phosphatidylethanolamine:Kdo2-lipid A phosphoethanolamine transferase activity based on UniProt/CARD determinant identity and the curated ARO->GO mapping.	Replace the broad or over-specific electronic term 'transferase activity, transferring phosphorus-containing groups' with phosphatidylethanolamine:Kdo2-lipid A phosphoethanolamine transferase activity based on UniProt/CARD determinant identity and the curated ARO->GO mapping.	genes/ECOLX/mcr2/mcr2-ai-review.yaml
deeper_than	InterPro2GO	HETGA	Cd44	GO:0016323	basolateral plasma membrane	KEEP_AS_NON_CORE	GO:0016020	membrane	MODIFY	A polarity-specific sub-compartment claim that applies only in polarised epithelia and has no naked mole-rat support. It sits alongside an apical plasma membrane annotation projected from a different human study, and the two cannot both be the general case; of the pair, the basolateral assignment is	The InterPro2GO mapping is deliberately conservative and stops at the root membrane term. The compartment is established for this protein - UniProt records cell membrane, single-pass type I, and a transmembrane helix at 609-630 - so the specific child term should be used. This is a granularity corre	genes/HETGA/Cd44/Cd44-ai-review.yaml
deeper_than	InterPro2GO	HETGA	Scn9a	GO:0035725	sodium ion transmembrane transport	ACCEPT	GO:0006811	monoatomic ion transport	MODIFY	Core biological process, at the right level of specificity, and directly supported by the naked-mole-rat electrophysiology, which measures voltage-gated sodium currents in this species' nociceptors and their block by protons.	A strict ancestor of GO:0035725, which is already present on this gene product and which the evidence supports directly. Keeping the generic parent adds no information about what this channel does.	genes/HETGA/Scn9a/Scn9a-ai-review.yaml
deeper_than	InterPro2GO	HETGA	Scn9a	GO:0035725	sodium ion transmembrane transport	ACCEPT	GO:0006814	sodium ion transport	MODIFY	Core biological process, at the right level of specificity, and directly supported by the naked-mole-rat electrophysiology, which measures voltage-gated sodium currents in this species' nociceptors and their block by protons.	Correct in substance and one level too shallow. GO:0035725 states both the ion and the fact that transport is across a membrane, which is what a NaV alpha subunit does and what the naked-mole-rat electrophysiology measures.	genes/HETGA/Scn9a/Scn9a-ai-review.yaml
deeper_than	InterPro2GO	HETGA	Scn9a	GO:0035725	sodium ion transmembrane transport	ACCEPT	GO:0055085	transmembrane transport	MODIFY	Core biological process, at the right level of specificity, and directly supported by the naked-mole-rat electrophysiology, which measures voltage-gated sodium currents in this species' nociceptors and their block by protons.	A strict ancestor of GO:0035725. It says only that something crosses a membrane, which for a well-characterized sodium-selective channel is a loss of information.	genes/HETGA/Scn9a/Scn9a-ai-review.yaml
deeper_than	InterPro2GO	HETGA	Trpv1	GO:0098703	calcium ion import across plasma membrane	ACCEPT	GO:0006811	monoatomic ion transport	ACCEPT	Capsaicin application to naked mole-rat DRG neurons produces a rise in intracellular Ca2+ measured by fura-2 ratiometric imaging, of the same incidence and magnitude as in mouse [PMID:18232734], and the same Ca2+ response is seen for the cloned protein in naked mole-rat fibroblasts [PMID:27732851]. 	The InterPro signatures that generate this term (IPR005821 ion transport domain, IPR008347 TrpV1-4, IPR024862 TRPV) are all genuinely present in G9DCX1, and the protein does conduct ions: capsaicin evokes inward currents and Ca2+ entry in naked mole-rat sensory neurons [PMID:18232734, PMID:40705105]	genes/HETGA/Trpv1/Trpv1-ai-review.yaml
deeper_than	InterPro2GO	HETGA	Trpv1	GO:0098703	calcium ion import across plasma membrane	ACCEPT	GO:0055085	transmembrane transport	ACCEPT	Capsaicin application to naked mole-rat DRG neurons produces a rise in intracellular Ca2+ measured by fura-2 ratiometric imaging, of the same incidence and magnitude as in mouse [PMID:18232734], and the same Ca2+ response is seen for the cloned protein in naked mole-rat fibroblasts [PMID:27732851]. 	Naked mole-rat TRPV1 moves cations across the plasma membrane when gated by capsaicin, heat or protons [PMID:27732851, PMID:40705105]. The term is correct at a coarse level and carries the domain-based inference honestly; it is retained rather than modified because GO:0098703 in this same set alread	genes/HETGA/Trpv1/Trpv1-ai-review.yaml
deeper_than	InterPro2GO	METBS	Pks1	GO:0004312	fatty acid synthase activity	REMOVE	GO:0016740	transferase activity	MODIFY		The MAT domain's acyltransferase chemistry is one partial activity of the iterative polyketide synthase; the informative whole-protein function is polyketide synthase activity (same treatment as the GO:0016746 acyltransferase row).	genes/METBS/Pks1/Pks1-ai-review.yaml
deeper_than	InterPro2GO	METBS	Pks1	GO:0004312	fatty acid synthase activity	REMOVE	GO:0016746	acyltransferase activity	MODIFY			genes/METBS/Pks1/Pks1-ai-review.yaml
deeper_than	InterPro2GO	METEA	mdh	GO:0004459	L-lactate dehydrogenase (NAD+) activity	REMOVE	GO:0003824	catalytic activity	KEEP_AS_NON_CORE			genes/METEA/mdh/mdh-ai-review.yaml
deeper_than	InterPro2GO	METEA	mdh	GO:0004459	L-lactate dehydrogenase (NAD+) activity	REMOVE	GO:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	ACCEPT		Accurate mechanistic parent term. The NAD-dependence underlying this term is directly supported by the AM1-specific crystallographic and kinetic study summarized in the falcon deep research (NAD+ bound in the structure; NADH used as reductant).	genes/METEA/mdh/mdh-ai-review.yaml
deeper_than	InterPro2GO	METEA	mdh	GO:0006089	lactate metabolic process	REMOVE	GO:0019752	carboxylic acid metabolic process	KEEP_AS_NON_CORE			genes/METEA/mdh/mdh-ai-review.yaml
deeper_than	InterPro2GO	METEA	mluA	GO:0015344	siderophore uptake transmembrane transporter activity	MODIFY	GO:0015343	siderophore-iron transmembrane transporter activity	MODIFY			genes/METEA/mluA/mluA-ai-review.yaml
deeper_than	InterPro2GO	MISSI	MnSOD	GO:0030145	manganese ion binding	ACCEPT	GO:0046872	metal ion binding	KEEP_AS_NON_CORE	Manganese binding is the specific metal cofactor association for MnSOD catalysis.	The specific manganese ion binding annotation should represent the core cofactor-binding aspect; the parent metal-binding term is non-core.	genes/MISSI/MnSOD/MnSOD-ai-review.yaml
deeper_than	InterPro2GO	NICAT	NaPMT1.1	GO:0004766	spermidine synthase activity	REMOVE	GO:0003824	catalytic activity	MARK_AS_OVER_ANNOTATED	Distinct chemistry, not merely a less specific term. GO:0004766 is defined as S-adenosylmethioninamine + putrescine = 5'-methylthioadenosine + spermidine, an aminopropyl transfer from decarboxylated SAM (EC 2.5.1.16). PMT1 catalyzes putrescine + S-adenosyl-L-methionine = N-methylputrescine + S-adeno	GO:0030750 putrescine N-methyltransferase activity captures the actual chemistry; the generic catalytic parent term adds no useful biological resolution.	genes/NICAT/NaPMT1.1/NaPMT1.1-ai-review.yaml
deeper_than	InterPro2GO	NICAT	NaPMT1.2	GO:0004766	spermidine synthase activity	REMOVE	GO:0003824	catalytic activity	MARK_AS_OVER_ANNOTATED	Distinct chemistry, not merely a less specific term. GO:0004766 is defined as S-adenosylmethioninamine + putrescine = 5'-methylthioadenosine + spermidine, an aminopropyl transfer from decarboxylated SAM (EC 2.5.1.16). PMT2 catalyzes putrescine + S-adenosyl-L-methionine = N-methylputrescine + S-adeno	GO:0030750 putrescine N-methyltransferase activity already captures the actual chemistry performed by PMT2.	genes/NICAT/NaPMT1.2/NaPMT1.2-ai-review.yaml
deeper_than	InterPro2GO	NICAT	NaPMT3	GO:0004766	spermidine synthase activity	REMOVE	GO:0003824	catalytic activity	ACCEPT	PMT proteins evolved from spermidine synthase but now catalyze putrescine N-methylation in alkaloid biosynthesis. The target carries the PMT-specific IPR025803/PROSITE assignment and the SAM-dependent methylation reaction. The existing reports support a PMT-versus-SPDS functional divergence, not los	Catalytic activity is an entailed broad molecular function of the accepted putrescine N-methyltransferase activity. Its generality is not over-annotation.	genes/NICAT/NaPMT3/NaPMT3-ai-review.yaml
deeper_than	InterPro2GO	NICAT	NaUGT1_candidate_UGT85A2_0	GO:0080043	quercetin 3-O-glucosyltransferase activity	UNDECIDED	GO:0008194	UDP-glycosyltransferase activity	ACCEPT	Primary 2026 data support nicotinate N-glucosylation at the mapped g26396 locus, with a documented construct-boundary caveat. They do not assay every alternative acceptor. Neither the positive nicotine function nor sequence-family distance establishes that quercetin or 7-deoxyloganetic acid cannot a	UDP-glycosyltransferase activity is a valid broad parent of the accepted UDP-glucosyltransferase function. The more specific donor assignment does not invalidate this broad InterPro inference.	genes/NICAT/NaUGT1_candidate_UGT85A2_0/NaUGT1_candidate_UGT85A2_0-ai-review.yaml
deeper_than	InterPro2GO	NICAT	NaUGT1_candidate_UGT85A2_0	GO:0080044	quercetin 7-O-glucosyltransferase activity	UNDECIDED	GO:0008194	UDP-glycosyltransferase activity	ACCEPT	Primary 2026 data support nicotinate N-glucosylation at the mapped g26396 locus, with a documented construct-boundary caveat. They do not assay every alternative acceptor. Neither the positive nicotine function nor sequence-family distance establishes that quercetin or 7-deoxyloganetic acid cannot a	UDP-glycosyltransferase activity is a valid broad parent of the accepted UDP-glucosyltransferase function. The more specific donor assignment does not invalidate this broad InterPro inference.	genes/NICAT/NaUGT1_candidate_UGT85A2_0/NaUGT1_candidate_UGT85A2_0-ai-review.yaml
deeper_than	InterPro2GO	NOVAD	Saro_0802	GO:0010436	carotenoid dioxygenase activity	REMOVE	GO:0016702	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen	ACCEPT	Rule/tree-based over-annotation contradicted by the enzyme's structural and functional characterization as a resveratrol/stilbene dioxygenase. The correct specific term is GO:7770086 (resveratrol dioxygenase activity, RHEA:73735; added go-ontology master Jul 2026); the real activity is already cover	Accurate general dioxygenase MF; the specific activity (resveratrol/stilbene cleavage) sits under this term.	genes/NOVAD/Saro_0802/Saro_0802-ai-review.yaml
deeper_than	InterPro2GO	NOVAD	Saro_2809	GO:0010436	carotenoid dioxygenase activity	REMOVE	GO:0016702	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen	ACCEPT	Rule/tree-based over-annotation of the wrong substrate class. Correct specific term is GO:7770086 (resveratrol dioxygenase activity; go-ontology PR #32332, merged 2026-07-17, live in QuickGO); the general activity is covered by GO:0016702. Same error as NOV1 and cao-1.	Accurate general dioxygenase MF; consistent with the demonstrated stilbenoid cleavage.	genes/NOVAD/Saro_2809/Saro_2809-ai-review.yaml
deeper_than	InterPro2GO	OSCPE	TLN	GO:0098609	cell-cell adhesion	MODIFY	GO:0007155	cell adhesion	ACCEPT	Talin's established role is in integrin-based attachment of cells to the extracellular matrix, whereas cell-cell contacts (adherens junctions) are built on cadherins and catenins. Nothing links O. pearsei talin to cell-cell contacts. The essence (adhesion) is right, but cell-matrix adhesion is the a	Talin does part of the work of integrin-mediated adhesion (it links and activates integrins and recruits vinculin and actin), so the general term is appropriate for a talin with conserved domain architecture.	genes/OSCPE/TLN/TLN-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	PP_0892	GO:0008808	cardiolipin synthase activity	UNDECIDED	GO:0003824	catalytic activity	MODIFY	TreeGrafter and PANTHER place PP_0892 in a ClsB-like node, but the current UniProt record remains generic and supplies no reaction or experimental substrate evidence.	Use phosphatidyltransferase activity as the cautious function supported by the PLD-family architecture while substrate specificity remains unresolved.	genes/PSEPK/PP_0892/PP_0892-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	PP_1084	GO:0008379	thioredoxin peroxidase activity	ACCEPT	GO:0016209	antioxidant activity	MARK_AS_OVER_ANNOTATED	The UniProt entry identifies the protein as a thiol-specific/thioredoxin peroxidase that reduces peroxides, and the directly studied KT2440 protein PpPrx (PP_1084) is experimentally a thioredoxin-dependent peroxidase.	The annotation should prioritize the direct enzymatic activity rather than a generic antioxidant-function parent.	genes/PSEPK/PP_1084/PP_1084-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	PP_1084	GO:0008379	thioredoxin peroxidase activity	ACCEPT	GO:0016491	oxidoreductase activity	MARK_AS_OVER_ANNOTATED	The UniProt entry identifies the protein as a thiol-specific/thioredoxin peroxidase that reduces peroxides, and the directly studied KT2440 protein PpPrx (PP_1084) is experimentally a thioredoxin-dependent peroxidase.	The specific peroxide-reduction terms are available and should carry the functional interpretation.	genes/PSEPK/PP_1084/PP_1084-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	PP_1084	GO:0008379	thioredoxin peroxidase activity	ACCEPT	GO:0051920	peroxiredoxin activity	ACCEPT	The UniProt entry identifies the protein as a thiol-specific/thioredoxin peroxidase that reduces peroxides, and the directly studied KT2440 protein PpPrx (PP_1084) is experimentally a thioredoxin-dependent peroxidase.	UniProt identifies the protein as a thioredoxin peroxidase/peroxiredoxin family member that reduces peroxides, and the KT2440-specific study confirms typical 2-Cys peroxiredoxin classification.	genes/PSEPK/PP_1084/PP_1084-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	PP_1257	GO:0008840	4-hydroxy-tetrahydrodipicolinate synthase activity	REMOVE	GO:0016829	lyase activity	REMOVE	PP_1257 has a DapA-like fold, but its product name and exact EC mapping identify 1-pyrroline-4-hydroxy-2-carboxylate deaminase. The adjacent hydroxyproline-pathway enzymes provide independent genomic context, so the DapA activity is a paralog transfer.	EC 3.5.4.22 and GO:0047425 describe hydrolytic deamination and place the activity under hydrolase/deaminase terms, not lyase activity. The DapA/NAL-like fold does not justify transfer of the ancestral lyase class.	genes/PSEPK/PP_1257/PP_1257-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	PP_1969	GO:0061798	GTP 3',8'-cyclase activity	UNDECIDED	GO:0003824	catalytic activity	UNDECIDED	Reverted from ACCEPT (2026-10-15) to UNDECIDED (2026-10-16) after scoring the function-level models. NCBIfam TIGR02666 (moaA): Q88LG4 scores 269.2 bits, 14.8 below the trusted cutoff (284.05) and 1.8 below the noise cutoff (270.95), against 370-403 bits for every reviewed MoaA tested, including both	Restored to UNDECIDED (2026-10-16). It had been marked TOO_GENERAL beside an accepted GO:0061798, which is again UNDECIDED. Intact cluster and SAM sites make catalysis likely, but the reaction is not resolved, and this row is not used as a stand-in for it.	genes/PSEPK/PP_1969/PP_1969-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	PP_1969	GO:0061799	cyclic pyranopterin monophosphate synthase activity	REMOVE	GO:0003824	catalytic activity	UNDECIDED	Wrong step of a two-enzyme sequence, verifiable from the term definition. GO:0061799 is defined as (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate = cyclic pyranopterin phosphate + diphosphate - that is, it consumes the product of the MoaA reaction, and is the MoaC step. This protein is a MoaA-	Restored to UNDECIDED (2026-10-16). It had been marked TOO_GENERAL beside an accepted GO:0061798, which is again UNDECIDED. Intact cluster and SAM sites make catalysis likely, but the reaction is not resolved, and this row is not used as a stand-in for it.	genes/PSEPK/PP_1969/PP_1969-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	PP_2482	GO:0061798	GTP 3',8'-cyclase activity	UNDECIDED	GO:0003824	catalytic activity	UNDECIDED	Reverted from ACCEPT (2026-10-15) to UNDECIDED (2026-10-16) after scoring the function-level models. NCBIfam TIGR02666 (moaA): Q88K11 scores 268.1 bits, 15.9 below the trusted cutoff (284.05) and 2.9 below the noise cutoff (270.95), against 370-403 bits for every reviewed MoaA tested, including both	Restored to UNDECIDED (2026-10-16). It had been marked TOO_GENERAL beside an accepted GO:0061798, which is again UNDECIDED. Intact cluster and SAM sites make catalysis likely, but the reaction is not resolved, and this row is not used as a stand-in for it.	genes/PSEPK/PP_2482/PP_2482-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	PP_2482	GO:0061799	cyclic pyranopterin monophosphate synthase activity	REMOVE	GO:0003824	catalytic activity	UNDECIDED	Wrong step of a two-enzyme sequence, verifiable from the term definition. GO:0061799 is defined as (8S)-3',8-cyclo-7,8-dihydroguanosine 5'-triphosphate = cyclic pyranopterin phosphate + diphosphate - that is, it consumes the product of the MoaA reaction, and is the MoaC step. This protein is a MoaA-	Restored to UNDECIDED (2026-10-16). It had been marked TOO_GENERAL beside an accepted GO:0061798, which is again UNDECIDED. Intact cluster and SAM sites make catalysis likely, but the reaction is not resolved, and this row is not used as a stand-in for it.	genes/PSEPK/PP_2482/PP_2482-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	PP_2528	GO:0004124	cysteine synthase activity	MARK_AS_OVER_ANNOTATED	GO:0016765	transferase activity, transferring alkyl or aryl (other than methyl) groups	MODIFY	Downgraded from removal because the activity cannot be excluded on architectural grounds. GO:0004124 is O3-acetyl-L-serine + hydrogen sulfide = L-cysteine + acetate, differing from the propagated-and-accepted GO:0003961 (O-acetyl-L- homoserine + a thiol) by a single methylene in the substrate, and O	PP_2528 is predicted as an O-acetylhomoserine (thiol)-lyase, and the GOA table already carries the corresponding specific term.	genes/PSEPK/PP_2528/PP_2528-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	PP_2528	GO:0071269	L-homocysteine biosynthetic process	UNDECIDED	GO:0006520	amino acid metabolic process	MARK_AS_OVER_ANNOTATED	O-acetylhomoserine sulfhydrylase chemistry would form homocysteine, but the pathway-level review identifies MetXS plus MetZ as the substrate-matched O-succinylhomoserine route. Keep this process unresolved for PP_2528 until substrate use or mutant phenotypes are available.	The broad InterPro2GO process loses the specific homocysteine/methionine biosynthetic context supported by the O-acetylhomoserine sulfhydrylase assignment.	genes/PSEPK/PP_2528/PP_2528-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	PP_3394	GO:0004419	hydroxymethylglutaryl-CoA lyase activity	REMOVE	GO:0003824	catalytic activity	ACCEPT	The focused paralog analysis resolved the conflict left by the first pass. PP_3394 retains the DRE-TIM catalytic core but fails the HMG-CoA-lyase-specific PROSITE signature and carries an isopropylmalate/homocitrate-synthase-like motif, whereas MvaB/PP_3540 is an ortholog-level match to the experime	The DRE-TIM/HMGL-like and alpha-isopropylmalate/homocitrate-synthase signatures imply catalysis. Their disagreement concerns substrate and reaction class, not whether PP_3394 is catalytic; no target-specific loss of catalysis has been established.	genes/PSEPK/PP_3394/PP_3394-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	PP_3571	GO:0008777	acetylornithine deacetylase activity	MODIFY	GO:0019213	deacetylase activity	UNDECIDED	Re-reviewed after a blinded OpenScientist control run (file:PSEPK/PP_3571/PP_3571-hypotheses/function-hypothesis-go-0008777/openscientist.md). The run and a local re-computation agree on the facts: (i) all seven E. coli ArgE (P23908) active-site and Zn-ligand residues (H80, D82, D112, E144, E145, E1	ArgE-like signals support deacetylation, whereas the same PANTHER branch also contains succinyl-amino-acid hydrolases. Current evidence does not distinguish acetyl from succinyl chemistry for Q88GZ4.	genes/PSEPK/PP_3571/PP_3571-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	PP_3599	GO:0008840	4-hydroxy-tetrahydrodipicolinate synthase activity	REMOVE	GO:0016829	lyase activity	MARK_AS_OVER_ANNOTATED	Different reaction on a different substrate, not a coarse term. GO:0008840 is the aldol condensation of pyruvate with L-aspartate-4-semialdehyde in lysine/DAP biosynthesis; Q88GW8 catalyzes 5-dehydro-4-deoxy-D-glucarate + H+ = 2,5-dioxopentanoate + CO2 + H2O (EC 4.2.1.41, RHEA:24608), a dehydration 	GO:0047448 captures the exact 5-dehydro-4-deoxyglucarate dehydratase activity supported by the reviewed record and should be preferred.	genes/PSEPK/PP_3599/PP_3599-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	PP_3995	GO:1990228	sulfurtransferase complex	ACCEPT	GO:0005737	cytoplasm	ACCEPT	The TusB family assignment directly supports complex membership.	The protein lacks export or transmembrane features and functions in a soluble complex.	genes/PSEPK/PP_3995/PP_3995-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	accD	GO:0009329	acetate CoA-transferase complex	ACCEPT	GO:0009317	acetyl-CoA carboxylase complex	ACCEPT	"The rejection recorded here read the term's label rather than its definition. GO defines GO:0009329 as ""A heterotetrameric enzyme complex made up of two alpha subunits and two beta subunits. Part of the acetyl-CoA carboxylase complex. Catalyzes the transfer of a carboxyl group to form malonyl-CoA"" -"	Reviewed UniProt describes the heteromeric AccABCD complex.	genes/PSEPK/accD/accD-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	aceF	GO:0016407	acetyltransferase activity	KEEP_AS_NON_CORE	GO:0016746	acyltransferase activity	KEEP_AS_NON_CORE	AceF is an acetyltransferase, but GO:0004742 captures the PDH-specific lipoyl-lysine acceptor and is the informative core molecular function.	AceF transfers the acetyl group from a lipoyl-lysine arm to CoA, but the specific GO:0004742 child is already present and better represents this PDH E2 chemistry.	genes/PSEPK/aceF/aceF-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	aceK	GO:0004721	phosphoprotein phosphatase activity	ACCEPT	GO:0016791	phosphatase activity	ACCEPT	Both existing adjudications support phosphoprotein phosphatase activity in substance. A more specific substrate term is useful in the core summary, but its availability does not make the TreeGrafter parent assertion biologically incorrect.	Phosphatase activity is entailed by the accepted specific phosphoprotein dephosphorylation reaction. Retain the correct InterPro parent term.	genes/PSEPK/aceK/aceK-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	acoA	GO:0004739	pyruvate dehydrogenase (acetyl-transferring) activity	REMOVE	GO:0016624	oxidoreductase activity, acting on the aldehyde or oxo group of donors, disulfide as acceptor	REMOVE	PTN002264059 places this acetoin-specific E1 alpha paralog in a broad pyruvate-dehydrogenase lineage. The locus paper instead identifies AcoA as E1 alpha of the acetoin-cleaving system. The available GO molecular function that captures its complex-level redox chemistry is GO:0016624, and AcoA contri	AcoA and AcoB form an alpha2-beta2 E1 component in the experimentally characterized H16 exemplar. The term should therefore use contributes_to for this individual subunit rather than enables. The enables assertion is removed and replaced by the qualifier-correct row below.	genes/PSEPK/acoA/acoA-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	ahpC	GO:0008379	thioredoxin peroxidase activity	MODIFY	GO:0016209	antioxidant activity	ACCEPT	QuickGO checked on 2026-09-20 marks GO:0008379 obsolete; preserve the source GOA identifier and refine its review to the active peroxiredoxin term. Independently, the existing reports support a typical AhpC/AhpF system and distinguish its immediate protein reductant from free thioredoxin. Their dono	The broad antioxidant activity follows from the accepted peroxiredoxin reaction; it is the same core function at broader granularity.	genes/PSEPK/ahpC/ahpC-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	ahpC	GO:0008379	thioredoxin peroxidase activity	MODIFY	GO:0016491	oxidoreductase activity	ACCEPT	QuickGO checked on 2026-09-20 marks GO:0008379 obsolete; preserve the source GOA identifier and refine its review to the active peroxiredoxin term. Independently, the existing reports support a typical AhpC/AhpF system and distinguish its immediate protein reductant from free thioredoxin. Their dono	This broad parent is chemically entailed by peroxiredoxin activity. It is acceptable alongside the specific function.	genes/PSEPK/ahpC/ahpC-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	amaC	GO:0004838	L-tyrosine:2-oxoglutarate transaminase activity	ACCEPT	GO:0003824	catalytic activity	MARK_AS_OVER_ANNOTATED	Best-supported molecular function. The protein has a class-I PLP aminotransferase domain, belongs to the PANTHER aromatic-amino-acid aminotransferase subfamily, and local KT2440 functional data support reannotation of AmaC as an L-Tyr aminotransferase.	Correct but uninformative. The specific aminotransferase terms, especially GO:0004838 and GO:0008483, capture the function more usefully.	genes/PSEPK/amaC/amaC-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	argF	GO:0019240	L-citrulline biosynthetic process	ACCEPT	GO:0006520	amino acid metabolic process	MARK_AS_OVER_ANNOTATED	This is the immediate biological outcome of the RHEA:19513 reaction.	It adds no pathway-level information beyond the retained child terms.	genes/PSEPK/argF/argF-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	bglX	GO:0009251	glucan catabolic process	KEEP_AS_NON_CORE	GO:0005975	carbohydrate metabolic process	KEEP_AS_NON_CORE	The GH3 architecture and terminal beta-D-glucosyl-residue hydrolysis support breakdown of beta-glucosyl oligosaccharides or glucans, although the physiological substrate has not been identified.	The predicted beta-glucosidase reaction provides the more useful functional description.	genes/PSEPK/bglX/bglX-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	bhbP	GO:0005886	plasma membrane	ACCEPT	GO:0016020	membrane	KEEP_AS_NON_CORE	Seven Phobius-predicted transmembrane segments support membrane localization.	The generic membrane term is redundant with the more precise plasma membrane call.	genes/PSEPK/bhbP/bhbP-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	cbcW	GO:1902603	carnitine transmembrane transport	ACCEPT	GO:0055085	transmembrane transport	KEEP_AS_NON_CORE	The CbcWV core is experimentally required for carnitine uptake in related Pseudomonas systems.	Substrate-specific transport terms provide the core biological roles.	genes/PSEPK/cbcW/cbcW-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	davD	GO:0004777	succinate-semialdehyde dehydrogenase (NAD+) activity	REMOVE	GO:0009013	succinate-semialdehyde dehydrogenase [NAD(P)+] activity	REMOVE	DavD is assigned to oxidation of 5-oxopentanoate in the lysine-derived Dav pathway, whereas GO:0004777 specifies succinate semialdehyde. This substrate mismatch is independent of the unresolved NAD versus NADP preference of Q88RC0.	Family membership does not override the exact 5-oxopentanoate reaction assigned to DavD.	genes/PSEPK/davD/davD-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	davD	GO:0004777	succinate-semialdehyde dehydrogenase (NAD+) activity	REMOVE	GO:0016491	oxidoreductase activity	MARK_AS_OVER_ANNOTATED	DavD is assigned to oxidation of 5-oxopentanoate in the lysine-derived Dav pathway, whereas GO:0004777 specifies succinate semialdehyde. This substrate mismatch is independent of the unresolved NAD versus NADP preference of Q88RC0.	The substrate- and cofactor-specific activity GO:0102810 is available.	genes/PSEPK/davD/davD-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	dnaJ	GO:0042026	protein refolding	ACCEPT	GO:0006457	protein folding	ACCEPT	Refolding of denatured proteins, via DnaK-coupled ATP-dependent cycles and autonomous disaggregation, is a direct, core biological process for DnaJ.	Protein folding is a direct, core biological process for this J-domain co-chaperone of the DnaK folding cycle.	genes/PSEPK/dnaJ/dnaJ-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	dnaN	GO:0006271	DNA strand elongation involved in DNA replication	ACCEPT	GO:0006260	DNA replication	ACCEPT	The beta clamp confers processivity during replicative DNA strand elongation.	DnaN is required for processive bacterial chromosome replication.	genes/PSEPK/dnaN/dnaN-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	dnaQ	GO:0045004	DNA replication proofreading	ACCEPT	GO:0006260	DNA replication	ACCEPT	Removal of misincorporated 3'-terminal nucleotides is replication proofreading.	DnaQ proofreads newly synthesized DNA as part of polymerase III.	genes/PSEPK/dnaQ/dnaQ-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	dnaX	GO:0006261	DNA-templated DNA replication	ACCEPT	GO:0006260	DNA replication	ACCEPT	DnaX acts directly in template-dependent chromosome duplication.	DnaX loads the processivity clamp and couples polymerase cores during chromosome replication.	genes/PSEPK/dnaX/dnaX-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	dxr	GO:0030145	manganese ion binding	KEEP_AS_NON_CORE	GO:0046872	metal ion binding	MARK_AS_OVER_ANNOTATED	UniProt allows Mn2+ or Mg2+ as the divalent cofactor, while the specific reductoisomerase activity remains the core function.	The entry specifies Mg2+ or Mn2+, and metal binding is mechanistic context rather than an independent core function.	genes/PSEPK/dxr/dxr-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	fabV	GO:0050343	trans-2-enoyl-CoA reductase (NADH) activity	MARK_AS_OVER_ANNOTATED	GO:0016491	oxidoreductase activity	MARK_AS_OVER_ANNOTATED	Reviewed UniProt specifies an ACP-linked enoyl substrate for KT2440 FabV. A characterized FabV ortholog can also reduce a crotonyl-CoA model substrate, so CoA activity is not refuted, but it has not been demonstrated for Q88E33 or established as its physiological role.	The ACP-substrate and NADH-specific reductase term is available.	genes/PSEPK/fabV/fabV-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	fadB	GO:0016509	long-chain (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity	ACCEPT	GO:0003824	catalytic activity	MARK_AS_OVER_ANNOTATED	Retain as the most specific dehydrogenase annotation.	Retain the specific FadB enzymatic activities instead.	genes/PSEPK/fadB/fadB-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	fadB	GO:0016509	long-chain (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity	ACCEPT	GO:0016491	oxidoreductase activity	MARK_AS_OVER_ANNOTATED	Retain as the most specific dehydrogenase annotation.	Retain GO:0003857 and GO:0016509 instead.	genes/PSEPK/fadB/fadB-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	fadB	GO:0016509	long-chain (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity	ACCEPT	GO:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	MARK_AS_OVER_ANNOTATED	Retain as the most specific dehydrogenase annotation.	Retain the specific dehydrogenase terms.	genes/PSEPK/fadB/fadB-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	fbp	GO:0005986	sucrose biosynthetic process	REMOVE	GO:0005975	carbohydrate metabolic process	MARK_AS_OVER_ANNOTATED	Sucrose biosynthesis is not a process of P. putida KT2440 nor a function of class 1 FBPase; this is an incorrect electronic transfer from plant-type enzymes in the same broad PANTHER family. The transfer source is the PANTHER subfamily PTHR11556:SF35, whose plant/chloroplast sedoheptulose-1,7-bispho	This is a correct but very broad parent of the specific gluconeogenesis process already captured, so it does not add informative content.	genes/PSEPK/fbp/fbp-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	fbp	GO:0006000	fructose metabolic process	KEEP_AS_NON_CORE	GO:0005975	carbohydrate metabolic process	MARK_AS_OVER_ANNOTATED	The term is in the correct general area but is broad and not the core process; gluconeogenesis is the specific informative term.	This is a correct but very broad parent of the specific gluconeogenesis process already captured, so it does not add informative content.	genes/PSEPK/fbp/fbp-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	fpvA	GO:0015344	siderophore uptake transmembrane transporter activity	ACCEPT	GO:0015343	siderophore-iron transmembrane transporter activity	ACCEPT	TreeGrafter/PANTHER assignment consistent with the receptor's role in importing the ferripyoverdine complex. Closely related to GO:0015343; both are acceptable family-level MF terms for this receptor.	This term accurately describes the activity of a TonB-dependent ferri-siderophore receptor that imports the iron-loaded siderophore complex. Well supported by family/domain evidence (TonB-dependent siderophore receptor, IPR010105) and by the gene's identity as the ferripyoverdine receptor.	genes/PSEPK/fpvA/fpvA-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	gabD-II	GO:0004777	succinate-semialdehyde dehydrogenase (NAD+) activity	UNDECIDED	GO:0016491	oxidoreductase activity	MODIFY	No direct Q88EN2 assay establishes either cofactor or substrate. Re-review against the OpenScientist control report: its decisive facts were checked. A BLOSUM62 global alignment gives Q88EN2 50.8% identity to NADP+-specific E. coli GabD (P25526; report 51.7%), 48.4% to human ALDH5A1 and 31.6% to E. 	The aldehyde-dehydrogenase domains support the more informative, substrate-neutral aldehyde dehydrogenase [NAD(P)+] activity term, but not a resolved physiological aldehyde.	genes/PSEPK/gabD-II/gabD-II-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	gbd	GO:0004022	alcohol dehydrogenase (NAD+) activity	MODIFY	GO:0016491	oxidoreductase activity	MODIFY	Replace this parent with GO:0047577, which captures the submitted 4-hydroxybutyrate substrate and NAD-dependent chemistry. Group III Fe-ADH signatures in Q88JJ9 and characterized bacterial homologs independently support the enzyme class, while the exact substrate assignment remains predictive.	Replace it with the submitted EC-matched GO:0047577 activity. The Q88JJ9 Fe-ADH architecture and bacterial homolog evidence support the enzyme class, but direct substrate testing of Q88JJ9 is still needed.	genes/PSEPK/gbd/gbd-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	glgP	GO:0005980	glycogen catabolic process	ACCEPT	GO:0005975	carbohydrate metabolic process	KEEP_AS_NON_CORE	The glycogen-phosphorylase family assignment and EC 2.4.1.1 reaction support a direct role in glycogen catabolism, while the imported claim that this is rate-limiting in KT2440 is not adopted.	The term is valid context; glycogen catabolic process is the more informative pathway annotation.	genes/PSEPK/glgP/glgP-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	glpF	GO:0015793	glycerol transmembrane transport	ACCEPT	GO:0055085	transmembrane transport	MARK_AS_OVER_ANNOTATED	This is the core transport process of GlpF.	The substrate-specific process term already captures the relevant biology.	genes/PSEPK/glpF/glpF-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	glpK	GO:0006071	glycerol metabolic process	KEEP_AS_NON_CORE	GO:0005975	carbohydrate metabolic process	MARK_AS_OVER_ANNOTATED			genes/PSEPK/glpK/glpK-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	gpmI	GO:0005829	cytosol	ACCEPT	GO:0005737	cytoplasm	ACCEPT	This is a specific, biologically appropriate annotation for this gene product.	This is a specific, biologically appropriate annotation for this gene product.	genes/PSEPK/gpmI/gpmI-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	guaD	GO:0019239	deaminase activity	KEEP_AS_NON_CORE	GO:0016787	hydrolase activity	MARK_AS_OVER_ANNOTATED	GO:0008892 guanine deaminase activity is_a GO:0019239 in the current ontology, so the broad term correctly describes the hydrolytic deamination (guanine + H2O = xanthine + NH4+, EC 3.5.4.3) assigned to Q88F18's guanine-deaminase family. Being less specific than the child term carried on another row 	Retain the leaf-level GO:0008892 annotation rather than this generic catalytic class.	genes/PSEPK/guaD/guaD-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	guaD	GO:0019239	deaminase activity	KEEP_AS_NON_CORE	GO:0016810	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	MARK_AS_OVER_ANNOTATED	GO:0008892 guanine deaminase activity is_a GO:0019239 in the current ontology, so the broad term correctly describes the hydrolytic deamination (guanine + H2O = xanthine + NH4+, EC 3.5.4.3) assigned to Q88F18's guanine-deaminase family. Being less specific than the child term carried on another row 	GO:0008892 provides the informative substrate-specific molecular function.	genes/PSEPK/guaD/guaD-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	hemB	GO:0006783	heme biosynthetic process	ACCEPT	GO:0033014	tetrapyrrole biosynthetic process	ACCEPT	The reaction is required upstream of hydroxymethylbilane, uroporphyrinogen III, and all subsequent heme-b intermediates.	ALAD produces porphobilinogen for the shared tetrapyrrole trunk, so the broad process term is accurate and does not force a single downstream tetrapyrrole endpoint.	genes/PSEPK/hemB/hemB-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	hemB	GO:0008270	zinc ion binding	ACCEPT	GO:0046872	metal ion binding	MODIFY	Three residues are annotated as catalytic Zn2+ ligands, and the sequence contains the corresponding cysteine-rich region. This architecture is absent from the KT2440 HemBB paralog.	Zinc binding is already represented by GO:0008270, while UniProt also identifies a distinct Mg2+-binding residue. GO:0000287 records that second metal requirement without retaining a generic parent term.	genes/PSEPK/hemB/hemB-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	hemBB	GO:0006783	heme biosynthetic process	ACCEPT	GO:0033014	tetrapyrrole biosynthetic process	ACCEPT	Its predicted porphobilinogen product feeds the shared reactions leading to uroporphyrinogen III, protoporphyrin IX, and heme b.	An active ALAD paralog would produce porphobilinogen for the shared tetrapyrrole trunk. The process term is appropriately broad given that HemBB's relative physiological contribution remains unresolved.	genes/PSEPK/hemBB/hemBB-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	hemBB	GO:0008270	zinc ion binding	MODIFY	GO:0046872	metal ion binding	KEEP_AS_NON_CORE	The current HemBB record predicts Mg2+ binding at residue 247 and does not identify the catalytic Zn2+-ligand triad found in HemB. Magnesium ion binding is therefore the conservative sequence-supported replacement.	GO:0046872 is true if the predicted Mg2+ site is functional, but it is less informative than the magnesium-ion-binding replacement proposed for the unsupported zinc transfer.	genes/PSEPK/hemBB/hemBB-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	hemE	GO:0006783	heme biosynthetic process	ACCEPT	GO:0006779	porphyrin-containing compound biosynthetic process	MODIFY	Coproporphyrinogen III is required for the subsequent HemF/HemN, protoporphyrinogen oxidase, and ferrochelatase reactions.	In KT2440, HemE supplies coproporphyrinogen III to the HemF/HemN, protoporphyrinogen oxidase, and ferrochelatase reactions that produce heme B, supporting the live endpoint term GO:0006785.	genes/PSEPK/hemE/hemE-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	hmgB	GO:0006572	L-tyrosine catabolic process	ACCEPT	GO:0009072	aromatic amino acid metabolic process	MARK_AS_OVER_ANNOTATED	The P. putida pathway study establishes that tyrosine is converted to homogentisate and then catabolized by HmgABC.	HmgB can receive homogentisate-derived carbon from aromatic amino-acid catabolism, but this broad umbrella term is redundant with the existing accepted GO:1902000 homogentisate catabolic process annotation.	genes/PSEPK/hmgB/hmgB-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	hmgC	GO:0004364	glutathione transferase activity	MARK_AS_OVER_ANNOTATED	GO:0003824	catalytic activity	MARK_AS_OVER_ANNOTATED	GST-zeta family membership and use of glutathione as a regenerated catalytic cofactor do not establish a physiologically relevant net glutathione-transferase reaction for Q88E49. GO:0016034 captures the supported substrate-specific isomerase function.	Q88E49 has the specific maleylacetoacetate isomerase activity, so that term should replace generic catalytic activity.	genes/PSEPK/hmgC/hmgC-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	hmgC	GO:0006559	L-phenylalanine catabolic process	ACCEPT	GO:0009072	aromatic amino acid metabolic process	MARK_AS_OVER_ANNOTATED	The P. putida pathway study establishes that phenylalanine is converted to homogentisate and then catabolized by HmgABC.	HmgC can receive homogentisate-derived carbon from aromatic amino-acid catabolism, but this broad umbrella term is redundant with the specific GO:1902000 homogentisate catabolic process annotation added below.	genes/PSEPK/hmgC/hmgC-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	hpd	GO:0006572	L-tyrosine catabolic process	ACCEPT	GO:0009072	aromatic amino acid metabolic process	MODIFY	Accurate biological process; well supported by the homogentisate pathway literature in P. putida.	The annotation is correct but the generic metabolic term under-specifies the function. Replace with the catabolic process term, which captures the documented degradative role.	genes/PSEPK/hpd/hpd-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	hutF	GO:0019239	deaminase activity	MARK_AS_OVER_ANNOTATED	GO:0016787	hydrolase activity	MARK_AS_OVER_ANNOTATED	Unlike the redundant-parent cases, this term is not an is_a ancestor of HutF's activity: GO:0050416 formimidoylglutamate deiminase activity sits under GO:0016813, hydrolase activity acting on carbon-nitrogen bonds in linear amidines, whereas GO:0019239 deaminase activity is a separate branch under G	GO:0050416 identifies the biological substrate and reaction and should be used instead of propagating a generic hydrolase claim.	genes/PSEPK/hutF/hutF-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	hutF	GO:0019239	deaminase activity	MARK_AS_OVER_ANNOTATED	GO:0016810	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	MARK_AS_OVER_ANNOTATED	Unlike the redundant-parent cases, this term is not an is_a ancestor of HutF's activity: GO:0050416 formimidoylglutamate deiminase activity sits under GO:0016813, hydrolase activity acting on carbon-nitrogen bonds in linear amidines, whereas GO:0019239 deaminase activity is a separate branch under G	The class term is redundant with the substrate-specific formimidoylglutamate deiminase annotation.	genes/PSEPK/hutF/hutF-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	ilvA-I	GO:0006565	L-serine catabolic process	UNDECIDED	GO:0006520	amino acid metabolic process	ACCEPT	Family enzyme assays support a serine-dehydratase side activity, and PMID:30327426 shows that this chemistry can occur in vivo in a biosynthetic IlvA context. They do not determine the contribution of either KT2440 paralog to physiological serine turnover. The isoleucine role does not exclude such a	Its catalysis consumes L-threonine and supplies 2-oxobutanoate for L-isoleucine synthesis. Both the broad amino-acid process and the specific isoleucine biosynthetic process are correct; annotation breadth does not imply excess biological scope.	genes/PSEPK/ilvA-I/ilvA-I-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	ilvA-I	GO:0006567	L-threonine catabolic process	ACCEPT	GO:0006520	amino acid metabolic process	ACCEPT	GO:0006567 covers chemical reactions resulting in L-threonine breakdown. Conversion to 2-oxobutanoate and ammonium satisfies that definition. Subsequent use of the carbon skeleton in biosynthesis does not exclude threonine catabolism or require a dedicated energy-generating degradation pathway.	Its catalysis consumes L-threonine and supplies 2-oxobutanoate for L-isoleucine synthesis. Both the broad amino-acid process and the specific isoleucine biosynthetic process are correct; annotation breadth does not imply excess biological scope.	genes/PSEPK/ilvA-I/ilvA-I-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	ilvA-II	GO:0006565	L-serine catabolic process	UNDECIDED	GO:0006520	amino acid metabolic process	ACCEPT	Family enzyme assays support a serine-dehydratase side activity, and PMID:30327426 shows that this chemistry can occur in vivo in a biosynthetic IlvA context. They do not determine the contribution of either KT2440 paralog to physiological serine turnover. The isoleucine role does not exclude such a	Its catalysis consumes L-threonine and supplies 2-oxobutanoate for L-isoleucine synthesis. Both the broad amino-acid process and the specific isoleucine biosynthetic process are correct; annotation breadth does not imply excess biological scope.	genes/PSEPK/ilvA-II/ilvA-II-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	ilvA-II	GO:0006567	L-threonine catabolic process	ACCEPT	GO:0006520	amino acid metabolic process	ACCEPT	GO:0006567 covers chemical reactions resulting in L-threonine breakdown. Conversion to 2-oxobutanoate and ammonium satisfies that definition. Subsequent use of the carbon skeleton in biosynthesis does not exclude threonine catabolism or require a dedicated energy-generating degradation pathway.	Its catalysis consumes L-threonine and supplies 2-oxobutanoate for L-isoleucine synthesis. Both the broad amino-acid process and the specific isoleucine biosynthetic process are correct; annotation breadth does not imply excess biological scope.	genes/PSEPK/ilvA-II/ilvA-II-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	katA	GO:0042542	response to hydrogen peroxide	KEEP_AS_NON_CORE	GO:0006979	response to oxidative stress	KEEP_AS_NON_CORE	This term reflects the physiological context of katA induction and stress defense, but the direct catalytic process term GO:0042744 is the more specific core annotation.	KatA contributes to oxidative-stress survival, yet the more specific core process is hydrogen peroxide catabolism. This term is better treated as contextual rather than as the primary evolved function.	genes/PSEPK/katA/katA-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	katG	GO:0070301	cellular response to hydrogen peroxide	KEEP_AS_NON_CORE	GO:0006979	response to oxidative stress	ACCEPT	The annotation is biologically reasonable for an H2O2-scavenging enzyme, but the direct H2O2 catabolic process term more precisely captures the enzyme's core contribution; this response term is retained as non-core.	H2O2 decomposition by catalase-peroxidase is a principal mechanism of defense against oxidative stress, consistent with the bifunctional H2O2-detoxifying activity recorded in UniProt.	genes/PSEPK/katG/katG-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	lysS	GO:0000049	tRNA binding	KEEP_AS_NON_CORE	GO:0003676	nucleic acid binding	MARK_AS_OVER_ANNOTATED	The exact reaction identifies tRNA(Lys).	tRNA(Lys) is explicitly identified.	genes/PSEPK/lysS/lysS-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	mdh	GO:0004459	L-lactate dehydrogenase (NAD+) activity	REMOVE	GO:0003824	catalytic activity	KEEP_AS_NON_CORE	This IEA (TreeGrafter/PANTHER) annotation reflects an electronic mis-assignment within the shared LDH/MDH superfamily node. UniProt and InterPro (Malate_DH_type3, IPR011275) classify Q88Q44 as a malate dehydrogenase (EC 1.1.1.37, GO:0030060), and experimental assays in KT2440 measured malate dehydro	The gene product is an enzyme so catalytic activity is true, but this is a very general parent of the specific malate dehydrogenase activity (GO:0030060) and carries no specific information. Retained as non-core.	genes/PSEPK/mdh/mdh-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	mdh	GO:0004459	L-lactate dehydrogenase (NAD+) activity	REMOVE	GO:0016491	oxidoreductase activity	KEEP_AS_NON_CORE	This IEA (TreeGrafter/PANTHER) annotation reflects an electronic mis-assignment within the shared LDH/MDH superfamily node. UniProt and InterPro (Malate_DH_type3, IPR011275) classify Q88Q44 as a malate dehydrogenase (EC 1.1.1.37, GO:0030060), and experimental assays in KT2440 measured malate dehydro	True but general parent of GO:0030060. Retained as non-core background.	genes/PSEPK/mdh/mdh-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	mdh	GO:0004459	L-lactate dehydrogenase (NAD+) activity	REMOVE	GO:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	KEEP_AS_NON_CORE	This IEA (TreeGrafter/PANTHER) annotation reflects an electronic mis-assignment within the shared LDH/MDH superfamily node. UniProt and InterPro (Malate_DH_type3, IPR011275) classify Q88Q44 as a malate dehydrogenase (EC 1.1.1.37, GO:0030060), and experimental assays in KT2440 measured malate dehydro	Accurately describes the enzyme class (NAD-linked CH-OH oxidoreductase) but is a parent of the specific GO:0030060 L-malate dehydrogenase (NAD+) activity. Retained as non-core.	genes/PSEPK/mdh/mdh-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	metH	GO:0046653	tetrahydrofolate metabolic process	KEEP_AS_NON_CORE	GO:0042558	pteridine-containing compound metabolic process	MARK_AS_OVER_ANNOTATED	MetH remethylates its cobalamin cofactor using methyltetrahydrofolate, so tetrahydrofolate metabolism is related but secondary to methionine biosynthesis.	MetH uses 5-methyltetrahydrofolate, but the biologically specific process for this enzyme is L-methionine biosynthesis, not a broad pteridine-metabolism process.	genes/PSEPK/metH/metH-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	mexB	GO:0042910	xenobiotic transmembrane transporter activity	ACCEPT	GO:0022857	transmembrane transporter activity	KEEP_AS_NON_CORE			genes/PSEPK/mexB/mexB-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	mnmA	GO:0002143	tRNA wobble position uridine thiolation	ACCEPT	GO:0008033	tRNA processing	KEEP_AS_NON_CORE	The reviewed UniProt record and MnmA family assignment explicitly support U34 thiolation.	The specific tRNA thiolation term is preferred.	genes/PSEPK/mnmA/mnmA-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	moaA	GO:0061799	cyclic pyranopterin monophosphate synthase activity	REMOVE	GO:0003824	catalytic activity	MODIFY	MoaA makes the cyclic GTP intermediate; the distinct MoaC enzyme converts that intermediate to cPMP.	Reviewed UniProt/HAMAP assigns EC 4.1.99.22 GTP 3',8'-cyclase activity to Q88E69.	genes/PSEPK/moaA/moaA-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	mobA	GO:1902758	bis(molybdopterin guanine dinucleotide)molybdenum biosynthetic process	ACCEPT	GO:0006777	Mo-molybdopterin cofactor biosynthetic process	ACCEPT	The previous rejection read the single-MGD reaction equation as excluding the bis-MGD product, but bis-MGD is assembled by two successive MobA guanylyl transfers onto Mo-MPT, and the process term is how GO records that contribution: the characterised E. coli ortholog MobA (P32173) carries GO:1902758	The exact MobA reaction produces the Mo-MGD cofactor variant, so this broad biosynthetic-process term is accurate without asserting downstream bis-MGD assembly.	genes/PSEPK/mobA/mobA-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	nspC	GO:0008836	diaminopimelate decarboxylase activity	REMOVE	GO:0003824	catalytic activity	MARK_AS_OVER_ANNOTATED			genes/PSEPK/nspC/nspC-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	nspC	GO:0008836	diaminopimelate decarboxylase activity	REMOVE	GO:0016831	carboxy-lyase activity	ACCEPT			genes/PSEPK/nspC/nspC-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	nuoE	GO:0003954	NADH dehydrogenase activity	MODIFY	GO:0016491	oxidoreductase activity	MARK_AS_OVER_ANNOTATED	GO:0003954 (NADH + H+ + acceptor = NAD+ + reduced acceptor) is an is_a ancestor of GO:0008137 NADH dehydrogenase (ubiquinone) activity, the reaction catalysed by the assembled 13-subunit NDH-1 complex of which NuoE is an obligate component. NuoE carries a single [2Fe-2S] cluster and no FMN or NADH-b	The complete NADH:quinone oxidoreductase reaction is an emergent activity of assembled complex I; this subunit contributes to it but does not independently enable the full reaction.	genes/PSEPK/nuoE/nuoE-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	nuoG	GO:0003954	NADH dehydrogenase activity	KEEP_AS_NON_CORE	GO:0016491	oxidoreductase activity	MARK_AS_OVER_ANNOTATED	GO:0003954 (NADH + H+ + acceptor = NAD+ + reduced acceptor) is an is_a ancestor of GO:0008137 NADH dehydrogenase (ubiquinone) activity, the reaction catalysed by the assembled 13-subunit NDH-1 complex of which NuoG is an obligate component. NuoG carries one [2Fe-2S] and three [4Fe-4S] clusters and n	The complete NADH:quinone oxidoreductase reaction is an emergent activity of assembled complex I; this subunit contributes to it but does not independently enable the full reaction.	genes/PSEPK/nuoG/nuoG-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	nuoG	GO:0003954	NADH dehydrogenase activity	KEEP_AS_NON_CORE	GO:0016651	oxidoreductase activity, acting on NAD(P)H	MARK_AS_OVER_ANNOTATED	GO:0003954 (NADH + H+ + acceptor = NAD+ + reduced acceptor) is an is_a ancestor of GO:0008137 NADH dehydrogenase (ubiquinone) activity, the reaction catalysed by the assembled 13-subunit NDH-1 complex of which NuoG is an obligate component. NuoG carries one [2Fe-2S] and three [4Fe-4S] clusters and n	The complete NADH:quinone oxidoreductase reaction is an emergent activity of assembled complex I; this subunit contributes to it but does not independently enable the full reaction.	genes/PSEPK/nuoG/nuoG-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	nuoI	GO:0003954	NADH dehydrogenase activity	MODIFY	GO:0016651	oxidoreductase activity, acting on NAD(P)H	MARK_AS_OVER_ANNOTATED	GO:0003954 (NADH + H+ + acceptor = NAD+ + reduced acceptor) is an is_a ancestor of GO:0008137 NADH dehydrogenase (ubiquinone) activity, the reaction catalysed by the assembled 13-subunit NDH-1 complex of which NuoI is an obligate component. NuoI carries two [4Fe-4S] clusters and no FMN or NADH-bindi	The complete NADH:quinone oxidoreductase reaction is an emergent activity of assembled complex I; this subunit contributes to it but does not independently enable the full reaction.	genes/PSEPK/nuoI/nuoI-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	opgG	GO:0051274	beta-glucan biosynthetic process	MODIFY	GO:0005975	carbohydrate metabolic process	MODIFY	OpgG is assigned to osmoregulated periplasmic glucan biosynthesis; GO:1900727 captures that pathway more specifically than beta-glucan biosynthetic process.	UniProt places OpgG specifically in the osmoregulated periplasmic glucan biosynthesis pathway; the broad carbohydrate metabolic process term should be replaced by the specific OPG biosynthesis term.	genes/PSEPK/opgG/opgG-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	opgG	GO:0051274	beta-glucan biosynthetic process	MODIFY	GO:0016051	carbohydrate biosynthetic process	MODIFY	OpgG is assigned to osmoregulated periplasmic glucan biosynthesis; GO:1900727 captures that pathway more specifically than beta-glucan biosynthetic process.	The OpgG-specific process is osmoregulated periplasmic glucan biosynthesis, so the broad carbohydrate biosynthetic process term should be replaced by GO:1900727.	genes/PSEPK/opgG/opgG-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	paaH	GO:0006635	fatty acid beta-oxidation	MARK_AS_OVER_ANNOTATED	GO:0006631	fatty acid metabolic process	MARK_AS_OVER_ANNOTATED	"The rejection is retained on substrate grounds rather than on the propagation alone. GO:0006635 is defined as the process that ""results in the complete oxidation of a long-chain fatty acid"". The exact target is named 3-hydroxyadipyl-CoA dehydrogenase and sits in the paa locus, acting on the 3-hydrox"	The exact target is named 3-hydroxyadipyl-CoA dehydrogenase and is encoded in the phenylacetate catabolic locus, not a general fatty-acid metabolic enzyme.	genes/PSEPK/paaH/paaH-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	pcaK	GO:0046943	carboxylic acid transmembrane transporter activity	MODIFY	GO:0022857	transmembrane transporter activity	MODIFY	GO has the more specific existing term GO:0008028 monocarboxylic acid transmembrane transporter activity, which better matches the demonstrated substrate class for 4-HBA transport. A dedicated 4-hydroxybenzoate transporter term is not currently available and is proposed below.	The generic transporter term should be replaced by terms that capture both substrate class and mechanism. The best existing GO terms are GO:0008028 monocarboxylic acid transmembrane transporter activity and GO:0015293 symporter activity. A still more specific 4-hydroxybenzoate transporter term does 	genes/PSEPK/pcaK/pcaK-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	pgi1	GO:0051156	glucose 6-phosphate metabolic process	ACCEPT	GO:1901135	carbohydrate derivative metabolic process	MARK_AS_OVER_ANNOTATED	Pgi acts directly on glucose-6-phosphate; this is a specific and accurate process annotation for the gene.	A high-level metabolic parent that adds no specificity beyond the more precise process terms already annotated.	genes/PSEPK/pgi1/pgi1-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	pgi2	GO:0051156	glucose 6-phosphate metabolic process	ACCEPT	GO:1901135	carbohydrate derivative metabolic process	MARK_AS_OVER_ANNOTATED	This is a specific, biologically appropriate annotation for this gene product.	The annotation is not necessarily false, but it is less informative than the specific molecular function already present.	genes/PSEPK/pgi2/pgi2-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	pgm	GO:0008973	phosphopentomutase activity	MARK_AS_OVER_ANNOTATED	GO:0016868	intramolecular phosphotransferase activity	KEEP_AS_NON_CORE	Rejection confirmed on re-review, with the reason strengthened. GO:0008973 is defined as catalysis of D-ribose 1-phosphate = D-ribose 5-phosphate, a pentose-phosphate substrate, whereas Q88GY7 carries the glucose-specific classifiers NCBIfam TIGR01132 and InterPro IPR005852 PGM_a-D-Glc-sp and is ass	Retain as a supporting/non-core annotation rather than using it as the main functional summary.	genes/PSEPK/pgm/pgm-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	prs	GO:0006164	purine nucleotide biosynthetic process	KEEP_AS_NON_CORE	GO:0009165	nucleotide biosynthetic process	MARK_AS_OVER_ANNOTATED	PRPP supplies purine biosynthesis, so the involvement is real, but the specific direct process (PRPP biosynthesis, GO:0006015) is the core BP. The deep research confirms PRPP is required for purine and pyrimidine nucleotide biosynthesis.	Prs directly synthesizes PRPP, a precursor for nucleotide biosynthesis; GO:0006015 is the specific process. The deep research frames PRPP as a central activated-ribose donor feeding nucleotide pathways.	genes/PSEPK/prs/prs-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	ptxD	GO:0016618	hydroxypyruvate reductase [NAD(P)H] activity	UNDECIDED	GO:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	MODIFY	"Re-review: changed from REMOVE to UNDECIDED. The stated ground was only the absence of a target-specific assay, which is not by itself a refutation of a phylogenetic inference. Q88HI1 carries no experimentally determined substrate: UniProt gives only the EMBL-derived SubName ""Phosphonate dehydrogena"	Direct locus genetics and conserved pathway order support phosphogluconate 2-dehydrogenase activity more specifically.	genes/PSEPK/ptxD/ptxD-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	ptxD	GO:0030267	glyoxylate reductase (NADPH) activity	UNDECIDED	GO:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	MODIFY	Re-reviewed against the OpenScientist control report, which recommended retaining GO:0030267 and adding GO:0016618 on the grounds that the nearest characterized homolog is E. coli GhrB (P37666). Verified in this re-review: a BLOSUM62 global alignment gives 53.1% identity of Q88HI1 to GhrB, 40.0% to 	Direct locus genetics and conserved pathway order support phosphogluconate 2-dehydrogenase activity more specifically.	genes/PSEPK/ptxD/ptxD-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	pvdD	GO:0047527	2,3-dihydroxybenzoate-serine ligase activity	MODIFY	GO:0003824	catalytic activity	ACCEPT	The target is a pyoverdine NRPS with target PP_4219 genetic and domain support; DHB-serine ligation is the distinct enterobactin chemistry. Keep the NRPS amino-acid-ligation replacement without assigning the threonine-rich substrate map of P. aeruginosa PvdD to this three-module KT2440 protein.	PvdD directly catalyzes amino-acid activation and peptide assembly. A broad catalytic ancestor remains valid even when a specific NRPS term is available.	genes/PSEPK/pvdD/pvdD-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	pydB	GO:0005829	cytosol	ACCEPT	GO:0005737	cytoplasm	MARK_AS_OVER_ANNOTATED	Retain the more precise TreeGrafter localization.	GO:0005829 already captures the soluble compartment at useful specificity.	genes/PSEPK/pydB/pydB-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	pydB	GO:0016812	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides	KEEP_AS_NON_CORE	GO:0016787	hydrolase activity	MARK_AS_OVER_ANNOTATED	Correct but less informative than GO:0004157.	The specific cyclic-amide hydrolase activity supersedes this root-like parent.	genes/PSEPK/pydB/pydB-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	pyrC	GO:0006207	'de novo' pyrimidine nucleobase biosynthetic process	MARK_AS_OVER_ANNOTATED	GO:0019856	pyrimidine nucleobase biosynthetic process	MARK_AS_OVER_ANNOTATED	Retain the more specific de novo UMP process.	Retain GO:0044205.	genes/PSEPK/pyrC/pyrC-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	pyrC'	GO:0004038	allantoinase activity	REMOVE	GO:0016810	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	REMOVE	The TreeGrafter transfer reflects broad amidohydrolase-family similarity. Direct work on the P. putida complex instead identifies this protein as a catalytically inactive PyrC-like partner of PyrB.	Family resemblance does not establish catalysis in this experimentally characterized pseudoenzyme.	genes/PSEPK/pyrC'/pyrC'-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	quiA	GO:0008876	quinoprotein glucose dehydrogenase activity	MARK_AS_OVER_ANNOTATED	GO:0016614	oxidoreductase activity, acting on CH-OH group of donors	MARK_AS_OVER_ANNOTATED	The specific EC2GO term GO:0047519 quinate dehydrogenase (quinone) activity is present and better matches the protein name, EC assignment, and pathway context. Glucose dehydrogenase specificity is not supported for this gene in the supplied evidence.	GO:0047519 captures the specific molecular function; this parent term adds little.	genes/PSEPK/quiA/quiA-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	recB	GO:0000725	recombinational repair	KEEP_AS_NON_CORE	GO:0006281	DNA repair	KEEP_AS_NON_CORE	Accurate but more general than the specific DSB-via-HR term, which better represents the core process; retain as supporting/non-core.	Correct but general; subsumed by GO:0000724.	genes/PSEPK/recB/recB-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	recD	GO:0017116	single-stranded DNA helicase activity	KEEP_AS_NON_CORE	GO:0004386	helicase activity	KEEP_AS_NON_CORE	GO:0017116 is not a parent of the 5-prime-to-3-prime term and is biologically true, but GO:0043139 better captures RecD's defining polarity in the core-function summary.	Retain the true broad molecular function while using GO:0043139, 5-prime-to-3-prime DNA helicase activity, as the defining core term.	genes/PSEPK/recD/recD-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	rlmE	GO:0008173	RNA methyltransferase activity	KEEP_AS_NON_CORE	GO:0008168	methyltransferase activity	MARK_AS_OVER_ANNOTATED	"The over-annotation call is relaxed and the ancestor is retained as non-core. GO:0008173 is defined as transfer of a methyl group to a nucleoside residue in an RNA molecule, which is exactly what RlmE does (EC 2.1.1.166; UniProt ""Specifically methylates the uridine in position 2552 of 23S""). It is a"	GO:0008650 (rRNA uridine-2'-O-ribose methyltransferase activity) captures the specific rRNA substrate and modified nucleotide. Falcon deep research confirms RlmE is a SAM-dependent RNA 2'-O-methyltransferase specific for the 23S rRNA ribose 2'-hydroxyl.	genes/PSEPK/rlmE/rlmE-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	rnc	GO:0003725	double-stranded RNA binding	ACCEPT	GO:0003723	RNA binding	MARK_AS_OVER_ANNOTATED	Substrate recognition of double-stranded RNA is intrinsic to RNase III activity and is structurally supported by the dedicated DRBM domain.	RNA binding is a generic parent of double-stranded RNA binding (GO:0003725), which is already annotated and better captures the substrate-recognition activity mediated by the DRBM domain.	genes/PSEPK/rnc/rnc-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	sdhA	GO:0000104	succinate dehydrogenase activity	ACCEPT	GO:0016491	oxidoreductase activity	KEEP_AS_NON_CORE	Strongly supported by family/domain assignment (TIGR01816 sdhA_forward, Pfam FAD_binding_2, FRD/SDH subfamily), conserved active-site and FAD-binding residues, and UniProt EC 1.3.5.1. Consistent across all lines of evidence.	Correct but uninformative high-level term; subsumed by GO:0000104 succinate dehydrogenase activity for SdhA. Retain as non-core.	genes/PSEPK/sdhA/sdhA-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	treY	GO:0005992	trehalose biosynthetic process	ACCEPT	GO:0005975	carbohydrate metabolic process	MARK_AS_OVER_ANNOTATED	The submitted treY product, EC assignment, and TreY-specific family identify the first reaction of maltooligosyltrehalose-dependent trehalose synthesis.	Trehalose biosynthesis and alpha-glucan use provide more informative pathway context.	genes/PSEPK/treY/treY-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	treY	GO:0030980	alpha-glucan catabolic process	KEEP_AS_NON_CORE	GO:0005975	carbohydrate metabolic process	MARK_AS_OVER_ANNOTATED	The coupled TreY/TreZ route draws on alpha-glucan, but TreY's defining role in this batch is synthesis of the trehalose-containing intermediate.	Trehalose biosynthesis and alpha-glucan use provide more informative pathway context.	genes/PSEPK/treY/treY-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	ttgB	GO:0042910	xenobiotic transmembrane transporter activity	ACCEPT	GO:0022857	transmembrane transporter activity	ACCEPT	This is an excellent annotation from TreeGrafter that captures the core molecular function at the right level of specificity. TtgB specifically transports xenobiotic compounds (antibiotics, plant antimicrobials, bipyridyls) across the inner membrane. The broad substrate specificity spanning multiple	This is a correct but general parent term of GO:0015562 (efflux transmembrane transporter activity). Since both annotations are IEA, retaining the broader term from a different InterPro mapping (IPR001036 vs IPR004764) is acceptable. TtgB unambiguously has transmembrane transporter activity as the R	genes/PSEPK/ttgB/ttgB-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	ttgR	GO:0000976	transcription cis-regulatory region binding	ACCEPT	GO:0003677	DNA binding	KEEP_AS_NON_CORE	TtgR is a TetR-family local regulator of the ttgR-ttgABC promoter/operator region; transcription cis-regulatory region binding is the directly supported and most informative DNA-binding molecular function. Falcon deep research confirms TtgR binds a pseudo-palindromic operator that overlaps the diver	DNA binding is true for this HTH regulator but is less specific than the transcription cis-regulatory region binding term, so it should be retained only as a broad non-core parent.	genes/PSEPK/ttgR/ttgR-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	tusD	GO:0002143	tRNA wobble position uridine thiolation	ACCEPT	GO:0008033	tRNA processing	KEEP_AS_NON_CORE	The TusD family and neighboring tusBCDE locus support the specific pathway assignment.	GO:0002143 captures the actual pathway role.	genes/PSEPK/tusD/tusD-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	tyrB	GO:0004838	L-tyrosine:2-oxoglutarate transaminase activity	ACCEPT	GO:0003824	catalytic activity	MARK_AS_OVER_ANNOTATED	Domain/family evidence (class-I PLP aminotransferase, PANTHER ArAT subfamily SF37) plus genetic evidence in KT2440 (tyrB mutants show a tyrosine-utilization phenotype; PMID:20050871) support tyrosine aminotransferase activity. The enzyme is likely promiscuous across aromatic amino acids (also acting	"""catalytic activity"" is the MF root and conveys no specific information. The more precise terms GO:0008483 (transaminase activity) and GO:0004838 (L-tyrosine:2-oxoglutarate transaminase activity) capture the actual function."	genes/PSEPK/tyrB/tyrB-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	ubiX	GO:0016831	carboxy-lyase activity	REMOVE	GO:0003824	catalytic activity	MARK_AS_OVER_ANNOTATED	UbiX synthesizes prenylated FMN, whereas the partner UbiD protein performs the 4-hydroxy-3-polyprenylbenzoate decarboxylation. This TreeGrafter propagation confuses cofactor supply with the UbiD reaction.	GO:0106141 captures the specific evolved activity of UbiX.	genes/PSEPK/ubiX/ubiX-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	uppS	GO:0045547	ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific] activity	KEEP_AS_NON_CORE	GO:0016765	transferase activity, transferring alkyl or aryl (other than methyl) groups	MARK_AS_OVER_ANNOTATED	Relaxed from MARK_AS_OVER_ANNOTATED with a proposed replacement. QuickGO confirms GO:0008834 (the undecaprenyl-specific term this record already carries and accepts) is_a GO:0045547, so the flagged row is a true ancestor of the enzyme's actual reaction rather than a competing or less accurate claim.	GO:0008834 states the reaction and product-chain specificity.	genes/PSEPK/uppS/uppS-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	ydiJ	GO:0004458	D-lactate dehydrogenase (cytochrome) activity	MODIFY	GO:0003824	catalytic activity	MODIFY	The frozen TG graft PTN001714929 lies below broad lactate IBD PTN000202298 but itself contains the characterized E. coli YdiJ P77748, in PTHR11748 SF119. PMID:36144368 purified E. coli and Pantoea YdiJ and found no D-lactate activity at 5-10 mM in PES/DCIP assays. Together with PP_4493 mutant D-2HG 	Catalysis is central to this enzyme, but GO:0003824 does not identify the reaction. Use the specific molecular function already supported elsewhere in this review; this is a specificity refinement, not a claim that catalysis is peripheral or absent.	genes/PSEPK/ydiJ/ydiJ-ai-review.yaml
deeper_than	InterPro2GO	PSEPK	ydiJ	GO:0008720	D-lactate dehydrogenase (NAD+) activity	MODIFY	GO:0003824	catalytic activity	MODIFY	The frozen TG graft PTN001714929 lies below broad lactate IBD PTN000202298 but itself contains the characterized E. coli YdiJ P77748, in PTHR11748 SF119. PMID:36144368 purified E. coli and Pantoea YdiJ and found no D-lactate activity at 5-10 mM in PES/DCIP assays. Together with PP_4493 mutant D-2HG 	Catalysis is central to this enzyme, but GO:0003824 does not identify the reaction. Use the specific molecular function already supported elsewhere in this review; this is a specificity refinement, not a claim that catalysis is peripheral or absent.	genes/PSEPK/ydiJ/ydiJ-ai-review.yaml
deeper_than	InterPro2GO	RAMVA	RvY_01767	GO:0030145	manganese ion binding	ACCEPT	GO:0046872	metal ion binding	KEEP_AS_NON_CORE			genes/RAMVA/RvY_01767/RvY_01767-ai-review.yaml
deeper_than	InterPro2GO	SACEN	ermE	GO:0031167	rRNA methylation	ACCEPT	GO:0000154	rRNA modification	ACCEPT	Accurate biological process.	Accurate (general) biological process; the specific GO:0031167 rRNA methylation is also annotated.	genes/SACEN/ermE/ermE-ai-review.yaml
deeper_than	InterPro2GO	SACEN	eryAI	GO:0004312	fatty acid synthase activity	MODIFY	GO:0016740	transferase activity	ACCEPT	Wrong product class. Replace with GO:0016218 (polyketide synthase activity).	Accurate (general) molecular function.	genes/SACEN/eryAI/eryAI-ai-review.yaml
deeper_than	InterPro2GO	SACEN	eryAI	GO:0004312	fatty acid synthase activity	MODIFY	GO:0016746	acyltransferase activity	ACCEPT	Wrong product class. Replace with GO:0016218 (polyketide synthase activity).	Correct component (AT-domain) molecular function (UniProt Acyltransferase keyword).	genes/SACEN/eryAI/eryAI-ai-review.yaml
deeper_than	InterPro2GO	SACEN	eryAII	GO:0004312	fatty acid synthase activity	MODIFY	GO:0016740	transferase activity	ACCEPT	Wrong product class. Replace with GO:0016218 (polyketide synthase activity).	Accurate (general) molecular function.	genes/SACEN/eryAII/eryAII-ai-review.yaml
deeper_than	InterPro2GO	SACEN	eryAII	GO:0004312	fatty acid synthase activity	MODIFY	GO:0016746	acyltransferase activity	ACCEPT	Wrong product class. Replace with GO:0016218 (polyketide synthase activity).	Correct component (AT-domain) molecular function.	genes/SACEN/eryAII/eryAII-ai-review.yaml
deeper_than	InterPro2GO	SACEN	eryAIII	GO:0004312	fatty acid synthase activity	MODIFY	GO:0016740	transferase activity	ACCEPT	The characterized assembly-line product is 6-deoxyerythronolide B, a macrolide polyketide. This supports a polyketide-synthase refinement of the fatty-acid-synthase assignment. Shared acyl-carrier/condensation chemistry is real; absence of DH/ER domains from this particular subunit is not, by itself	Accurate (general) molecular function.	genes/SACEN/eryAIII/eryAIII-ai-review.yaml
deeper_than	InterPro2GO	SACEN	eryAIII	GO:0004312	fatty acid synthase activity	MODIFY	GO:0016746	acyltransferase activity	ACCEPT	The characterized assembly-line product is 6-deoxyerythronolide B, a macrolide polyketide. This supports a polyketide-synthase refinement of the fatty-acid-synthase assignment. Shared acyl-carrier/condensation chemistry is real; absence of DH/ER domains from this particular subunit is not, by itself	Correct component (AT-domain) molecular function.	genes/SACEN/eryAIII/eryAIII-ai-review.yaml
deeper_than	InterPro2GO	SALRS	PTSG_05882	GO:0016339	calcium-dependent cell-cell adhesion	MARK_AS_OVER_ANNOTATED	GO:0098609	cell-cell adhesion	MARK_AS_OVER_ANNOTATED	Calcium-dependent cell-cell adhesion is a general cadherin capability, so it is not impossible for this protein. But it is untested, the donor biology is classical-cadherin adhesion in bilaterian tissues, and the EC-like repeats of F2UD23 lack the canonical calcium-binding motifs. Kept as an over-an	The family entry is dominated by animal cadherins, whose cell-cell adhesion function does not transfer automatically to a premetazoan cadherin of unknown function. Possible roles in prey capture or substrate attachment are equally consistent with the domain content.	genes/SALRS/PTSG_05882/PTSG_05882-ai-review.yaml
deeper_than	InterPro2GO	SALRS	PTSG_05882	GO:0044331	cell-cell adhesion mediated by cadherin	MARK_AS_OVER_ANNOTATED	GO:0098609	cell-cell adhesion	MARK_AS_OVER_ANNOTATED	The definition fits any cadherin that mediates cell-cell attachment, so the term is not excluded. But it is untested, and the S. rosetta rosette is held together by other means (cytoplasmic bridges, a C-type lectin-containing extracellular matrix). Premetazoan cadherins may well serve non-adhesive o	The family entry is dominated by animal cadherins, whose cell-cell adhesion function does not transfer automatically to a premetazoan cadherin of unknown function. Possible roles in prey capture or substrate attachment are equally consistent with the domain content.	genes/SALRS/PTSG_05882/PTSG_05882-ai-review.yaml
deeper_than	InterPro2GO	SALRS	PTSG_06458	GO:0016339	calcium-dependent cell-cell adhesion	MARK_AS_OVER_ANNOTATED	GO:0007155	cell adhesion	KEEP_AS_NON_CORE	Calcium-dependent cell-cell adhesion is a general cadherin capability, and the EC repeats of this protein keep canonical calcium-binding motifs, so the term is not impossible. But it is untested, the donor biology is classical-cadherin adhesion in bilaterian tissues, and S. rosetta rosettes are held	Broad and plausible for a cell-surface EC-repeat protein: it covers adhesion to prey, matrix or substrate as well as to other cells. Kept as non-core because no adhesive activity has been measured.	genes/SALRS/PTSG_06458/PTSG_06458-ai-review.yaml
deeper_than	InterPro2GO	SALRS	PTSG_06458	GO:0016339	calcium-dependent cell-cell adhesion	MARK_AS_OVER_ANNOTATED	GO:0098609	cell-cell adhesion	MARK_AS_OVER_ANNOTATED	Calcium-dependent cell-cell adhesion is a general cadherin capability, and the EC repeats of this protein keep canonical calcium-binding motifs, so the term is not impossible. But it is untested, the donor biology is classical-cadherin adhesion in bilaterian tissues, and S. rosetta rosettes are held	The family entry is dominated by animal cadherins, whose cell-cell adhesion function does not transfer automatically to a premetazoan cadherin of unknown function. Possible roles in prey capture or substrate attachment are equally consistent with the domain content.	genes/SALRS/PTSG_06458/PTSG_06458-ai-review.yaml
deeper_than	InterPro2GO	SALRS	PTSG_06458	GO:0016342	catenin complex	REMOVE	GO:0005886	plasma membrane	ACCEPT	Without a cytoplasmic cadherin domain, the protein cannot enter the cadherin-beta-catenin-alpha-catenin complex. The assembled complex is an animal feature not found in choanoflagellates.	A signal peptide, a large ectodomain and a single transmembrane helix fit plasma membrane localization. The one choanoflagellate cadherin that has been localized, M. brevicollis MBCDH1, is on the microvillar collar, a plasma-membrane structure. Accepted as a sequence-based inference.	genes/SALRS/PTSG_06458/PTSG_06458-ai-review.yaml
deeper_than	InterPro2GO	SALRS	PTSG_06458	GO:0044331	cell-cell adhesion mediated by cadherin	MARK_AS_OVER_ANNOTATED	GO:0007155	cell adhesion	KEEP_AS_NON_CORE	The definition fits any cadherin that mediates cell-cell attachment, so the term is not excluded. But it is untested, and the S. rosetta rosette is held together by other means (cytoplasmic bridges, a C-type lectin-containing extracellular matrix). Premetazoan cadherins may well serve non-adhesive o	Broad and plausible for a cell-surface EC-repeat protein: it covers adhesion to prey, matrix or substrate as well as to other cells. Kept as non-core because no adhesive activity has been measured.	genes/SALRS/PTSG_06458/PTSG_06458-ai-review.yaml
deeper_than	InterPro2GO	SALRS	PTSG_06458	GO:0044331	cell-cell adhesion mediated by cadherin	MARK_AS_OVER_ANNOTATED	GO:0098609	cell-cell adhesion	MARK_AS_OVER_ANNOTATED	The definition fits any cadherin that mediates cell-cell attachment, so the term is not excluded. But it is untested, and the S. rosetta rosette is held together by other means (cytoplasmic bridges, a C-type lectin-containing extracellular matrix). Premetazoan cadherins may well serve non-adhesive o	The family entry is dominated by animal cadherins, whose cell-cell adhesion function does not transfer automatically to a premetazoan cadherin of unknown function. Possible roles in prey capture or substrate attachment are equally consistent with the domain content.	genes/SALRS/PTSG_06458/PTSG_06458-ai-review.yaml
deeper_than	InterPro2GO	SALRS	PTSG_11235	GO:0016339	calcium-dependent cell-cell adhesion	MARK_AS_OVER_ANNOTATED	GO:0007155	cell adhesion	KEEP_AS_NON_CORE	Calcium-dependent cell-cell adhesion is a general cadherin capability, and the EC repeats of this protein keep canonical calcium-binding motifs, so the term is not impossible. But it is untested, the donor biology is classical-cadherin adhesion in bilaterian tissues, and S. rosetta rosettes are held	Broad and plausible for a cell-surface EC-repeat protein: it covers adhesion to prey, matrix or substrate as well as to other cells. Kept as non-core because no adhesive activity has been measured.	genes/SALRS/PTSG_11235/PTSG_11235-ai-review.yaml
deeper_than	InterPro2GO	SALRS	PTSG_11235	GO:0016339	calcium-dependent cell-cell adhesion	MARK_AS_OVER_ANNOTATED	GO:0098609	cell-cell adhesion	MARK_AS_OVER_ANNOTATED	Calcium-dependent cell-cell adhesion is a general cadherin capability, and the EC repeats of this protein keep canonical calcium-binding motifs, so the term is not impossible. But it is untested, the donor biology is classical-cadherin adhesion in bilaterian tissues, and S. rosetta rosettes are held	The family entry is dominated by animal cadherins, whose cell-cell adhesion function does not transfer automatically to a premetazoan cadherin of unknown function. Possible roles in prey capture or substrate attachment are equally consistent with the domain content.	genes/SALRS/PTSG_11235/PTSG_11235-ai-review.yaml
deeper_than	InterPro2GO	SALRS	PTSG_11235	GO:0016342	catenin complex	REMOVE	GO:0016020	membrane	ACCEPT	Without a cytoplasmic cadherin domain, the protein cannot enter the cadherin-beta-catenin-alpha-catenin complex. The assembled complex is an animal feature not found in choanoflagellates.	The signal peptide plus a single transmembrane helix make membrane insertion a sound sequence-based prediction. The term is broad (plasma membrane is also annotated), and localization has not been examined.	genes/SALRS/PTSG_11235/PTSG_11235-ai-review.yaml
deeper_than	InterPro2GO	SALRS	PTSG_11235	GO:0044331	cell-cell adhesion mediated by cadherin	MARK_AS_OVER_ANNOTATED	GO:0007155	cell adhesion	KEEP_AS_NON_CORE	The definition fits any cadherin that mediates cell-cell attachment, so the term is not excluded. But it is untested, and the S. rosetta rosette is held together by other means (cytoplasmic bridges, a C-type lectin-containing extracellular matrix). Premetazoan cadherins may well serve non-adhesive o	Broad and plausible for a cell-surface EC-repeat protein: it covers adhesion to prey, matrix or substrate as well as to other cells. Kept as non-core because no adhesive activity has been measured.	genes/SALRS/PTSG_11235/PTSG_11235-ai-review.yaml
deeper_than	InterPro2GO	SALRS	PTSG_11235	GO:0044331	cell-cell adhesion mediated by cadherin	MARK_AS_OVER_ANNOTATED	GO:0098609	cell-cell adhesion	MARK_AS_OVER_ANNOTATED	The definition fits any cadherin that mediates cell-cell attachment, so the term is not excluded. But it is untested, and the S. rosetta rosette is held together by other means (cytoplasmic bridges, a C-type lectin-containing extracellular matrix). Premetazoan cadherins may well serve non-adhesive o	The family entry is dominated by animal cadherins, whose cell-cell adhesion function does not transfer automatically to a premetazoan cadherin of unknown function. Possible roles in prey capture or substrate attachment are equally consistent with the domain content.	genes/SALRS/PTSG_11235/PTSG_11235-ai-review.yaml
deeper_than	InterPro2GO	SALRS	couscous	GO:0000026	alpha-1,2-mannosyltransferase activity	ACCEPT	GO:0016757	glycosyltransferase activity	ACCEPT	The catalytic domain places Couscous within a family whose characterized members (S. cerevisiae Mnn2, Mnn5) are alpha-1,2-mannosyltransferases, and the DXD motif is retained, so there is no sequence evidence of catalytic loss. Loss-of-function mutants show a specific, rescuable glycan (jacalin) defe	Correct at the general level and consistent with the more specific alpha-1,2-mannosyltransferase prediction. Retained as a companion IEA; it is the safest statement of the activity given that sugar and linkage specificity have not been measured.	genes/SALRS/couscous/couscous-ai-review.yaml
deeper_than	InterPro2GO	SALSP	mcr-4	GO:0016776	phosphotransferase activity, phosphate group as acceptor	MODIFY	GO:0016772	transferase activity, transferring phosphorus-containing groups	MODIFY	Replace the broad or over-specific electronic term 'phosphotransferase activity, phosphate group as acceptor' with phosphatidylethanolamine:Kdo2-lipid A phosphoethanolamine transferase activity based on UniProt/CARD determinant identity and the curated ARO->GO mapping.	Replace the broad or over-specific electronic term 'transferase activity, transferring phosphorus-containing groups' with phosphatidylethanolamine:Kdo2-lipid A phosphoethanolamine transferase activity based on UniProt/CARD determinant identity and the curated ARO->GO mapping.	genes/SALSP/mcr-4/mcr-4-ai-review.yaml
deeper_than	InterPro2GO	SPHPI	Q53353	GO:0010436	carotenoid dioxygenase activity	REMOVE	GO:0016702	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen	ACCEPT	LSD-I is an experimentally characterized lignostilbene dioxygenase (EC 1.13.11.43), not a carotenoid enzyme; the correct specific MF (GO:0050054) is already present by IDA. Same substrate-class error as LSD-III, NOV1/NOV2, Rco1, and cao-1.	Accurate general dioxygenase MF.	genes/SPHPI/Q53353/Q53353-ai-review.yaml
deeper_than	InterPro2GO	SPHPI	lsdB	GO:0010436	carotenoid dioxygenase activity	REMOVE	GO:0016702	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen, incorporation of two atoms of oxygen	ACCEPT	LSD-III is an experimentally characterized lignostilbene dioxygenase (EC 1.13.11.43), not a carotenoid enzyme; the correct specific MF (GO:0050054) is already present by IDA. Same substrate-class error as cao-1 (IBA) and NOV1 (IEA/TreeGrafter).	Accurate general dioxygenase MF, consistent with the experimental activity.	genes/SPHPI/lsdB/lsdB-ai-review.yaml
deeper_than	InterPro2GO	STABO	mdr	GO:0005743	mitochondrial inner membrane	REMOVE	GO:0016020	membrane	ACCEPT	The focused report resolved all three mitochondrial/oligopeptide claims to the same GO_REF:0000118 TreeGrafter source, PTN008681462, with no independent evidence line. The current PTHR43394 tree recovers that node in an Embryophyta subtree rather than as an H6TB12 leaf, and H6TB12 has a full-length 	Correct; the transmembrane domains place the protein in a membrane, and the more specific plasma membrane location is separately annotated.	genes/STABO/mdr/mdr-ai-review.yaml
deeper_than	InterPro2GO	STABO	mdr	GO:0015421	ABC-type oligopeptide transporter activity	REMOVE	GO:0140359	ABC-type transporter activity	ACCEPT	H6TB12 is experimentally tied to sophorolipid secretion and has two ABC nucleotide- binding domains in a full-length MDR architecture. The focused report found that the oligopeptide row shares its sole TreeGrafter provenance with the two mitochondrial rows and inherits from the Mdl1-named PTHR43394 	Primary deletion studies demonstrate a major reduction in extracellular sophorolipids; sequence architecture supports ATP-binding/hydrolytic coupling and transmembrane export. Plasma-membrane placement is the functional/topological inference for secretion, not a directly imaged exclusive localizatio	genes/STABO/mdr/mdr-ai-review.yaml
deeper_than	InterPro2GO	STABO	mdr	GO:0090374	oligopeptide export from mitochondrion	REMOVE	GO:0055085	transmembrane transport	ACCEPT	All three narrow mitochondrial/oligopeptide claims depend on a single GO_REF:0000118 TreeGrafter source, PTN008681462, and the current PTHR43394 reconstruction no longer places H6TB12 on that recovered internal subtree. The target is a full-length MDR transporter with direct sophorolipid-export evid	Primary deletion studies demonstrate a major reduction in extracellular sophorolipids; sequence architecture supports ATP-binding/hydrolytic coupling and transmembrane export. Plasma-membrane placement is the functional/topological inference for secretion, not a directly imaged exclusive localizatio	genes/STABO/mdr/mdr-ai-review.yaml
deeper_than	InterPro2GO	STAWA	cfr	GO:0030488	tRNA methylation	REMOVE	GO:0006400	tRNA modification	REMOVE	Retained. Cfr's characterized substrate is 23S rRNA: it methylates C8 of adenosine 2503 (PMID:19144912), and the record's rRNA methyltransferase, rRNA base methylation and rRNA binding rows are accepted. The tRNA specificity in this family belongs to the paralogous radical-SAM enzyme RlmN, which met	The Cfr record and Cfr mechanism literature identify 23S rRNA A2503 as the substrate. This review found no support that Cfr modifies tRNA.	genes/STAWA/cfr/cfr-ai-review.yaml
deeper_than	UniProt keyword	ACET2	P15329	GO:0004622	phosphatidylcholine lysophospholipase A1 activity	MODIFY	GO:0016787	hydrolase activity	ACCEPT	The SGNH hydrolase domain correctly identifies the enzyme family, but lysophospholipase activity is unlikely for a cellulosome-associated enzyme. The biological context (cellulosome, plant cell wall degradation) strongly suggests this enzyme functions as a carbohydrate esterase involved in lignocell	The SGNH hydrolase domain definitively encodes hydrolase activity. The broad term is appropriate given uncertainty about the specific substrate. This correctly captures the enzymatic function without the problematic over-specificity of the glycoside hydrolase or lysophospholipase annotations.	genes/ACET2/P15329/P15329-ai-review.yaml
deeper_than	UniProt keyword	ACET2	celC	GO:0008422	beta-glucosidase activity	REMOVE	GO:0016787	hydrolase activity	ACCEPT	This annotation is incorrect. CelC (EC 3.2.1.4) is an endoglucanase that cleaves internal beta-1,4-glucosidic linkages in cellulose chains. Beta-glucosidase (EC 3.2.1.21) is a distinct enzyme class that removes terminal glucose residues. The TreeGrafter prediction appears to be based on broad sequen	This annotation is correct but very general. CelC is indeed a hydrolase (it catalyzes hydrolysis of beta-1,4-glucosidic bonds). The annotation derives from UniProtKB keyword mapping. More specific child terms provide better functional characterization.	genes/ACET2/celC/celC-ai-review.yaml
deeper_than	UniProt keyword	ACET2	celC	GO:0008422	beta-glucosidase activity	REMOVE	GO:0016798	hydrolase activity, acting on glycosyl bonds	ACCEPT	This annotation is incorrect. CelC (EC 3.2.1.4) is an endoglucanase that cleaves internal beta-1,4-glucosidic linkages in cellulose chains. Beta-glucosidase (EC 3.2.1.21) is a distinct enzyme class that removes terminal glucose residues. The TreeGrafter prediction appears to be based on broad sequen	CelC hydrolyzes glycosidic (glycosyl) bonds, specifically beta-1,4-glucosidic linkages. This annotation from UniProtKB keyword mapping correctly places CelC within the glycoside hydrolase functional category.	genes/ACET2/celC/celC-ai-review.yaml
deeper_than	UniProt keyword	DESRO	K9IFT7	GO:0050829	defense response to Gram-negative bacterium	ACCEPT	GO:0042742	defense response to bacterium	ACCEPT	The secreted beta-defensin 1-like architecture supports the ancestral antimicrobial-spectrum inference, and no target-specific loss of this defense role is established. Human beta-defensin 1 activity can depend strongly on redox conditions, so this term does not assert equal potency against every ba	This is a secreted beta-defensin 1-like peptide from salivary gland. Conserved antimicrobial family function supports defense response and defense response to bacterium; the broader label remains biologically correct.	genes/DESRO/K9IFT7/K9IFT7-ai-review.yaml
deeper_than	UniProt keyword	DESRO	K9IFT7	GO:0050830	defense response to Gram-positive bacterium	ACCEPT	GO:0042742	defense response to bacterium	ACCEPT	The secreted beta-defensin 1-like architecture supports the ancestral antimicrobial-spectrum inference, and no target-specific loss of this defense role is established. Human beta-defensin 1 activity can depend strongly on redox conditions, so this term does not assert equal potency against every ba	This is a secreted beta-defensin 1-like peptide from salivary gland. Conserved antimicrobial family function supports defense response and defense response to bacterium; the broader label remains biologically correct.	genes/DESRO/K9IFT7/K9IFT7-ai-review.yaml
deeper_than	UniProt keyword	DESRO	K9IMD0	GO:0019731	antibacterial humoral response	KEEP_AS_NON_CORE	GO:0002376	immune system process	KEEP_AS_NON_CORE	The focused report treats antibacterial and broader immune annotations as weak family-level carry-over, supported by salivary antimicrobial grouping but not by a direct draculin bactericidal assay. Keep the term as a peripheral lactotransferrin inference rather than the demonstrated draculin anticoa	The focused report treats immune annotations as weak family-level carry-over, supported by salivary antimicrobial grouping but not by a direct draculin immune assay. Keep this broad immune term as a peripheral lactotransferrin inference rather than the demonstrated draculin anticoagulant core.	genes/DESRO/K9IMD0/K9IMD0-ai-review.yaml
deeper_than	UniProt keyword	DESRO	K9IMD0	GO:0019731	antibacterial humoral response	KEEP_AS_NON_CORE	GO:0042742	defense response to bacterium	KEEP_AS_NON_CORE	The focused report treats antibacterial and broader immune annotations as weak family-level carry-over, supported by salivary antimicrobial grouping but not by a direct draculin bactericidal assay. Keep the term as a peripheral lactotransferrin inference rather than the demonstrated draculin anticoa	The focused report treats antibacterial and broader immune annotations as weak family-level carry-over, supported by salivary antimicrobial grouping but not by a direct draculin bactericidal assay. Keep the term as a peripheral lactotransferrin inference rather than the demonstrated draculin anticoa	genes/DESRO/K9IMD0/K9IMD0-ai-review.yaml
deeper_than	UniProt keyword	DESRO	K9IWH5	GO:0050829	defense response to Gram-negative bacterium	ACCEPT	GO:0042742	defense response to bacterium	ACCEPT	Consistent with the characterised spectrum of mammalian c-type lysozyme and with the same TreeGrafter propagation applied to the human orthologue. Retained at the specific level.	Correct and directly supported. Retained as the general parent alongside the specific Gram-positive and Gram-negative terms.	genes/DESRO/K9IWH5/K9IWH5-ai-review.yaml
deeper_than	UniProt keyword	DESRO	K9IWH5	GO:0050830	defense response to Gram-positive bacterium	ACCEPT	GO:0042742	defense response to bacterium	ACCEPT	This is the well-supported, mechanistically explained specificity of c-type lysozyme, and the broad parent is annotated separately. Keep the specific term.	Correct and directly supported. Retained as the general parent alongside the specific Gram-positive and Gram-negative terms.	genes/DESRO/K9IWH5/K9IWH5-ai-review.yaml
deeper_than	UniProt keyword	DESRO	K9J287	GO:0004530	deoxyribonuclease I activity	ACCEPT	GO:0004519	endonuclease activity	MODIFY	UniProt names this protein deoxyribonuclease-1-like 1, consistent with DNase I activity.	Use the specific deoxyribonuclease I activity term.	genes/DESRO/K9J287/K9J287-ai-review.yaml
deeper_than	UniProt keyword	DESRO	K9J287	GO:0004530	deoxyribonuclease I activity	ACCEPT	GO:0016787	hydrolase activity	MODIFY	UniProt names this protein deoxyribonuclease-1-like 1, consistent with DNase I activity.	Use the specific deoxyribonuclease I activity term.	genes/DESRO/K9J287/K9J287-ai-review.yaml
deeper_than	UniProt keyword	DESVH	Q725T8	GO:0071805	potassium ion transmembrane transport	ACCEPT	GO:0006811	monoatomic ion transport	MARK_AS_OVER_ANNOTATED	KdpC is an essential subunit of the KdpFABC potassium-transporting ATPase. Contemporary structural and mechanistic studies confirm that KdpC is required for proper complex function, even though it does not directly catalyze transport. The 'involved_in' qualifier is appropriate for an accessory subun	While technically correct (potassium is a monoatomic ion), this annotation adds no information beyond what GO:0006813 (potassium ion transport) and GO:0071805 (potassium ion transmembrane transport) already provide. The KdpFABC complex is specifically a potassium transporter, not a general ion trans	genes/DESVH/Q725T8/Q725T8-ai-review.yaml
deeper_than	UniProt keyword	METEA	mdcD	GO:0003989	acetyl-CoA carboxylase activity	REMOVE	GO:0016874	ligase activity	REMOVE	The target has the MdcD-specific family assignment and neighboring mdcA/C/E genes. Its inferred reaction is decarboxylation of specialized ACP-bound malonyl substrate; it is not the ATP/biotin-dependent acetyl-CoA-to-malonyl-CoA reaction. Shared carboxyltransferase-fold ancestry does not establish r	The inferred MdcD-MdcE reaction is a biotin-independent decarboxylation, not energy-dependent joining of substrates. The target is a catalytic component of the malonate-degradation complex; related ACC/PCC ligase chemistry is not retained merely because of shared fold.	genes/METEA/mdcD/mdcD-ai-review.yaml
deeper_than	UniProt subcellular location	9POAL	NCGR_LOCUS10166	GO:0009570	chloroplast stroma	UNDECIDED	GO:0009507	chloroplast	UNDECIDED	The strong HDH-like N-terminus supports the ancestral localization, while the fused membrane region raises a real targeting question. Rejecting stroma solely because another domain predicts ER localization assumed exclusivity and model error without evidence.	The N-terminus is strongly conserved with a separate predicted plant HDH. A C-terminal membrane region does not categorically preclude plastid import or processing, but no target localization or authentic fusion transcript has been established.	genes/9POAL/NCGR_LOCUS10166/NCGR_LOCUS10166-ai-review.yaml
deeper_than	UniProt subcellular location	CAPO3	coITGB2	GO:0008305	integrin complex	ACCEPT	GO:0005886	plasma membrane	ACCEPT	Membership of an alpha/beta heterodimer is the defining property of an integrin beta subunit. Every element needed for it is conserved, so the inference is sound even though the Capsaspora heterodimer has not been isolated. Note that the graft node itself (vertebrate ITGBL1, a TM-less protein) is a 	Signal peptide plus a single transmembrane helix and filopodial staining are consistent with plasma membrane localization. Blocking adhesion by an antibody added to live cells also implies an exposed ectodomain.	genes/CAPO3/coITGB2/coITGB2-ai-review.yaml
deeper_than	UniProt subcellular location	CAPO3	coITGB2	GO:0008305	integrin complex	ACCEPT	GO:0016020	membrane	KEEP_AS_NON_CORE	Membership of an alpha/beta heterodimer is the defining property of an integrin beta subunit. Every element needed for it is conserved, so the inference is sound even though the Capsaspora heterodimer has not been isolated. Note that the graft node itself (vertebrate ITGBL1, a TM-less protein) is a 	True (one transmembrane helix) but redundant with the more specific plasma membrane annotation.	genes/CAPO3/coITGB2/coITGB2-ai-review.yaml
deeper_than	UniProt subcellular location	CERSP	dorR	GO:0005829	cytosol	ACCEPT	GO:0005737	cytoplasm	ACCEPT			genes/CERSP/dorR/dorR-ai-review.yaml
deeper_than	UniProt subcellular location	CRIGR	HSPH1	GO:0005829	cytosol	ACCEPT	GO:0005737	cytoplasm	ACCEPT	Cytosol is the primary localization for HSPH1, consistent with UniProt annotation of cytoplasm and with its known functions as a cytoplasmic chaperone and NEF.	Cytoplasm is the primary subcellular localization for HSPH1. UniProt annotation (by similarity) and the protein's established cytoplasmic functions support this.	genes/CRIGR/HSPH1/HSPH1-ai-review.yaml
deeper_than	UniProt subcellular location	DORPE	cpx	GO:0031201	SNARE complex	MARK_AS_OVER_ANNOTATED	GO:0016020	membrane	ACCEPT	Complexin is not a core subunit of the SNARE complex; it binds to the exterior surface of the assembled SNARE four-helix bundle as an accessory regulatory protein. The part_of qualifier used in the GOA annotation implies complexin is a structural component of the SNARE complex, which is inaccurate. 	Complexin is farnesylated at Cys149 (S-farnesyl cysteine), providing a lipid anchor for membrane association. The membrane annotation is consistent with this post-translational modification. Although a more specific membrane compartment (e.g. presynaptic membrane) would be preferable, the broad memb	genes/DORPE/cpx/cpx-ai-review.yaml
deeper_than	UniProt subcellular location	HYPJE	IRE1	GO:1990604	IRE1-TRAF2-ASK1 complex	REMOVE	GO:0005789	endoplasmic reticulum membrane	ACCEPT	The focused report confirms that GO:1990604 requires an IRE1, TRAF2 and ASK1 complex, but Trichoderma encodes neither TRAF2 nor ASK1/MAP3K5; ASK1 was also absent across the Fungi kingdom query. The mammalian complex evidence sits on human/rat metazoan systems and the mammalian PTHR13954:SF17 subfami	Correct. IRE1 is a type I ER transmembrane protein with lumenal and cytoplasmic domains. Confirmed by topology and transmembrane helix prediction in UniProt.	genes/HYPJE/IRE1/IRE1-ai-review.yaml
deeper_than	UniProt subcellular location	PSEPK	bioD	GO:0005829	cytosol	KEEP_AS_NON_CORE	GO:0005737	cytoplasm	KEEP_AS_NON_CORE	Relaxed from MARK_AS_OVER_ANNOTATED on re-review, per the rule that broad-but-true terms are not over-annotations. BioD is a soluble cytoplasmic enzyme with no signal peptide, transmembrane segment or lipobox, so it resides in the cytosol; carrying the more general cytoplasm term on another row make	UniProt explicitly predicts cytoplasmic localization; the duplicate cytosol annotation adds no distinct localization information.	genes/PSEPK/bioD/bioD-ai-review.yaml
deeper_than	UniProt subcellular location	PSEPK	fabB	GO:0005829	cytosol	KEEP_AS_NON_CORE	GO:0005737	cytoplasm	KEEP_AS_NON_CORE	FabB is a soluble homodimeric FAS-II enzyme acting on ACP-bound substrates, with a UniProt cytoplasmic subcellular location and no transmembrane segment, so the TreeGrafter cytosol call is true; redundancy with the broader cytoplasm annotation is not grounds for rejection. It is kept as non-core bec	Retain the localization annotation without using it to define the catalytic core function.	genes/PSEPK/fabB/fabB-ai-review.yaml
deeper_than	UniProt subcellular location	PSEPK	fur	GO:0005829	cytosol	ACCEPT	GO:0005737	cytoplasm	ACCEPT	Consistent with the cytoplasm annotation and the soluble nature of Fur; cytosol is the appropriate specific component for this regulator.	Correct localization for a cytoplasmic metal-sensing transcription factor.	genes/PSEPK/fur/fur-ai-review.yaml
deeper_than	UniProt subcellular location	PSEPK	kdpE	GO:0005829	cytosol	ACCEPT	GO:0005737	cytoplasm	KEEP_AS_NON_CORE			genes/PSEPK/kdpE/kdpE-ai-review.yaml
deeper_than	UniProt subcellular location	PSEPK	lolC	GO:0098797	plasma membrane protein complex	ACCEPT	GO:0005886	plasma membrane	ACCEPT			genes/PSEPK/lolC/lolC-ai-review.yaml
deeper_than	UniProt subcellular location	PSEPK	lolE	GO:0098797	plasma membrane protein complex	ACCEPT	GO:0005886	plasma membrane	ACCEPT			genes/PSEPK/lolE/lolE-ai-review.yaml
deeper_than	UniProt subcellular location	PSEPK	secA	GO:0005829	cytosol	ACCEPT	GO:0005737	cytoplasm	MARK_AS_OVER_ANNOTATED	The specific cytosol term captures the soluble half of the approximately 50:50 distribution reported by UniProt and is retained as a core location.	Retaining both cytoplasm and cytosol is redundant; cytosol better identifies the soluble pool.	genes/PSEPK/secA/secA-ai-review.yaml
deeper_than	UniRule	EMENI	sfgA	GO:0000976	transcription cis-regulatory region binding	ACCEPT	GO:0003677	DNA binding	ACCEPT	Zn(II)2Cys6 binuclear-cluster factors bind upstream activating and repressing sequences, so the prediction fits SfgA's domain. No SfgA DNA-binding assay is cited in this review, so the row rests on the domain call.	Unsigned keyword-level parent of the terms above; uninformative on its own.	genes/EMENI/sfgA/sfgA-ai-review.yaml
deeper_than	UniRule	PSEPK	aceK	GO:0004721	phosphoprotein phosphatase activity	ACCEPT	GO:0016788	hydrolase activity, acting on ester bonds	ACCEPT	Both existing adjudications support phosphoprotein phosphatase activity in substance. A more specific substrate term is useful in the core summary, but its availability does not make the TreeGrafter parent assertion biologically incorrect.	Hydrolase activity acting on ester bonds is a valid broad function of the enzyme. Redundancy with substrate-specific phosphatase activity is not a biological error.	genes/PSEPK/aceK/aceK-ai-review.yaml
deeper_than	UniRule	PSEPK	flgE	GO:0071978	bacterial-type flagellum-dependent swarming motility	KEEP_AS_NON_CORE	GO:0071973	bacterial-type flagellum-dependent cell motility	ACCEPT	GO:0071978 is a child of GO:0071973 bacterial-type flagellum-dependent cell motility, which is accepted on another row, and swarming is flagellum-driven movement of a group of cells over a surface. The hook transmits motor torque to the filament during swimming and swarming alike, so a strain lackin		genes/PSEPK/flgE/flgE-ai-review.yaml
deeper_than	UniRule	PSEPK	fur	GO:0000976	transcription cis-regulatory region binding	ACCEPT	GO:0003677	DNA binding	KEEP_AS_NON_CORE	Captures the specific DNA-binding mode of Fur (operator/Fur-box binding) and is supported by the canonical Fur mechanism and by purified Fur binding to Fur boxes in pseudomonads (e.g. P. aeruginosa Fur on pvdS/pchR promoters).	True but generic; the more specific GO:0000976 (transcription cis-regulatory region binding) better captures the function. Retained as a non-core, broader supporting term rather than removed.	genes/PSEPK/fur/fur-ai-review.yaml
deeper_than	UniRule	PSEPK	glnK	GO:0005524	ATP binding	ACCEPT	GO:0000166	nucleotide binding	ACCEPT	Well supported by conserved PII structural biology and InterPro/PANTHER family assignment.	Consistent with PII-family biology and the UniProt Nucleotide-binding keyword; a true molecular property of the protein.	genes/PSEPK/glnK/glnK-ai-review.yaml
deeper_than	UniRule	PSEPK	gltB	GO:0019676	ammonia assimilation cycle	ACCEPT	GO:0006541	L-glutamine metabolic process	KEEP_AS_NON_CORE			genes/PSEPK/gltB/gltB-ai-review.yaml
deeper_than	UniRule	PSEPK	mnmA	GO:0002143	tRNA wobble position uridine thiolation	ACCEPT	GO:0006400	tRNA modification	KEEP_AS_NON_CORE	The reviewed UniProt record and MnmA family assignment explicitly support U34 thiolation.	GO:0002143 captures the direct modification pathway.	genes/PSEPK/mnmA/mnmA-ai-review.yaml
deeper_than	UniRule	PSEPK	mobA	GO:1902758	bis(molybdopterin guanine dinucleotide)molybdenum biosynthetic process	ACCEPT	GO:0019720	Mo-molybdopterin cofactor metabolic process	MARK_AS_OVER_ANNOTATED	The previous rejection read the single-MGD reaction equation as excluding the bis-MGD product, but bis-MGD is assembled by two successive MobA guanylyl transfers onto Mo-MPT, and the process term is how GO records that contribution: the characterised E. coli ortholog MobA (P32173) carries GO:1902758	GO:0006777 more specifically captures the biosynthetic context of MobA-catalyzed Mo-MGD formation.	genes/PSEPK/mobA/mobA-ai-review.yaml
deeper_than	UniRule	PSEPK	nadA	GO:0034628	'de novo' NAD+ biosynthetic process from L-aspartate	ACCEPT	GO:0019363	pyridine nucleotide biosynthetic process	MODIFY	NadA consumes the iminoaspartate generated from L-aspartate and supplies quinolinate to NadC.	NadA specifically participates in de novo NAD+ biosynthesis from L-aspartate, captured by GO:0034628.	genes/PSEPK/nadA/nadA-ai-review.yaml
deeper_than	UniRule	PSEPK	nadB	GO:0034628	'de novo' NAD+ biosynthetic process from L-aspartate	ACCEPT	GO:0019363	pyridine nucleotide biosynthetic process	MODIFY	L-aspartate oxidation by NadB is the entry reaction for this de novo NAD+ biosynthetic route.	The exact pathway is de novo NAD+ biosynthesis from L-aspartate, which is captured by GO:0034628.	genes/PSEPK/nadB/nadB-ai-review.yaml
deeper_than	UniRule	PSEPK	opgG	GO:0051274	beta-glucan biosynthetic process	MODIFY	GO:0009250	glucan biosynthetic process	MODIFY	OpgG is assigned to osmoregulated periplasmic glucan biosynthesis; GO:1900727 captures that pathway more specifically than beta-glucan biosynthetic process.	UniProt assigns OpgG to OPG biosynthesis, and GO:1900727 captures this pathway more specifically than generic glucan biosynthesis.	genes/PSEPK/opgG/opgG-ai-review.yaml
deeper_than	UniRule	PSEPK	queA	GO:0002099	tRNA wobble guanine modification	ACCEPT	GO:0006400	tRNA modification	MODIFY	The reaction converts preQ1-tRNA at position 34 to epoxyqueuosine(34)-tRNA, so it directly participates in wobble guanine modification.	QueA performs the specific preQ1-tRNA to epoxyqueuosine-tRNA conversion, so GO:0008616 is the informative process term.	genes/PSEPK/queA/queA-ai-review.yaml
deeper_than	UniRule	PSEPK	tatC-I	GO:0009977	proton motive force dependent protein transmembrane transporter activity	MARK_AS_OVER_ANNOTATED	GO:0008320	transmembrane protein transporter activity	MARK_AS_OVER_ANNOTATED	TatC contributes to this whole-complex activity but does not independently enable it.	TatC is a receptor/scaffold subunit and does not independently transport protein.	genes/PSEPK/tatC-I/tatC-I-ai-review.yaml
deeper_than	UniRule	PSEPK	tatC-II	GO:0009977	proton motive force dependent protein transmembrane transporter activity	MARK_AS_OVER_ANNOTATED	GO:0008320	transmembrane protein transporter activity	MARK_AS_OVER_ANNOTATED	TatC contributes to this whole-complex activity but does not independently enable it.	TatC is a receptor/scaffold subunit and does not independently transport protein.	genes/PSEPK/tatC-II/tatC-II-ai-review.yaml
deeper_than	combined IEA	9POAL	NCGR_LOCUS27674	GO:0009570	chloroplast stroma	UNDECIDED	GO:0005737	cytoplasm	ACCEPT	While chloroplast localization is plausible for a plant UMP-CMP kinase, the specific annotation to chloroplast stroma (GO:0009570) is uncertain. The closest characterized ortholog, rice YL2, is a thylakoid membrane-localized protein [PMID:29392476]. Furthermore, the TreeGrafter PANTHER match could r	Cytoplasmic localization is well-supported for plant UMP-CMP kinases. Arabidopsis has cytosolic UMK isoforms alongside the plastid-localized PUMPKIN. Even if this particular gene model is chimeric, the UMP-CMP kinase portion would likely localize to the cytoplasm or plastids.	genes/9POAL/NCGR_LOCUS27674/NCGR_LOCUS27674-ai-review.yaml
deeper_than	combined IEA	ACET2	celC	GO:0009251	glucan catabolic process	ACCEPT	GO:0000272	polysaccharide catabolic process	ACCEPT	This annotation is accurate. CelC breaks down cellulose, which is a glucan (polymer of glucose). The TreeGrafter annotation correctly infers this biological process from sequence homology to characterized cellulases.	The annotation is accurate as cellulose is a polysaccharide and CelC participates in its degradation. This parent term complements the more specific cellulose catabolic process annotation. IEA evidence from InterPro domain and UniProtKB keyword mappings is appropriate for this general term.	genes/ACET2/celC/celC-ai-review.yaml
deeper_than	combined IEA	CANLF	ALB	GO:0072562	blood microparticle	KEEP_AS_NON_CORE	GO:0005576	extracellular region	ACCEPT	Plausible plasma-derived localization; not a distinguishing functional compartment.	Albumin functions in blood plasma (extracellular region).	genes/CANLF/ALB/ALB-ai-review.yaml
deeper_than	combined IEA	CERSP	dorR	GO:0000976	transcription cis-regulatory region binding	ACCEPT	GO:0003677	DNA binding	REMOVE			genes/CERSP/dorR/dorR-ai-review.yaml
deeper_than	combined IEA	DESPS	nrfA	GO:0030288	outer membrane-bounded periplasmic space	ACCEPT	GO:0042597	periplasmic space	ACCEPT	NrfA is annotated as a precursor and belongs to the periplasmic cytochrome c nitrite reductase family. The TreeGrafter localization is consistent with the biology of Gram-negative respiratory nitrite reductases. The available support is family-level rather than a DESPS-specific fractionation or loca	This duplicates the more specific outer membrane-bounded periplasmic space annotation but is still biologically consistent with exported NrfA respiratory nitrite reductases.	genes/DESPS/nrfA/nrfA-ai-review.yaml
deeper_than	combined IEA	DESRO	K9IFT7	GO:0002227	innate immune response in mucosa	ACCEPT	GO:0006952	defense response	ACCEPT	The beta-defensin fold and conserved secretory architecture support an inherited innate effector function. The target transcript was obtained from salivary gland and the native vampirome study reports defensin-family expression in accessory glands, consistent with an oral mucosal context. No lineage	This is a secreted beta-defensin 1-like peptide from salivary gland. Conserved antimicrobial family function supports defense response and defense response to bacterium; the broader label remains biologically correct.	genes/DESRO/K9IFT7/K9IFT7-ai-review.yaml
deeper_than	combined IEA	DESRO	K9IFT7	GO:0050829	defense response to Gram-negative bacterium	ACCEPT	GO:0006952	defense response	ACCEPT	The secreted beta-defensin 1-like architecture supports the ancestral antimicrobial-spectrum inference, and no target-specific loss of this defense role is established. Human beta-defensin 1 activity can depend strongly on redox conditions, so this term does not assert equal potency against every ba	This is a secreted beta-defensin 1-like peptide from salivary gland. Conserved antimicrobial family function supports defense response and defense response to bacterium; the broader label remains biologically correct.	genes/DESRO/K9IFT7/K9IFT7-ai-review.yaml
deeper_than	combined IEA	DESRO	K9IFT7	GO:0050830	defense response to Gram-positive bacterium	ACCEPT	GO:0006952	defense response	ACCEPT	The secreted beta-defensin 1-like architecture supports the ancestral antimicrobial-spectrum inference, and no target-specific loss of this defense role is established. Human beta-defensin 1 activity can depend strongly on redox conditions, so this term does not assert equal potency against every ba	This is a secreted beta-defensin 1-like peptide from salivary gland. Conserved antimicrobial family function supports defense response and defense response to bacterium; the broader label remains biologically correct.	genes/DESRO/K9IFT7/K9IFT7-ai-review.yaml
deeper_than	combined IEA	DESRO	K9IJK6	GO:0031639	plasminogen activation	ACCEPT	GO:0006508	proteolysis	ACCEPT	Plasminogen activation is the specific proteolytic function inferred for this salivary plasminogen-activator homolog; it names conversion of the zymogen rather than a generic vascular phenotype. The previous UNDECIDED treated the PRU00121 warning as loss of catalytic residues. The actual rule concer	Proteolysis is direct peptide-bond cleavage performed by the enzyme during plasminogen activation, so it is part of its core work. The previous UNDECIDED treated the PRU00121 warning as loss of catalytic residues. The actual rule concerns kringle-domain disulfide features, not the protease catalytic	genes/DESRO/K9IJK6/K9IJK6-ai-review.yaml
deeper_than	combined IEA	DESRO	K9J287	GO:0004530	deoxyribonuclease I activity	ACCEPT	GO:0004518	nuclease activity	MODIFY	UniProt names this protein deoxyribonuclease-1-like 1, consistent with DNase I activity.	Use the specific deoxyribonuclease I activity term.	genes/DESRO/K9J287/K9J287-ai-review.yaml
deeper_than	combined IEA	DESVH	Q725T8	GO:0071805	potassium ion transmembrane transport	ACCEPT	GO:0006813	potassium ion transport	ACCEPT	KdpC is an essential subunit of the KdpFABC potassium-transporting ATPase. Contemporary structural and mechanistic studies confirm that KdpC is required for proper complex function, even though it does not directly catalyze transport. The 'involved_in' qualifier is appropriate for an accessory subun	KdpC is required for proper function of the KdpFABC complex, which mediates high-affinity K+ uptake. The annotation correctly captures KdpC's involvement in the biological process of potassium ion transport. However, GO:0071805 (potassium ion transmembrane transport) is more specific and also presen	genes/DESVH/Q725T8/Q725T8-ai-review.yaml
deeper_than	combined IEA	DESVH	Q72DT2	GO:0000104	succinate dehydrogenase activity	REMOVE	GO:0016491	oxidoreductase activity	ACCEPT	AprA has the APS-reductase substrate chemistry, AprA-specific domain assignment and sulfate-reduction pathway context, rather than succinate dehydrogenation. Existing OpenScientist and Falcon reports corroborate this distinction. Their assertion that a covalent FAD-binding histidine is universally n	AprA catalyzes the reduction of APS through its FAD-containing active site. GO:0009973 provides the more specific reaction, while GO:0016491 remains a correct description of the same core catalytic work. A valid broad parent is not an over-annotation simply because a more specific enzyme term coexis	genes/DESVH/Q72DT2/Q72DT2-ai-review.yaml
deeper_than	combined IEA	DOROP	ADAR2	GO:0003725	double-stranded RNA binding	ACCEPT	GO:0003723	RNA binding	ACCEPT	dsRNA binding is a core molecular function of sqADAR2, demonstrated directly using recombinant protein with quantitative binding assays. The three dsRBD architecture of sqADAR2a is a defining and unique feature of this enzyme. This is at the right level of specificity for the binding function.	RNA binding is required for engagement of the duplex RNA substrate by the ADAR2 dsRNA-binding domains; it describes direct molecular work in editing. The broad RNA-binding term is entailed by directly supported dsRNA binding. It is part of the core substrate-recognition mechanism, not peripheral sim	genes/DOROP/ADAR2/ADAR2-ai-review.yaml
deeper_than	combined IEA	DOROP	ADAR2	GO:0005730	nucleolus	UNDECIDED	GO:0005634	nucleus	ACCEPT	Retain UNDECIDED because the available squid localization evidence resolves nucleus versus cytoplasm but not nucleolus. Vertebrate nucleolar localization can support a phylogenetic hypothesis; missing target-specific microscopy alone is not a refutation. An explicit comparison of nucleolar-targeting	Nuclear localization is well-supported for ADAR2 enzymes generally, as co-transcriptional editing of pre-mRNAs occurs in the nucleus. While sqADAR2 is also found in the cytoplasm, nuclear localization remains valid.	genes/DOROP/ADAR2/ADAR2-ai-review.yaml
deeper_than	combined IEA	EMENI	sfgA	GO:0045944	positive regulation of transcription by RNA polymerase II	MARK_AS_OVER_ANNOTATED	GO:0006355	regulation of DNA-templated transcription	ACCEPT	This is an IEA:TreeGrafter propagation from the PTHR37534 zinc-cluster family (whose named member is the transcriptional *activator* Uga3), not an SfgA-specific inference. The primary characterization of sfgA shows the opposite direction - loss of sfgA bypasses fluG and derepresses conidiation, and 	Generic unsigned process parent. SfgA's characterised role is repression relieved by FluG signalling, so a signed negative-regulation term would be more informative than this one.	genes/EMENI/sfgA/sfgA-ai-review.yaml
deeper_than	combined IEA	FELCA	ALB	GO:0072562	blood microparticle	KEEP_AS_NON_CORE	GO:0005576	extracellular region	ACCEPT	Plausible plasma-derived localization; not a distinguishing functional compartment.	Albumin functions in blood plasma (extracellular region).	genes/FELCA/ALB/ALB-ai-review.yaml
deeper_than	combined IEA	FELCA	CSTA	GO:0005829	cytosol	ACCEPT	GO:0005737	cytoplasm	ACCEPT	Consistent with documented cytoplasmic/cytosolic localization.	Directly supported by the curated subcellular location.	genes/FELCA/CSTA/CSTA-ai-review.yaml
deeper_than	combined IEA	FUSNU	pepV	GO:0008777	acetylornithine deacetylase activity	REMOVE	GO:0016787	hydrolase activity	MARK_AS_OVER_ANNOTATED	"PTHR43808 spans several catalytically distinct M20A subfamilies. The acetylornithine deacetylase (ArgE) function belongs to a different subfamily from PepV dipeptidases. Because the protein carries PepV-specific CDD/TIGRFAM/InterPro signatures and is named ""Putative dipeptidase PepV,"" the acetylorni"	GO:0016787 (hydrolase activity) is not wrong, but it is far too general for a protein whose family identity supports the specific dipeptidase activity (GO:0016805) and metallopeptidase activity (GO:0008237). Per curation best practice, prefer the most specific defensible term; the specific terms are	genes/FUSNU/pepV/pepV-ai-review.yaml
deeper_than	combined IEA	HETGA	Cd44	GO:0016323	basolateral plasma membrane	KEEP_AS_NON_CORE	GO:0005886	plasma membrane	ACCEPT	A polarity-specific sub-compartment claim that applies only in polarised epithelia and has no naked mole-rat support. It sits alongside an apical plasma membrane annotation projected from a different human study, and the two cannot both be the general case; of the pair, the basolateral assignment is	Supported by three independent strands: the UniProt subcellular-location statement for this entry, the transmembrane helix in its own feature table, and the functional requirement that a cell-impermeant blocking antibody reach the receptor on living naked mole-rat cells. Note that the plasma membran	genes/HETGA/Cd44/Cd44-ai-review.yaml
deeper_than	combined IEA	METEA	ackA	GO:0005829	cytosol	ACCEPT	GO:0005737	cytoplasm	KEEP_AS_NON_CORE			genes/METEA/ackA/ackA-ai-review.yaml
deeper_than	combined IEA	METEA	glyA	GO:0005829	cytosol	ACCEPT	GO:0005737	cytoplasm	ACCEPT			genes/METEA/glyA/glyA-ai-review.yaml
deeper_than	combined IEA	METEA	mdh	GO:0004459	L-lactate dehydrogenase (NAD+) activity	REMOVE	GO:0016491	oxidoreductase activity	KEEP_AS_NON_CORE			genes/METEA/mdh/mdh-ai-review.yaml
deeper_than	combined IEA	METEA	mxbM	GO:0000976	transcription cis-regulatory region binding	KEEP_AS_NON_CORE	GO:0003677	DNA binding	ACCEPT			genes/METEA/mxbM/mxbM-ai-review.yaml
deeper_than	combined IEA	METEA	pckA	GO:0005829	cytosol	ACCEPT	GO:0005737	cytoplasm	KEEP_AS_NON_CORE			genes/METEA/pckA/pckA-ai-review.yaml
deeper_than	combined IEA	NICAT	NaBGL1_candidate_BGLU18_6	GO:0008422	beta-glucosidase activity	ACCEPT	GO:0004553	hydrolase activity, hydrolyzing O-glycosyl compounds	MODIFY	UniProt and GH1 family assignment support beta-glucosidase chemistry, and the pathway paper makes beta-GD1 the late nicotine hydrolase.	GO:0008422 captures the relevant GH1 catalytic specificity more directly.	genes/NICAT/NaBGL1_candidate_BGLU18_6/NaBGL1_candidate_BGLU18_6-ai-review.yaml
deeper_than	combined IEA	NICAT	NaBGL2_candidate_BGLU18_1	GO:0008422	beta-glucosidase activity	ACCEPT	GO:0004553	hydrolase activity, hydrolyzing O-glycosyl compounds	MODIFY	UniProt and GH1 family assignment support beta-glucosidase chemistry for this beta-GD2-like candidate.	GO:0008422 is the more informative GH1 activity term for this candidate.	genes/NICAT/NaBGL2_candidate_BGLU18_1/NaBGL2_candidate_BGLU18_1-ai-review.yaml
deeper_than	combined IEA	PSEAI	merA	GO:0003955	NAD(P)H dehydrogenase (quinone) activity	REMOVE	GO:0016491	oxidoreductase activity	KEEP_AS_NON_CORE	Wrong electron acceptor, not merely a coarse term. GO:0003955 is defined as NAD(P)H + H+ + a quinone = NAD(P)+ + a quinol; MerA catalyzes Hg(2+) + NADPH = Hg(0) + NADP+ + H+ (EC 1.16.1.1, RHEA:23856), experimentally characterized in PubMed:6412751, with reduction proceeding through a redox-active ac	Too general - more specific mercury reductase term available	genes/PSEAI/merA/merA-ai-review.yaml
deeper_than	combined IEA	PSEPK	PP_3394	GO:0004419	hydroxymethylglutaryl-CoA lyase activity	REMOVE	GO:0016833	oxo-acid-lyase activity	UNDECIDED	The focused paralog analysis resolved the conflict left by the first pass. PP_3394 retains the DRE-TIM catalytic core but fails the HMG-CoA-lyase-specific PROSITE signature and carries an isopropylmalate/homocitrate-synthase-like motif, whereas MvaB/PP_3540 is an ortholog-level match to the experime	GO:0016833 specifies nonhydrolytic, nonoxidative C-C cleavage of a 3-hydroxy acid (QuickGO definition checked 2026-09-20). HMG-CoA cleavage fits, whereas a synthase-family assignment alone does not establish this cleavage activity. This uncertainty is about chemistry, not excessive generality.	genes/PSEPK/PP_3394/PP_3394-ai-review.yaml
deeper_than	combined IEA	PSEPK	PP_3571	GO:0008777	acetylornithine deacetylase activity	MODIFY	GO:0016787	hydrolase activity	KEEP_AS_NON_CORE	Re-reviewed after a blinded OpenScientist control run (file:PSEPK/PP_3571/PP_3571-hypotheses/function-hypothesis-go-0008777/openscientist.md). The run and a local re-computation agree on the facts: (i) all seven E. coli ArgE (P23908) active-site and Zn-ligand residues (H80, D82, D112, E144, E145, E1	This broad chemistry remains credible even though the physiological substrate is unresolved.	genes/PSEPK/PP_3571/PP_3571-ai-review.yaml
deeper_than	combined IEA	PSEPK	accD	GO:0009329	acetate CoA-transferase complex	ACCEPT	GO:0005737	cytoplasm	ACCEPT	"The rejection recorded here read the term's label rather than its definition. GO defines GO:0009329 as ""A heterotetrameric enzyme complex made up of two alpha subunits and two beta subunits. Part of the acetyl-CoA carboxylase complex. Catalyzes the transfer of a carboxyl group to form malonyl-CoA"" -"	The reviewed UniProt record places AccD in the cytoplasm.	genes/PSEPK/accD/accD-ai-review.yaml
deeper_than	combined IEA	PSEPK	acpP	GO:0005829	cytosol	ACCEPT	GO:0005737	cytoplasm	MARK_AS_OVER_ANNOTATED	Cytosol is the more specific existing annotation and is consistent with UniProt's cytoplasmic localization and the absence of membrane or secretion features.	The existing cytosol annotation is the more specific location for this soluble bacterial protein, so retaining both parent and child adds no information.	genes/PSEPK/acpP/acpP-ai-review.yaml
deeper_than	combined IEA	PSEPK	ahcY	GO:0005829	cytosol	ACCEPT	GO:0005737	cytoplasm	KEEP_AS_NON_CORE	The protein is annotated as cytoplasmic in UniProt and lacks targeting or membrane features; GO:0005829 captures the soluble cytoplasmic compartment.	UniProt explicitly supports cytoplasmic localization. The annotation is valid but redundant with the more specific cytosol annotation already present from an independent source, so it is retained as non-core rather than replaced by a duplicate GO:0005829 annotation.	genes/PSEPK/ahcY/ahcY-ai-review.yaml
deeper_than	combined IEA	PSEPK	ahpC	GO:0005829	cytosol	ACCEPT	GO:0005737	cytoplasm	ACCEPT	The current cytosol definition excludes organelles but includes soluble proteins and protein complexes. It applies to bacteria; the existing cytoplasm annotation does not justify replacing this correct, more specific localization.	The available evidence supports AhpC as a soluble cytoplasmic protein.	genes/PSEPK/ahpC/ahpC-ai-review.yaml
deeper_than	combined IEA	PSEPK	ahpC	GO:0008379	thioredoxin peroxidase activity	MODIFY	GO:0004601	peroxidase activity	ACCEPT	QuickGO checked on 2026-09-20 marks GO:0008379 obsolete; preserve the source GOA identifier and refine its review to the active peroxiredoxin term. Independently, the existing reports support a typical AhpC/AhpF system and distinguish its immediate protein reductant from free thioredoxin. Their dono	Peroxiredoxin activity is peroxidase activity. The broad parent does not become wrong because the catalytic subfamily is known.	genes/PSEPK/ahpC/ahpC-ai-review.yaml
deeper_than	combined IEA	PSEPK	ahpC	GO:0008379	thioredoxin peroxidase activity	MODIFY	GO:0051920	peroxiredoxin activity	ACCEPT	QuickGO checked on 2026-09-20 marks GO:0008379 obsolete; preserve the source GOA identifier and refine its review to the active peroxiredoxin term. Independently, the existing reports support a typical AhpC/AhpF system and distinguish its immediate protein reductant from free thioredoxin. Their dono	This term captures the core catalytic identity of the protein without overcommitting to donor-specific chemistry at the single-gene-product level.	genes/PSEPK/ahpC/ahpC-ai-review.yaml
deeper_than	combined IEA	PSEPK	alaS	GO:0005829	cytosol	KEEP_AS_NON_CORE	GO:0005737	cytoplasm	KEEP_AS_NON_CORE	Retain as non-core because TreeGrafter supplies no independent target-level localization experiment.	The location is biologically coherent but is not the catalytic function and lacks direct KT2440 localization evidence.	genes/PSEPK/alaS/alaS-ai-review.yaml
deeper_than	combined IEA	PSEPK	amaC	GO:0004838	L-tyrosine:2-oxoglutarate transaminase activity	ACCEPT	GO:0008483	transaminase activity	KEEP_AS_NON_CORE	Best-supported molecular function. The protein has a class-I PLP aminotransferase domain, belongs to the PANTHER aromatic-amino-acid aminotransferase subfamily, and local KT2440 functional data support reannotation of AmaC as an L-Tyr aminotransferase.	Correct parent term, but less specific than the L-tyrosine/aromatic aminotransferase activity that represents the core function.	genes/PSEPK/amaC/amaC-ai-review.yaml
deeper_than	combined IEA	PSEPK	argH	GO:0005829	cytosol	KEEP_AS_NON_CORE	GO:0005737	cytoplasm	KEEP_AS_NON_CORE	The location is electronically propagated and compatible with ArgH chemistry, but it is secondary to the catalytic reaction.	UniProt/HAMAP explicitly assigns ArgH to the cytoplasm. The location is valid but secondary to the substrate-specific catalytic reaction.	genes/PSEPK/argH/argH-ai-review.yaml
deeper_than	combined IEA	PSEPK	aroK	GO:0005829	cytosol	ACCEPT	GO:0005737	cytoplasm	ACCEPT	Accurate and slightly more specific localization than GO:0005737; both are appropriate for this enzyme.	Correct localization for a cytoplasmic biosynthetic enzyme; consistent with the cytosol annotation below.	genes/PSEPK/aroK/aroK-ai-review.yaml
deeper_than	combined IEA	PSEPK	bioB	GO:0051537	2 iron, 2 sulfur cluster binding	KEEP_AS_NON_CORE	GO:0051536	iron-sulfur cluster binding	MARK_AS_OVER_ANNOTATED	The reviewed UniProt record assigns one 2Fe-2S cluster coordinated by three cysteines and one arginine.	UniProt assigns both a 4Fe-4S radical-SAM cluster and an auxiliary 2Fe-2S cluster.	genes/PSEPK/bioB/bioB-ai-review.yaml
deeper_than	combined IEA	PSEPK	clpB	GO:0034605	cellular response to heat	ACCEPT	GO:0009408	response to heat	KEEP_AS_NON_CORE		This is the broad parent of the more specific 'cellular response to heat' (GO:0034605) that is also annotated; the specific child is retained as core while this parent is kept as non-core for consistency with parent-child handling elsewhere.	genes/PSEPK/clpB/clpB-ai-review.yaml
deeper_than	combined IEA	PSEPK	cysS	GO:0005829	cytosol	KEEP_AS_NON_CORE	GO:0005737	cytoplasm	KEEP_AS_NON_CORE	TreeGrafter IEA; not a defining activity.	HAMAP-rule-based localization IEA.	genes/PSEPK/cysS/cysS-ai-review.yaml
deeper_than	combined IEA	PSEPK	dapA__Q88NH2	GO:0005829	cytosol	KEEP_AS_NON_CORE	GO:0005737	cytoplasm	KEEP_AS_NON_CORE	Relaxed from MARK_AS_OVER_ANNOTATED on re-review, per the rule that broad-but-true terms are not over-annotations. DapA-I (PP_1237) is a soluble cytoplasmic enzyme with no signal peptide, transmembrane segment or lipobox, so the cytosol is where it resides; carrying the broader cytoplasm term on ano	The location is supported but is secondary to the reaction.	genes/PSEPK/dapA__Q88NH2/dapA__Q88NH2-ai-review.yaml
deeper_than	combined IEA	PSEPK	dapB	GO:0005829	cytosol	KEEP_AS_NON_CORE	GO:0005737	cytoplasm	KEEP_AS_NON_CORE	Relaxed from MARK_AS_OVER_ANNOTATED on re-review, per the rule that broad-but-true terms are not over-annotations. DapB is a soluble cytoplasmic enzyme with no signal peptide, transmembrane segment or lipobox, so the cytosol is where it resides; carrying the broader cytoplasm term on another row mak	The location is valid but secondary to the reaction.	genes/PSEPK/dapB/dapB-ai-review.yaml
deeper_than	combined IEA	PSEPK	dapE	GO:0008777	acetylornithine deacetylase activity	REMOVE	GO:0016787	hydrolase activity	MARK_AS_OVER_ANNOTATED	Q88MP5 is assigned to the proteobacterial DapE subfamily and EC 3.5.1.18; no evidence supports acetylornithine as its physiological substrate.	GO:0009014 captures the substrate-specific reaction.	genes/PSEPK/dapE/dapE-ai-review.yaml
deeper_than	combined IEA	PSEPK	dapF__Q88CF3	GO:0005829	cytosol	KEEP_AS_NON_CORE	GO:0005737	cytoplasm	KEEP_AS_NON_CORE	Relaxed from MARK_AS_OVER_ANNOTATED on re-review, per the rule that broad-but-true terms are not over-annotations. DapF (Q88CF3, PP_5228) is a soluble cytoplasmic enzyme with no signal peptide, transmembrane segment or lipobox, so the cytosol is where it resides; carrying the broader cytoplasm term 	The location is valid but secondary to the substrate-specific reaction.	genes/PSEPK/dapF__Q88CF3/dapF__Q88CF3-ai-review.yaml
deeper_than	combined IEA	PSEPK	dapF__Q88GD4	GO:0005829	cytosol	KEEP_AS_NON_CORE	GO:0005737	cytoplasm	KEEP_AS_NON_CORE	Relaxed from MARK_AS_OVER_ANNOTATED on re-review, per the rule that broad-but-true terms are not over-annotations. DapF (Q88GD4, PP_3790) is a soluble cytoplasmic enzyme with no signal peptide, transmembrane segment or lipobox, so the cytosol is where it resides; carrying the broader cytoplasm term 	The location is valid but secondary to the substrate-specific reaction.	genes/PSEPK/dapF__Q88GD4/dapF__Q88GD4-ai-review.yaml
deeper_than	combined IEA	PSEPK	davA	GO:0050126	N-carbamoylputrescine amidase activity	REMOVE	GO:0016787	hydrolase activity	MARK_AS_OVER_ANNOTATED	GO:0050126 is defined as hydrolysis of N-carbamoylputrescine to putrescine, CO2 and ammonium, the carbamoyl-amide step of the agmatine route to putrescine. Q88QV2 is the Dav-pathway enzyme that hydrolyses the simple amide 5-aminopentanamide to 5-aminovalerate, the reaction captured by GO:0047588 on 	The enzyme-specific 5-aminopentanamidase activity is available and captures the physiological reaction.	genes/PSEPK/davA/davA-ai-review.yaml
deeper_than	combined IEA	PSEPK	davA	GO:0050126	N-carbamoylputrescine amidase activity	REMOVE	GO:0016811	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides	MARK_AS_OVER_ANNOTATED	GO:0050126 is defined as hydrolysis of N-carbamoylputrescine to putrescine, CO2 and ammonium, the carbamoyl-amide step of the agmatine route to putrescine. Q88QV2 is the Dav-pathway enzyme that hydrolyses the simple amide 5-aminopentanamide to 5-aminovalerate, the reaction captured by GO:0047588 on 	GO:0047588 identifies the actual linear amide substrate and should carry the core function.	genes/PSEPK/davA/davA-ai-review.yaml
deeper_than	combined IEA	PSEPK	ddlA	GO:0005829	cytosol	KEEP_AS_NON_CORE	GO:0005737	cytoplasm	ACCEPT	DdlA is a soluble ATP-grasp ligase with no transmembrane segment, and UniProt records a cytoplasmic subcellular location (HAMAP-Rule MF_00047), so the TreeGrafter cytosol call is true rather than an over-annotation. Redundancy with the parent cytoplasm term is not grounds for rejection; the location	The reviewed UniProt record assigns Q88EV6 to the cytoplasm.	genes/PSEPK/ddlA/ddlA-ai-review.yaml
deeper_than	combined IEA	PSEPK	dinB	GO:0005829	cytosol	KEEP_AS_NON_CORE	GO:0005737	cytoplasm	ACCEPT	Pol IV is a soluble monomer with a UniProt cytoplasmic subcellular location and no membrane or nucleoid-restricted architecture, so the TreeGrafter cytosol call is true rather than an over-annotation; a bacterial cell has no organelles to exclude, and redundancy with the parent cytoplasm term is not	UniProt records cytoplasmic localization, appropriate for a bacterial DNA polymerase.	genes/PSEPK/dinB/dinB-ai-review.yaml
deeper_than	combined IEA	PSEPK	fadB	GO:0016509	long-chain (3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity	ACCEPT	GO:0003857	(3S)-3-hydroxyacyl-CoA dehydrogenase (NAD+) activity	ACCEPT	Retain as the most specific dehydrogenase annotation.	Retain as a core beta-oxidation enzymatic activity.	genes/PSEPK/fadB/fadB-ai-review.yaml
deeper_than	combined IEA	PSEPK	fbp	GO:0005829	cytosol	ACCEPT	GO:0005737	cytoplasm	KEEP_AS_NON_CORE	The cytosol term is consistent with the UniProt cytoplasm localization and is the appropriate specific compartment for this soluble metabolic enzyme.	The localization is correct but the more specific term cytosol (GO:0005829) is also present, making this broader cytoplasm term redundant as a distinct annotation.	genes/PSEPK/fbp/fbp-ai-review.yaml
deeper_than	combined IEA	PSEPK	flgE	GO:0009424	bacterial-type flagellum hook	ACCEPT	GO:0009288	bacterial-type flagellum	ACCEPT			genes/PSEPK/flgE/flgE-ai-review.yaml
deeper_than	combined IEA	PSEPK	flgG	GO:0071978	bacterial-type flagellum-dependent swarming motility	KEEP_AS_NON_CORE	GO:0071973	bacterial-type flagellum-dependent cell motility	KEEP_AS_NON_CORE	GO:0071978 is a child of GO:0071973 bacterial-type flagellum-dependent cell motility, and FlgG polymerizes into the distal rod that transmits motor torque across the periplasm to the hook, so a cell lacking FlgG has no working flagellum and cannot swarm. The term is therefore true rather than false;	Correct downstream process; rod assembly is the direct role.	genes/PSEPK/flgG/flgG-ai-review.yaml
deeper_than	combined IEA	PSEPK	fur	GO:0045892	negative regulation of DNA-templated transcription	ACCEPT	GO:0006355	regulation of DNA-templated transcription	KEEP_AS_NON_CORE	Repression is the canonical and best-supported activity of Fur; UniProt also carries the Repressor keyword.	Correct but general relative to GO:0045892 (negative regulation of DNA-templated transcription). Retained as a broader supporting process term.	genes/PSEPK/fur/fur-ai-review.yaml
deeper_than	combined IEA	PSEPK	galE	GO:0033499	beta-D-galactose catabolic process via UDP-galactose, Leloir pathway	REMOVE	GO:0006012	galactose metabolic process	KEEP_AS_NON_CORE	This electronic propagation assigns a complete catabolic pathway that is not satisfiable in KT2440: the proteome lacks identifiable GalK and GalT, while GalE is supported as an anabolic nucleotide-sugar epimerase.	Retain this broad substrate-level context without implying that KT2440 has a complete galactose-catabolic route.	genes/PSEPK/galE/galE-ai-review.yaml
deeper_than	combined IEA	PSEPK	glk	GO:0005829	cytosol	ACCEPT	GO:0005737	cytoplasm	MODIFY	Specific and biologically appropriate localization term.	Cytoplasm is broader than needed for a soluble bacterial enzyme.	genes/PSEPK/glk/glk-ai-review.yaml
deeper_than	combined IEA	PSEPK	glnS	GO:0005829	cytosol	ACCEPT	GO:0005737	cytoplasm	KEEP_AS_NON_CORE	The bacterial soluble compartment is supported by UniProt; no membrane or export feature is present.	The reviewed entry supports a soluble intracellular location, while GO:0005829 records it more specifically.	genes/PSEPK/glnS/glnS-ai-review.yaml
deeper_than	combined IEA	PSEPK	glpD	GO:0046168	glycerol-3-phosphate catabolic process	ACCEPT	GO:0006072	glycerol-3-phosphate metabolic process	KEEP_AS_NON_CORE	This is the specific core biological process.	The directional glycerol-3-phosphate catabolic term is more informative.	genes/PSEPK/glpD/glpD-ai-review.yaml
deeper_than	combined IEA	PSEPK	glpF	GO:0005886	plasma membrane	ACCEPT	GO:0016020	membrane	MARK_AS_OVER_ANNOTATED	This is the specific membrane location of the glycerol channel.	Retain the specific GO:0005886 localization as core.	genes/PSEPK/glpF/glpF-ai-review.yaml
deeper_than	combined IEA	PSEPK	gltX	GO:0005829	cytosol	ACCEPT	GO:0005737	cytoplasm	KEEP_AS_NON_CORE	The protein is a soluble monomer with no membrane or export feature.	The reviewed entry assigns GltX to the cytoplasm, while GO:0005829 more precisely captures the soluble compartment used in the core function.	genes/PSEPK/gltX/gltX-ai-review.yaml
deeper_than	combined IEA	PSEPK	glyQ	GO:0005829	cytosol	KEEP_AS_NON_CORE	GO:0005737	cytoplasm	KEEP_AS_NON_CORE	Localization is compatible with the role but is not a defining function.	Localization is compatible with the role but is not a defining function.	genes/PSEPK/glyQ/glyQ-ai-review.yaml
deeper_than	combined IEA	PSEPK	glyS	GO:0005829	cytosol	KEEP_AS_NON_CORE	GO:0005737	cytoplasm	KEEP_AS_NON_CORE	Localization is compatible with the role but is not a defining function.	Localization is compatible with the role but is not a defining function.	genes/PSEPK/glyS/glyS-ai-review.yaml
deeper_than	combined IEA	PSEPK	gpsA	GO:0005829	cytosol	KEEP_AS_NON_CORE	GO:0005737	cytoplasm	ACCEPT	Consistent with the UniProt cytoplasm assignment; retained as a non-core location annotation.	GpsA is a soluble cytoplasmic enzyme; the UniProt record explicitly assigns it to the cytoplasm.	genes/PSEPK/gpsA/gpsA-ai-review.yaml
deeper_than	combined IEA	PSEPK	gpsA	GO:0046474	glycerophospholipid biosynthetic process	ACCEPT	GO:0006650	glycerophospholipid metabolic process	KEEP_AS_NON_CORE	G3P is described as the key precursor for phospholipid synthesis, and the UniPathway assignment is glycerophospholipid metabolism.	A correct parent process; the specific glycerophospholipid biosynthetic process term better represents the gene's role.	genes/PSEPK/gpsA/gpsA-ai-review.yaml
deeper_than	combined IEA	PSEPK	grpE	GO:0005829	cytosol	ACCEPT	GO:0005737	cytoplasm	ACCEPT	Correct and slightly more specific localization than the cytoplasm annotation. Both are biologically appropriate for GrpE; retaining the more specific cytosol term is reasonable.	Correct subcellular localization for a bacterial DnaK cofactor. Consistent with HAMAP rule and with the cytosolic localization of its DnaK/DnaJ partners.	genes/PSEPK/grpE/grpE-ai-review.yaml
deeper_than	combined IEA	PSEPK	hemE	GO:0005829	cytosol	ACCEPT	GO:0005737	cytoplasm	MARK_AS_OVER_ANNOTATED	The TreeGrafter cytosol call is consistent with UniProt's cytoplasm assignment and avoids retaining both a child term and its broader parent as equivalent annotations.	The more specific cytosol annotation is also present and supported for this soluble enzyme, making cytoplasm redundant as a distinct retained annotation.	genes/PSEPK/hemE/hemE-ai-review.yaml
deeper_than	combined IEA	PSEPK	hmp	GO:0071500	cellular response to nitrosative stress	ACCEPT	GO:0051409	response to nitrosative stress	KEEP_AS_NON_CORE	Specific and accurate; reflects the inducible intracellular response to nitrosative stress.	This is the broad parent of the more specific 'cellular response to nitrosative stress' (GO:0071500) that is also annotated; the specific child is retained as core while this parent is kept as non-core, consistent with parent-child handling elsewhere in this batch.	genes/PSEPK/hmp/hmp-ai-review.yaml
deeper_than	combined IEA	PSEPK	ileS	GO:0005829	cytosol	KEEP_AS_NON_CORE	GO:0005737	cytoplasm	KEEP_AS_NON_CORE	Localization is compatible with the role but is not a defining function.	Localization is compatible with the role but is not a defining function.	genes/PSEPK/ileS/ileS-ai-review.yaml
deeper_than	combined IEA	PSEPK	infA	GO:0005829	cytosol	ACCEPT	GO:0005737	cytoplasm	KEEP_AS_NON_CORE	The UniProt cytoplasmic assignment and soluble 30S-complex role support a cytosolic location.	GO:0005737 is a correct, directly supported broad location for the soluble factor. It is retained as non-core because the same GOA set already contains the more specific GO:0005829 cytosol annotation.	genes/PSEPK/infA/infA-ai-review.yaml
deeper_than	combined IEA	PSEPK	infB	GO:0005829	cytosol	ACCEPT	GO:0005737	cytoplasm	KEEP_AS_NON_CORE	UniProt assigns IF-2 to the cytoplasm and describes a soluble ribosome-associated initiation role.	GO:0005737 is a correct, directly supported broad location for soluble IF-2. It is retained as non-core because the same GOA set already contains the more specific GO:0005829 cytosol annotation.	genes/PSEPK/infB/infB-ai-review.yaml
deeper_than	combined IEA	PSEPK	infC	GO:0005829	cytosol	ACCEPT	GO:0005737	cytoplasm	KEEP_AS_NON_CORE	UniProt assigns IF-3 to the cytoplasm and describes its association with the soluble 30S ribosomal subunit.	GO:0005737 is a correct, directly supported broad location for soluble IF-3. It is retained as non-core because the same GOA set already contains the more specific GO:0005829 cytosol annotation.	genes/PSEPK/infC/infC-ai-review.yaml
deeper_than	combined IEA	PSEPK	kdpA	GO:0071805	potassium ion transmembrane transport	ACCEPT	GO:0006813	potassium ion transport	KEEP_AS_NON_CORE			genes/PSEPK/kdpA/kdpA-ai-review.yaml
deeper_than	combined IEA	PSEPK	kdpC	GO:0071805	potassium ion transmembrane transport	ACCEPT	GO:0006813	potassium ion transport	KEEP_AS_NON_CORE			genes/PSEPK/kdpC/kdpC-ai-review.yaml
deeper_than	combined IEA	PSEPK	kdpD	GO:0005886	plasma membrane	ACCEPT	GO:0016020	membrane	KEEP_AS_NON_CORE			genes/PSEPK/kdpD/kdpD-ai-review.yaml
deeper_than	combined IEA	PSEPK	kdsB	GO:0005829	cytosol	KEEP_AS_NON_CORE	GO:0005737	cytoplasm	KEEP_AS_NON_CORE	The TreeGrafter inference is biologically compatible but redundant with the retained cytoplasm row. Localization remains ancillary and cytoplasm is used once in the core-function summary.	Localization is coherent but ancillary to the exact synthetase function.	genes/PSEPK/kdsB/kdsB-ai-review.yaml
deeper_than	combined IEA	PSEPK	kguT	GO:0005886	plasma membrane	ACCEPT	GO:0016020	membrane	MARK_AS_OVER_ANNOTATED	This is the appropriate specific localization.	GO:0005886 is already present.	genes/PSEPK/kguT/kguT-ai-review.yaml
deeper_than	combined IEA	PSEPK	leuB	GO:0005829	cytosol	KEEP_AS_NON_CORE	GO:0005737	cytoplasm	KEEP_AS_NON_CORE	UniProt records LeuB as a cytoplasmic homodimeric NAD-dependent dehydrogenase with no membrane features, so cytosol is a true statement of where the soluble enzyme acts in a bacterium; the parent cytoplasm row is retained separately because it has explicit HAMAP support. Kept non-core because the co	UniProt's HAMAP annotation explicitly predicts cytoplasmic localization, so this parent row has source-specific support rather than being only a redundant ancestor of the TreeGrafter cytosol row.	genes/PSEPK/leuB/leuB-ai-review.yaml
deeper_than	combined IEA	PSEPK	leuS	GO:0005829	cytosol	KEEP_AS_NON_CORE	GO:0005737	cytoplasm	KEEP_AS_NON_CORE	This inferred localization is contextual and redundant with cytoplasm.	Localization is explicitly assigned in the reviewed record but is not a molecular function.	genes/PSEPK/leuS/leuS-ai-review.yaml
deeper_than	combined IEA	PSEPK	lolA	GO:0030288	outer membrane-bounded periplasmic space	ACCEPT	GO:0042597	periplasmic space	MARK_AS_OVER_ANNOTATED			genes/PSEPK/lolA/lolA-ai-review.yaml
deeper_than	combined IEA	PSEPK	lolC	GO:0098797	plasma membrane protein complex	ACCEPT	GO:0016020	membrane	MARK_AS_OVER_ANNOTATED			genes/PSEPK/lolC/lolC-ai-review.yaml
deeper_than	combined IEA	PSEPK	lolE	GO:0098797	plasma membrane protein complex	ACCEPT	GO:0016020	membrane	MARK_AS_OVER_ANNOTATED			genes/PSEPK/lolE/lolE-ai-review.yaml
deeper_than	combined IEA	PSEPK	lptA	GO:0030288	outer membrane-bounded periplasmic space	ACCEPT	GO:0042597	periplasmic space	KEEP_AS_NON_CORE	This taxon-appropriate periplasmic compartment matches the signal-peptide-dependent localization and LptA role.	The term is correct but redundant with outer membrane-bounded periplasmic space.	genes/PSEPK/lptA/lptA-ai-review.yaml
deeper_than	combined IEA	PSEPK	metG	GO:0005829	cytosol	KEEP_AS_NON_CORE	GO:0005737	cytoplasm	KEEP_AS_NON_CORE	The localization supports context, not the defining catalytic role.	This is a HAMAP-rule localization rather than direct localization evidence.	genes/PSEPK/metG/metG-ai-review.yaml
deeper_than	combined IEA	PSEPK	murB	GO:0005829	cytosol	KEEP_AS_NON_CORE	GO:0005737	cytoplasm	ACCEPT	MurB is a soluble FAD-dependent reductase with no transmembrane segments or signal peptide; UniProt (HAMAP MF_00037) places it in the cytoplasm, and in a bacterium with no organelles the cytosol is where a soluble cytoplasmic enzyme resides. GO:0005829 is a true descendant of the GO:0005737 cytoplas	UniProt explicitly assigns Q88LM5 to the cytoplasm.	genes/PSEPK/murB/murB-ai-review.yaml
deeper_than	combined IEA	PSEPK	nadA	GO:0005829	cytosol	ACCEPT	GO:0005737	cytoplasm	MARK_AS_OVER_ANNOTATED	Cytosol is consistent with the UniProt cytoplasmic assignment and captures NadA's soluble compartment without retaining a redundant parent annotation.	The accepted GO:0005829 child captures the soluble compartment more precisely, so the parent location adds no independent localization information.	genes/PSEPK/nadA/nadA-ai-review.yaml
deeper_than	combined IEA	PSEPK	nadA	GO:0034628	'de novo' NAD+ biosynthetic process from L-aspartate	ACCEPT	GO:0009435	NAD+ biosynthetic process	ACCEPT	NadA consumes the iminoaspartate generated from L-aspartate and supplies quinolinate to NadC.	NadA produces quinolinate in the L-aspartate de novo NAD+ route.	genes/PSEPK/nadA/nadA-ai-review.yaml
deeper_than	combined IEA	PSEPK	nadB	GO:0034628	'de novo' NAD+ biosynthetic process from L-aspartate	ACCEPT	GO:0009435	NAD+ biosynthetic process	ACCEPT	L-aspartate oxidation by NadB is the entry reaction for this de novo NAD+ biosynthetic route.	NadB supplies iminoaspartate at the first committed reaction of the L-aspartate de novo NAD+ route.	genes/PSEPK/nadB/nadB-ai-review.yaml
deeper_than	combined IEA	PSEPK	nicT	GO:0005886	plasma membrane	ACCEPT	GO:0016020	membrane	KEEP_AS_NON_CORE	UniProt describes NicT as a multi-pass membrane protein (12 predicted TM helices), and as an MFS secondary transporter it functions in the bacterial inner (cytoplasmic/plasma) membrane. The falcon deep research reaches the same conclusion from family assignment and homolog localization.	Retain the generic membrane annotation as a parent/location background term while treating GO:0005886 plasma membrane as the informative location for this inner-membrane MFS transporter.	genes/PSEPK/nicT/nicT-ai-review.yaml
deeper_than	combined IEA	PSEPK	opgG	GO:0030288	outer membrane-bounded periplasmic space	ACCEPT	GO:0042597	periplasmic space	MODIFY	UniProt places OpgG in the periplasm with an N-terminal signal peptide, and TreeGrafter provides the Gram-negative-specific periplasmic compartment term.	OpgG is a signal-peptide-bearing periplasmic protein in a Gram-negative bacterium; GO:0030288 is the more precise concurrent location term.	genes/PSEPK/opgG/opgG-ai-review.yaml
deeper_than	combined IEA	PSEPK	panC	GO:0005829	cytosol	KEEP_AS_NON_CORE	GO:0005737	cytoplasm	ACCEPT	TreeGrafter transferred the more specific cytosol term. It is not in conflict with the reviewed cytoplasmic assignment, but carrying both terms into the synthesized core function would be redundant.	UniProt explicitly assigns Q88DW8 to the cytoplasm and records no membrane or secretion feature.	genes/PSEPK/panC/panC-ai-review.yaml
deeper_than	combined IEA	PSEPK	pdxB	GO:0005829	cytosol	KEEP_AS_NON_CORE	GO:0005737	cytoplasm	KEEP_AS_NON_CORE	PdxB is a soluble NAD-dependent dehydrogenase with no transmembrane segments or signal peptide; UniProt (HAMAP MF_01825) places it in the cytoplasm, and in a bacterium the cytosol is where a soluble cytoplasmic enzyme resides. GO:0005829 is a true descendant of the GO:0005737 row kept as non-core; r	Cytoplasm is appropriate bacterial context but is not the core function.	genes/PSEPK/pdxB/pdxB-ai-review.yaml
deeper_than	combined IEA	PSEPK	pdxH	GO:0042823	pyridoxal 5'-phosphate biosynthetic process	ACCEPT	GO:0042816	vitamin B6 metabolic process	KEEP_AS_NON_CORE	This is the immediate product-forming step of PLP biosynthesis.	The broader process accurately spans both physiological contexts, but the specific de novo and salvage processes are more informative.	genes/PSEPK/pdxH/pdxH-ai-review.yaml
deeper_than	combined IEA	PSEPK	pdxJ	GO:0005829	cytosol	KEEP_AS_NON_CORE	GO:0005737	cytoplasm	KEEP_AS_NON_CORE	"GO:0005829 cytosol is ""the part of the cytoplasm that does not contain organelles""; UniProt records SUBCELLULAR LOCATION Cytoplasm (HAMAP-Rule MF_00279) for PdxJ, which has no transmembrane segments and forms a soluble TIM-barrel octamer. A broad but true location is not an over-annotation, and redu"	Cytoplasm is appropriate context but is not the core function.	genes/PSEPK/pdxJ/pdxJ-ai-review.yaml
deeper_than	combined IEA	PSEPK	pgi1	GO:0005829	cytosol	ACCEPT	GO:0005737	cytoplasm	ACCEPT	Consistent with the soluble cytoplasmic nature of the enzyme; the more specific cytosol term is acceptable alongside cytoplasm.	Cytoplasmic localization is appropriate for a soluble central carbohydrate-metabolism enzyme and is supported by the curated UniProt subcellular location.	genes/PSEPK/pgi1/pgi1-ai-review.yaml
deeper_than	combined IEA	PSEPK	pgi2	GO:0005829	cytosol	ACCEPT	GO:0005737	cytoplasm	ACCEPT	This is a specific, biologically appropriate annotation for this gene product.	This is a specific, biologically appropriate annotation for this gene product.	genes/PSEPK/pgi2/pgi2-ai-review.yaml
deeper_than	combined IEA	PSEPK	pgk	GO:0005829	cytosol	ACCEPT	GO:0005737	cytoplasm	KEEP_AS_NON_CORE			genes/PSEPK/pgk/pgk-ai-review.yaml
deeper_than	combined IEA	PSEPK	pgsA	GO:0005886	plasma membrane	ACCEPT	GO:0016020	membrane	KEEP_AS_NON_CORE	UniProt assigns PgsA to the membrane as a multi-pass membrane protein and Phobius predicts four transmembrane helices. In a Gram-negative bacterium the glycerophospholipid biosynthetic machinery operates in the inner (plasma) membrane, and lipidomics of Pseudomonas putida confirms that phosphatidylg	Retain as non-core localization context alongside plasma membrane.	genes/PSEPK/pgsA/pgsA-ai-review.yaml
deeper_than	combined IEA	PSEPK	pgsA	GO:0046474	glycerophospholipid biosynthetic process	ACCEPT	GO:0008654	phospholipid biosynthetic process	KEEP_AS_NON_CORE	PgsA performs a committed phosphatidylglycerol/glycerophospholipid biosynthetic reaction.	Retain as non-core context while using glycerophospholipid biosynthetic process as the pathway-level core process.	genes/PSEPK/pgsA/pgsA-ai-review.yaml
deeper_than	combined IEA	PSEPK	pheT	GO:0009328	phenylalanine-tRNA ligase complex	ACCEPT	GO:0005737	cytoplasm	KEEP_AS_NON_CORE	The reviewed record explicitly describes a tetramer containing two alpha and two beta subunits.	The reviewed record explicitly assigns cytoplasmic localization, although by HAMAP rule.	genes/PSEPK/pheT/pheT-ai-review.yaml
deeper_than	combined IEA	PSEPK	pncB	GO:0034355	NAD+ biosynthetic process via the salvage pathway	ACCEPT	GO:0009435	NAD+ biosynthetic process	ACCEPT	Phosphoribosylation of available nicotinate to NaMN is the defining entry step of the Preiss-Handler salvage route.	PncB supplies NaMN for conversion to NAD+ by NadD and NadE.	genes/PSEPK/pncB/pncB-ai-review.yaml
deeper_than	combined IEA	PSEPK	proB	GO:0005829	cytosol	KEEP_AS_NON_CORE	GO:0005737	cytoplasm	ACCEPT	Keep as compatible automated localization, but use one cytoplasmic location in the core-function summary.	UniProt records cytoplasmic localization for ProB.	genes/PSEPK/proB/proB-ai-review.yaml
deeper_than	combined IEA	PSEPK	proS	GO:0005829	cytosol	KEEP_AS_NON_CORE	GO:0005737	cytoplasm	KEEP_AS_NON_CORE	Localization is contextual rather than defining.	The evidence is a HAMAP family rule rather than direct localization.	genes/PSEPK/proS/proS-ai-review.yaml
deeper_than	combined IEA	PSEPK	purM	GO:0005829	cytosol	ACCEPT	GO:0005737	cytoplasm	ACCEPT	The target UniProt record assigns cytoplasmic localization through HAMAP MF_00741, and the standalone soluble AIR-synthetase architecture and conserved intracellular purine pathway support the inference. A direct localization assay is not required to retain a sound family-based location, and breadth	The target UniProt record assigns cytoplasmic localization through HAMAP MF_00741, and the standalone soluble AIR-synthetase architecture and conserved intracellular purine pathway support the inference. A direct localization assay is not required to retain a sound family-based location, and breadth	genes/PSEPK/purM/purM-ai-review.yaml
deeper_than	combined IEA	PSEPK	putP	GO:0015193	L-proline transmembrane transporter activity	MODIFY	GO:0022857	transmembrane transporter activity	MODIFY	The exact record establishes the transported substrate and sodium coupling, captured together by GO:0005298.	PutP has a defined L-proline substrate and sodium coupling, both captured by GO:0005298.	genes/PSEPK/putP/putP-ai-review.yaml
deeper_than	combined IEA	PSEPK	pvdD	GO:0009239	enterobactin biosynthetic process	MODIFY	GO:0044550	secondary metabolite biosynthetic process	ACCEPT	The enterobactin process is an over-transfer error. Falcon deep research confirms PvdD is the pyoverdine NRPS in KT2440 and that a pvdD mutant does not produce pyoverdine, so the correct process is pyoverdine biosynthesis, not enterobactin.	Pyoverdine is a secondary metabolite and PvdD directly builds its peptide scaffold. The broad process is valid; a siderophore-specific term does not contradict it.	genes/PSEPK/pvdD/pvdD-ai-review.yaml
deeper_than	combined IEA	PSEPK	pydB	GO:0016812	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides	KEEP_AS_NON_CORE	GO:0016810	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds	KEEP_AS_NON_CORE	Correct but less informative than GO:0004157.	Retain as a correct reaction-class parent of the specific activity.	genes/PSEPK/pydB/pydB-ai-review.yaml
deeper_than	combined IEA	PSEPK	rbsD	GO:0005829	cytosol	ACCEPT	GO:0005737	cytoplasm	KEEP_AS_NON_CORE			genes/PSEPK/rbsD/rbsD-ai-review.yaml
deeper_than	combined IEA	PSEPK	rbsD	GO:0016866	intramolecular transferase activity	KEEP_AS_NON_CORE	GO:0016853	isomerase activity	KEEP_AS_NON_CORE			genes/PSEPK/rbsD/rbsD-ai-review.yaml
deeper_than	combined IEA	PSEPK	rbsK	GO:0005829	cytosol	ACCEPT	GO:0005737	cytoplasm	KEEP_AS_NON_CORE			genes/PSEPK/rbsK/rbsK-ai-review.yaml
deeper_than	combined IEA	PSEPK	rbsR	GO:0000976	transcription cis-regulatory region binding	ACCEPT	GO:0003677	DNA binding	KEEP_AS_NON_CORE			genes/PSEPK/rbsR/rbsR-ai-review.yaml
deeper_than	combined IEA	PSEPK	recA	GO:0005829	cytosol	ACCEPT	GO:0005737	cytoplasm	ACCEPT	Appropriate, more specific localization consistent with the cytoplasmic location and PANTHER tree-based transfer.	Consistent with the UniProt subcellular location (Cytoplasm) and the nature of RecA as a soluble DNA-acting protein. Cytosol (GO:0005829) is the more specific term.	genes/PSEPK/recA/recA-ai-review.yaml
deeper_than	combined IEA	PSEPK	rhlB	GO:0005829	cytosol	ACCEPT	GO:0005737	cytoplasm	KEEP_AS_NON_CORE	Cytosol is the more specific of the two nested soluble-compartment annotations.	Cytoplasm is correct but broader than the accompanying cytosol annotation.	genes/PSEPK/rhlB/rhlB-ai-review.yaml
deeper_than	combined IEA	PSEPK	rhlE	GO:0005829	cytosol	ACCEPT	GO:0005737	cytoplasm	KEEP_AS_NON_CORE	Cytosol is the more specific of the two nested soluble-compartment annotations.	Cytoplasm is correct but broader than the accompanying cytosol annotation.	genes/PSEPK/rhlE/rhlE-ai-review.yaml
deeper_than	combined IEA	PSEPK	rnr	GO:0006402	mRNA catabolic process	ACCEPT	GO:0016070	RNA metabolic process	KEEP_AS_NON_CORE	The RNase R family assignment and target UniProt function support processive RNA degradation; the protein also has a distinct structured-RNA maturation role represented separately below.	The annotation is correct but broad relative to mRNA catabolism and the specific exoribonuclease activity.	genes/PSEPK/rnr/rnr-ai-review.yaml
deeper_than	combined IEA	PSEPK	rsmG	GO:0005829	cytosol	KEEP_AS_NON_CORE	GO:0005737	cytoplasm	KEEP_AS_NON_CORE	The UniProt cytoplasm annotation is sufficient location context for this soluble enzyme; the deep research likewise describes RsmG as a cytosolic enzyme acting on ribosomal RNA.	RsmG is a soluble cytoplasmic rRNA methyltransferase; location is accurate and consistent with the deep-research description of a cytosolic enzyme acting on rRNA, but it is supporting context rather than the core function.	genes/PSEPK/rsmG/rsmG-ai-review.yaml
deeper_than	combined IEA	PSEPK	sdhA	GO:0000104	succinate dehydrogenase activity	ACCEPT	GO:0016627	oxidoreductase activity, acting on the CH-CH group of donors	KEEP_AS_NON_CORE	Strongly supported by family/domain assignment (TIGR01816 sdhA_forward, Pfam FAD_binding_2, FRD/SDH subfamily), conserved active-site and FAD-binding residues, and UniProt EC 1.3.5.1. Consistent across all lines of evidence.	Correct grouping term but subsumed by the specific MF term; keep as non-core supporting annotation.	genes/PSEPK/sdhA/sdhA-ai-review.yaml
deeper_than	combined IEA	PSEPK	tal	GO:0005829	cytosol	KEEP_AS_NON_CORE	GO:0005737	cytoplasm	MARK_AS_OVER_ANNOTATED	Keep as location context while the catalytic activity remains the core function.	Avoid retaining both parent cytoplasm and child cytosol as equally informative locations.	genes/PSEPK/tal/tal-ai-review.yaml
deeper_than	combined IEA	PSEPK	thiI	GO:0002937	tRNA 4-thiouridine biosynthesis	ACCEPT	GO:0034227	tRNA thio-modification	MARK_AS_OVER_ANNOTATED	UniProt describes ATP-dependent sulfur transfer to tRNA to produce 4-thiouridine in position 8, and falcon deep research cites Fuchs et al. 2023 showing that a P. putida KT2440 deletion of thiI drastically reduces bulk-tRNA s4U (mass spectrometry), directly demonstrating that ThiI is the s4U writer 	GO:0002937 captures the product and position of ThiI's direct tRNA modification. Falcon deep research confirms ThiI installs 4-thiouridine (s4U) in cellular tRNA, the specific thio-modification, so the broad parent thio-modification term is redundant with the more specific s4U biosynthesis term.	genes/PSEPK/thiI/thiI-ai-review.yaml
deeper_than	combined IEA	PSEPK	thiI	GO:0005829	cytosol	KEEP_AS_NON_CORE	GO:0005737	cytoplasm	KEEP_AS_NON_CORE	The TreeGrafter cytosol row can be retained as non-core context.	Location is useful context but not the defining function. Falcon deep research notes that no KT2440-specific localization experiment exists, but the substrate is cellular tRNA, implying a cytosolic/intracellular site of action consistent with the UniProt cytoplasm annotation.	genes/PSEPK/thiI/thiI-ai-review.yaml
deeper_than	combined IEA	PSEPK	thrS	GO:0005829	cytosol	KEEP_AS_NON_CORE	GO:0005737	cytoplasm	KEEP_AS_NON_CORE	Localization is contextual.	This is not direct localization evidence.	genes/PSEPK/thrS/thrS-ai-review.yaml
deeper_than	combined IEA	PSEPK	tig	GO:0051083	'de novo' cotranslational protein folding	ACCEPT	GO:0006457	protein folding	MARK_AS_OVER_ANNOTATED	Supported by the combination of ribosome binding at the exit tunnel and chaperone activity on newly synthesized proteins, which together define a co-translational folding role. This is the core biological process for trigger factor.	True but redundant with the more specific child term 'de novo' cotranslational protein folding (GO:0051083), which better captures the co-translational, exit-tunnel role of trigger factor. Retaining the broad parent alongside the specific child is an over-annotation.	genes/PSEPK/tig/tig-ai-review.yaml
deeper_than	combined IEA	PSEPK	tpiA	GO:0005829	cytosol	ACCEPT	GO:0005737	cytoplasm	ACCEPT	Appropriate and more informative than the parent cytoplasm term; consistent with the soluble homodimeric nature of bacterial TIM.	TIM is a canonical cytosolic enzyme; the more specific cytosol annotation (GO:0005829) is also present. Both are biologically appropriate; cytoplasm is retained as the parent term.	genes/PSEPK/tpiA/tpiA-ai-review.yaml
deeper_than	combined IEA	PSEPK	trmB	GO:0030488	tRNA methylation	ACCEPT	GO:0006400	tRNA modification	ACCEPT	The specific TrmB reaction methylates guanosine at position 46 in tRNA using SAM, so the broader tRNA methylation process is valid even though GO:0106004 is the more precise process term.	UniProt/HAMAP describes TrmB as catalyzing formation of N7-methylguanine at tRNA position 46 and assigns the N7-methylguanine-tRNA biosynthesis pathway, so the broad tRNA modification process is appropriate.	genes/PSEPK/trmB/trmB-ai-review.yaml
deeper_than	combined IEA	PSEPK	trpS	GO:0005829	cytosol	KEEP_AS_NON_CORE	GO:0005737	cytoplasm	KEEP_AS_NON_CORE	Localization is contextual.	This is not direct localization evidence.	genes/PSEPK/trpS/trpS-ai-review.yaml
deeper_than	combined IEA	PSEPK	tusD	GO:0005829	cytosol	KEEP_AS_NON_CORE	GO:0005737	cytoplasm	ACCEPT	Cytosol is biologically compatible with the soluble TusBCD complex, but it adds little information beyond the accepted cytoplasm annotation.	The family architecture and UniProt localization mapping support cytoplasm.	genes/PSEPK/tusD/tusD-ai-review.yaml
deeper_than	combined IEA	PSEPK	tusD	GO:1990228	sulfurtransferase complex	ACCEPT	GO:0005737	cytoplasm	ACCEPT	The conserved TusBCD architecture supports complex membership.	The family architecture and UniProt localization mapping support cytoplasm.	genes/PSEPK/tusD/tusD-ai-review.yaml
deeper_than	combined IEA	PSEPK	tyrB	GO:0004838	L-tyrosine:2-oxoglutarate transaminase activity	ACCEPT	GO:0008483	transaminase activity	KEEP_AS_NON_CORE	Domain/family evidence (class-I PLP aminotransferase, PANTHER ArAT subfamily SF37) plus genetic evidence in KT2440 (tyrB mutants show a tyrosine-utilization phenotype; PMID:20050871) support tyrosine aminotransferase activity. The enzyme is likely promiscuous across aromatic amino acids (also acting	Accurately describes the enzymatic class but is a parent of the more specific aromatic aminotransferase term that represents the core function. Retain as supporting/non-core rather than as the primary MF.	genes/PSEPK/tyrB/tyrB-ai-review.yaml
deeper_than	combined IEA	PSEPK	tyrS	GO:0005829	cytosol	KEEP_AS_NON_CORE	GO:0005737	cytoplasm	KEEP_AS_NON_CORE	Localization is compatible with the role but is not a defining function.	Localization is compatible with the role but is not a defining function.	genes/PSEPK/tyrS/tyrS-ai-review.yaml
deeper_than	combined IEA	PSEPK	ubiC	GO:0005829	cytosol	KEEP_AS_NON_CORE	GO:0005737	cytoplasm	KEEP_AS_NON_CORE	Relaxed from MARK_AS_OVER_ANNOTATED. Chorismate pyruvate-lyase is a small soluble enzyme with no transmembrane segment or signal peptide acting on the soluble metabolite chorismate, so the bacterial cytoplasmic compartment it occupies is the cytosol (GO:0005829, the part of the cytoplasm not contain	Retain the broad cellular location, but do not promote it into the core function.	genes/PSEPK/ubiC/ubiC-ai-review.yaml
deeper_than	combined IEA	PSEPK	ubiK	GO:0005829	cytosol	KEEP_AS_NON_CORE	GO:0005737	cytoplasm	ACCEPT	Relaxed from MARK_AS_OVER_ANNOTATED. UbiK is a small soluble accessory protein of the cytoplasmic Ubi machinery with no membrane-spanning segment, so the cytosol is its actual compartment; GO:0005829 is simply the more precise statement of the GO:0005737 cytoplasm row this record also carries. Per t	UniProt explicitly assigns UbiK to the cytoplasm.	genes/PSEPK/ubiK/ubiK-ai-review.yaml
deeper_than	combined IEA	PSEPK	uppS	GO:0045547	ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific] activity	KEEP_AS_NON_CORE	GO:0004659	prenyltransferase activity	MARK_AS_OVER_ANNOTATED	Relaxed from MARK_AS_OVER_ANNOTATED with a proposed replacement. QuickGO confirms GO:0008834 (the undecaprenyl-specific term this record already carries and accepts) is_a GO:0045547, so the flagged row is a true ancestor of the enzyme's actual reaction rather than a competing or less accurate claim.	GO:0008834 captures the defined C55 cis-prenyltransferase reaction.	genes/PSEPK/uppS/uppS-ai-review.yaml
deeper_than	combined IEA	PSEPK	valS	GO:0005829	cytosol	KEEP_AS_NON_CORE	GO:0005737	cytoplasm	KEEP_AS_NON_CORE	Localization is compatible with the role but is not a defining function.	Localization is compatible with the role but is not a defining function.	genes/PSEPK/valS/valS-ai-review.yaml
deeper_than	combined IEA	PSEPK	visC	GO:0019168	2-polyprenylphenol 6-hydroxylase activity	ACCEPT	GO:0016705	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen	MARK_AS_OVER_ANNOTATED	The UbiI/VisC orthology assignment, KEGG K18800 placement, and complete three-hydroxylase pathway support this oxygen-dependent reaction. The assignment is inferred rather than directly assayed in Q88CI4.	GO:0019168 more precisely identifies the substrate and reaction.	genes/PSEPK/visC/visC-ai-review.yaml
deeper_than	combined IEA	PSEPK	xseB	GO:0005829	cytosol	ACCEPT	GO:0005737	cytoplasm	MARK_AS_OVER_ANNOTATED	Avoids retaining both cytoplasm and its cytosol child.	Retain one nonredundant leaf-level location.	genes/PSEPK/xseB/xseB-ai-review.yaml
deeper_than	combined IEA	PSEPK	zwf	GO:0009051	pentose-phosphate shunt, oxidative branch	KEEP_AS_NON_CORE	GO:0006098	pentose-phosphate shunt	MARK_AS_OVER_ANNOTATED	Relaxed from MARK_AS_OVER_ANNOTATED. GO:0009051 is the branch of the pentose-phosphate shunt in which glucose 6-phosphate is oxidized with NADP+ reduction, which is precisely the reaction catalysed by the glucose-6-phosphate dehydrogenase activity this record accepts (GO:0004345, with NADP binding a	The process assignment is inferred from enzyme class rather than a clear paralog-specific role in vivo.	genes/PSEPK/zwf/zwf-ai-review.yaml
deeper_than	combined IEA	PSEPK	zwfA	GO:0009051	pentose-phosphate shunt, oxidative branch	ACCEPT	GO:0006098	pentose-phosphate shunt	KEEP_AS_NON_CORE	The term matches both the UniProt pathway statement and the chemistry of the ZwfA step.	G6PDH is the canonical first step of the oxidative pentose-phosphate route, but GO:0009051 is the more specific core process term.	genes/PSEPK/zwfA/zwfA-ai-review.yaml
deeper_than	combined IEA	PSEPK	zwfB	GO:0009051	pentose-phosphate shunt, oxidative branch	ACCEPT	GO:0006098	pentose-phosphate shunt	ACCEPT	The term matches both the enzyme chemistry and the KT2440 paralog interpretation.	This is a direct pathway annotation for a major G6PDH paralog in KT2440.	genes/PSEPK/zwfB/zwfB-ai-review.yaml
deeper_than	combined IEA	SALRS	PTSG_05882	GO:0016342	catenin complex	REMOVE	GO:0016020	membrane	ACCEPT	Without a cytoplasmic cadherin domain, the protein cannot enter the cadherin-beta-catenin-alpha-catenin complex. The assembled complex is an animal feature not found in choanoflagellates.	The signal peptide plus a single transmembrane helix make membrane insertion a sound sequence-based prediction. The term is broad, and localization has not been examined.	genes/SALRS/PTSG_05882/PTSG_05882-ai-review.yaml
deeper_than	combined IEA	SALRS	PTSG_06458	GO:0016342	catenin complex	REMOVE	GO:0016020	membrane	ACCEPT	Without a cytoplasmic cadherin domain, the protein cannot enter the cadherin-beta-catenin-alpha-catenin complex. The assembled complex is an animal feature not found in choanoflagellates.	The signal peptide plus a single transmembrane helix make membrane insertion a sound sequence-based prediction. The term is broad, and localization has not been examined.	genes/SALRS/PTSG_06458/PTSG_06458-ai-review.yaml
deeper_than	combined IEA	SALRS	PTSG_11235	GO:0016342	catenin complex	REMOVE	GO:0005886	plasma membrane	ACCEPT	Without a cytoplasmic cadherin domain, the protein cannot enter the cadherin-beta-catenin-alpha-catenin complex. The assembled complex is an animal feature not found in choanoflagellates.	A signal peptide, a large ectodomain, a single transmembrane helix and a cytoplasmic catalytic domain fit plasma membrane localization. The one choanoflagellate cadherin that has been localized, M. brevicollis MBCDH1, is on the microvillar collar, a plasma-membrane structure. Accepted as a sequence-	genes/SALRS/PTSG_11235/PTSG_11235-ai-review.yaml
deeper_than	combined IEA	XENLA	uap1.S	GO:0003977	UDP-N-acetylglucosamine diphosphorylase activity	ACCEPT	GO:0070569	uridylyltransferase activity	MODIFY			genes/XENLA/uap1.S/uap1.S-ai-review.yaml
shallower_than	ARBA	9POAL	NCGR_LOCUS10166	GO:0005737	cytoplasm	ACCEPT	GO:0005783	endoplasmic reticulum	UNDECIDED	Both plastids and the endoplasmic reticulum are cytoplasmic organelles. The previous reasoning wrongly treated cytoplasm as equivalent to cytosol and used unresolved organelle targeting to reject a broad TreeGrafter inference. The UniProt compartment/architecture assignment is electronic supporting 	Arabidopsis ARV localization supports this possibility but does not determine targeting of the complete fusion. Conversely, an HDH-like N-terminus does not prove that ER localization is impossible. Model structure, processing and targeting remain unresolved.	genes/9POAL/NCGR_LOCUS10166/NCGR_LOCUS10166-ai-review.yaml
shallower_than	ARBA	PSEPK	PP_3157	GO:0042578	phosphoric ester hydrolase activity	KEEP_AS_NON_CORE	GO:0016791	phosphatase activity	MARK_AS_OVER_ANNOTATED	GO:0042578 phosphoric ester hydrolase activity is a verified ancestor of GO:0004401 histidinol-phosphatase activity, which this protein carries from InterPro IPR011809, EC 3.1.3.15 and UniRule, and whose reaction UniProt records as L-histidinol phosphate + H2O = L-histidinol + phosphate. The broad t	GO:0016791 adds no useful information beyond the specific histidinol-phosphatase activity already assigned.	genes/PSEPK/PP_3157/PP_3157-ai-review.yaml
shallower_than	ARBA	PSEPK	PP_3199	GO:0004497	monooxygenase activity	ACCEPT	GO:0016709	oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, NAD(P)H as one donor, and incorporation of one atom of oxygen	ACCEPT	The monooxygenase-family assignment is supported by the target's FAD-binding domain architecture and similarity to experimentally characterized Hsero_1007/FdeE.	This term captures the supported reaction class without asserting the untested target-specific substrate, regioselectivity, or NADH-versus-NADPH preference.	genes/PSEPK/PP_3199/PP_3199-ai-review.yaml
shallower_than	ARBA	PSEPK	ptxS	GO:0003700	DNA-binding transcription factor activity	MODIFY	GO:0001217	DNA-binding transcription repressor activity	ACCEPT	PtxS acts exclusively as a repressor (de-repressed by 2-ketogluconate); the precise child term GO:0001217 is more informative than the general transcription factor activity term.	PtxS is a dedicated transcriptional repressor that binds operators overlapping the RNA polymerase binding site to block transcription; this is the precise core MF and is experimentally supported.	genes/PSEPK/ptxS/ptxS-ai-review.yaml
shallower_than	ARBA	PSEPK	tktA	GO:0006098	pentose-phosphate shunt	KEEP_AS_NON_CORE	GO:0009052	pentose-phosphate shunt, non-oxidative branch	ACCEPT	Retain as parent pathway context; GO:0009052 is the direct branch-level process term.	GO:0009052 matches the direct pathway role of TktA.	genes/PSEPK/tktA/tktA-ai-review.yaml
shallower_than	EC2GO	PSEPK	betC	GO:0008484	sulfuric ester hydrolase activity	KEEP_AS_NON_CORE	GO:0047753	choline-sulfatase activity	ACCEPT	BetC hydrolyzes a sulfate ester, but the existing exact choline-sulfatase term is more informative for its core function.	The target has concordant EC 3.1.6.6 and choline-sulfatase-specific domain assignments, KT2440 betC genetics support choline-O-sulfate utilization, and the reviewed Sinorhizobium BetC exemplar has direct genetic and enzymatic evidence for the same reaction.	genes/PSEPK/betC/betC-ai-review.yaml
shallower_than	InterPro2GO	EMENI	sfgA	GO:0003700	DNA-binding transcription factor activity	ACCEPT	GO:0000981	DNA-binding transcription factor activity, RNA polymerase II-specific	ACCEPT	General TF term, subsumed by the Pol II-specific call; kept as its parent.	Pol II-specific TF activity predicted from the binuclear-cluster domain, and consistent with SfgA acting as a repressor whose removal is what permits FluG-dependent development.	genes/EMENI/sfgA/sfgA-ai-review.yaml
shallower_than	InterPro2GO	PSEPK	bcsA	GO:0016758	hexosyltransferase activity	MODIFY	GO:0016759	cellulose synthase activity	MODIFY	UniProt and GOA assign the specific UDP-forming cellulose synthase activity, which is more informative than the generic hexosyltransferase parent.	The BcsA reaction is explicitly Rhea/EC-mapped as cellulose synthase (UDP-forming) activity, so GO:0016760 is the preferred specific term.	genes/PSEPK/bcsA/bcsA-ai-review.yaml
shallower_than	InterPro2GO	PSEPK	betA	GO:0016491	oxidoreductase activity	KEEP_AS_NON_CORE	GO:0016614	oxidoreductase activity, acting on CH-OH group of donors	KEEP_AS_NON_CORE	Relaxed from MARK_AS_OVER_ANNOTATED on re-review. GO:0016491 is a true ancestor of the choline dehydrogenase activity that BetA is established to carry, and the more specific descendants (GO:0016614 and GO:0008812) are already present on other rows, so the parent is redundant but not an over-attribu	Retain as a mechanistic parent subordinate to GO:0008812.	genes/PSEPK/betA/betA-ai-review.yaml
shallower_than	InterPro2GO	PSEPK	fdx	GO:0022900	electron transport chain	MARK_AS_OVER_ANNOTATED	GO:0140647	P450-containing electron transport chain	REMOVE	A soluble Isc ferredoxin transfers reducing equivalents during cluster assembly and is not necessarily a respiratory chain component.	Q88PK3 belongs to IPR011536 Fdx_isc and is encoded with iscSUA-hscBA, not a P450 electron-transfer module.	genes/PSEPK/fdx/fdx-ai-review.yaml
shallower_than	InterPro2GO	PSEPK	ftsY	GO:0006605	protein targeting	MODIFY	GO:0006614	SRP-dependent cotranslational protein targeting to membrane	ACCEPT	This parent term is correct but too broad. Replace it with GO:0006614, which captures the SRP-dependent cotranslational mechanism documented for FtsY.	This annotation precisely describes the core biological process in which FtsY participates. FtsY is the bacterial SRP receptor that, together with SRP (Ffh + 4.5S RNA), mediates co-translational targeting of nascent membrane and secretory proteins to the SecYEG translocon. This is the primary and de	genes/PSEPK/ftsY/ftsY-ai-review.yaml
shallower_than	InterPro2GO	PSEPK	gpmI	GO:0005975	carbohydrate metabolic process	KEEP_AS_NON_CORE	GO:0006007	glucose catabolic process	ACCEPT	Retain as a supporting/non-core annotation rather than using it as the main functional summary.	This is a specific, biologically appropriate annotation for this gene product.	genes/PSEPK/gpmI/gpmI-ai-review.yaml
shallower_than	InterPro2GO	PSEPK	nuoG	GO:0003954	NADH dehydrogenase activity	KEEP_AS_NON_CORE	GO:0008137	NADH dehydrogenase (ubiquinone) activity	MODIFY	GO:0003954 (NADH + H+ + acceptor = NAD+ + reduced acceptor) is an is_a ancestor of GO:0008137 NADH dehydrogenase (ubiquinone) activity, the reaction catalysed by the assembled 13-subunit NDH-1 complex of which NuoG is an obligate component. NuoG carries one [2Fe-2S] and three [4Fe-4S] clusters and n	NuoG contributes an essential subunit role to assembled respiratory complex I but does not independently catalyze the complete NADH:quinone reaction; retain the term and replace enables with contributes_to.	genes/PSEPK/nuoG/nuoG-ai-review.yaml
shallower_than	InterPro2GO	PSEPK	nuoG	GO:0022904	respiratory electron transport chain	ACCEPT	GO:0042773	ATP synthesis coupled electron transport	ACCEPT	NuoG is the iron-sulfur relay subunit of respiratory complex I; its target GOA and UniProt records support the respiratory electron transport chain assignment.	NuoG is the iron-sulfur relay subunit of respiratory complex I; its target GOA and UniProt records support the ATP synthesis coupled electron transport assignment.	genes/PSEPK/nuoG/nuoG-ai-review.yaml
shallower_than	InterPro2GO	PSEPK	nuoL	GO:0003954	NADH dehydrogenase activity	KEEP_AS_NON_CORE	GO:0008137	NADH dehydrogenase (ubiquinone) activity	MODIFY	GO:0003954 (NADH + H+ + acceptor = NAD+ + reduced acceptor) is an is_a ancestor of GO:0008137 NADH dehydrogenase (ubiquinone) activity, the reaction catalysed by the assembled 13-subunit NDH-1 complex of which NuoL is an obligate component. NuoL is a 16-TM antiporter-like subunit of the membrane sec	NuoL contributes an essential subunit role to assembled respiratory complex I but does not independently catalyze the complete NADH:quinone reaction; retain the term and replace enables with contributes_to.	genes/PSEPK/nuoL/nuoL-ai-review.yaml
shallower_than	InterPro2GO	PSEPK	nuoM	GO:0003954	NADH dehydrogenase activity	KEEP_AS_NON_CORE	GO:0008137	NADH dehydrogenase (ubiquinone) activity	MODIFY	GO:0003954 (NADH + H+ + acceptor = NAD+ + reduced acceptor) is an is_a ancestor of GO:0008137 NADH dehydrogenase (ubiquinone) activity, the reaction catalysed by the assembled 13-subunit NDH-1 complex of which NuoM is an obligate component. NuoM is a 14-TM antiporter-like subunit of the membrane sec	NuoM contributes an essential subunit role to assembled respiratory complex I but does not independently catalyze the complete NADH:quinone reaction; retain the term and replace enables with contributes_to.	genes/PSEPK/nuoM/nuoM-ai-review.yaml
shallower_than	InterPro2GO	PSEPK	nuoM	GO:0009060	aerobic respiration	KEEP_AS_NON_CORE	GO:0042773	ATP synthesis coupled electron transport	ACCEPT	Complex I supports aerobic respiration, but this broad process is not subunit-specific.	NuoM is the antiporter-like proton-pump subunit of respiratory complex I; its target GOA and UniProt records support the ATP synthesis coupled electron transport assignment.	genes/PSEPK/nuoM/nuoM-ai-review.yaml
shallower_than	InterPro2GO	PSEPK	pvdE	GO:0042626	ATPase-coupled transmembrane transporter activity	KEEP_AS_NON_CORE	GO:0140359	ABC-type transporter activity	ACCEPT			genes/PSEPK/pvdE/pvdE-ai-review.yaml
shallower_than	InterPro2GO	PSEPK	pyrD	GO:0009220	pyrimidine ribonucleotide biosynthetic process	TOO_GENERAL	GO:0006222	UMP biosynthetic process	TOO_GENERAL	Retain GO:0044205.	Retain GO:0044205.	genes/PSEPK/pyrD/pyrD-ai-review.yaml
shallower_than	InterPro2GO	PSEPK	sdhA	GO:0000104	succinate dehydrogenase activity	ACCEPT	GO:0160308	succinate dehydrogenase (FAD) activity	ACCEPT	Strongly supported by family/domain assignment (TIGR01816 sdhA_forward, Pfam FAD_binding_2, FRD/SDH subfamily), conserved active-site and FAD-binding residues, and UniProt EC 1.3.5.1. Consistent across all lines of evidence.	Accurately captures the FAD-coupled catalytic step intrinsic to the SdhA subunit and complements GO:0000104. SdhA contributes to, but does not independently enable, the holo-enzyme quinone-coupled activity GO:0008177.	genes/PSEPK/sdhA/sdhA-ai-review.yaml
shallower_than	InterPro2GO	PSEPK	sdhB	GO:0009060	aerobic respiration	ACCEPT	GO:0006099	tricarboxylic acid cycle	ACCEPT	UniProt distinguishes aerobic succinate dehydrogenase from anaerobic fumarate reductase. SdhB is annotated as the succinate dehydrogenase iron-sulfur subunit and participates in aerobic respiratory electron transfer.	SdhB is part of the succinate dehydrogenase complex that oxidizes succinate to fumarate in the TCA cycle. UniProt places Q88FA8 in the bacterial route from succinate to fumarate, and the PSEPK pathway report identifies the complete sdhCDAB operon as covering step 6.	genes/PSEPK/sdhB/sdhB-ai-review.yaml
shallower_than	InterPro2GO	PSEPK	secD	GO:0015031	protein transport	KEEP_AS_NON_CORE	GO:0006886	intracellular protein transport	MARK_AS_OVER_ANNOTATED	The over-annotation call is relaxed and the ancestor is retained as non-core. GO:0015031 protein transport is the directed movement of proteins into, out of or within a cell, which secD does as part of the SecDF accessory complex that uses the proton motive force to complete translocation after the 	The broad intracellular-transport parent is less informative than GO:0043952.	genes/PSEPK/secD/secD-ai-review.yaml
shallower_than	InterPro2GO	PSEPK	secF	GO:0015031	protein transport	KEEP_AS_NON_CORE	GO:0006886	intracellular protein transport	MARK_AS_OVER_ANNOTATED	The over-annotation call is relaxed and the ancestor is retained as non-core. GO:0015031 protein transport is the directed movement of proteins into, out of or within a cell, which secF does as part of the SecDF accessory complex that uses the proton motive force to complete translocation after the 	The broad intracellular-transport parent is less informative than GO:0043952.	genes/PSEPK/secF/secF-ai-review.yaml
shallower_than	InterPro2GO	PSEPK	selB	GO:0006414	translational elongation	MODIFY	GO:0001514	selenocysteine incorporation	ACCEPT	SelB does not serve as the general aminoacyl-tRNA delivery factor. Its defining role is SECIS-dependent delivery of Sec-tRNA(Sec) at UGA, which is captured by GO:0001514.	The protein is annotated as a selenocysteyl-tRNA-specific elongation factor and contains the characteristic SelB GTPase and C-terminal winged-helix domains.	genes/PSEPK/selB/selB-ai-review.yaml
shallower_than	InterPro2GO	PSEPK	ubiA	GO:0016740	transferase activity	KEEP_AS_NON_CORE	GO:0004659	prenyltransferase activity	MARK_AS_OVER_ANNOTATED	Relaxed from MARK_AS_OVER_ANNOTATED. UbiA transfers an all-trans polyprenyl group to 4-hydroxybenzoate, so GO:0016740 transferase activity is a true root-level ancestor of the accepted GO:0008412 4-hydroxybenzoate polyprenyltransferase activity. A correct but very general parent is not an over-annot	GO:0008412 captures the 4-hydroxybenzoate substrate and evolved function.	genes/PSEPK/ubiA/ubiA-ai-review.yaml
shallower_than	UniProt subcellular location	9POAL	NCGR_LOCUS10166	GO:0005737	cytoplasm	ACCEPT	GO:0009507	chloroplast	UNDECIDED	Both plastids and the endoplasmic reticulum are cytoplasmic organelles. The previous reasoning wrongly treated cytoplasm as equivalent to cytosol and used unresolved organelle targeting to reject a broad TreeGrafter inference. The UniProt compartment/architecture assignment is electronic supporting 	The N-terminus is strongly conserved with a separate predicted plant HDH. A C-terminal membrane region does not categorically preclude plastid import or processing, but no target localization or authentic fusion transcript has been established.	genes/9POAL/NCGR_LOCUS10166/NCGR_LOCUS10166-ai-review.yaml
shallower_than	UniProt subcellular location	9POAL	NCGR_LOCUS1270	GO:0005737	cytoplasm	ACCEPT	GO:0009507	chloroplast	MODIFY	GO:0005737 includes subcellular structures outside the nucleus and plasma membrane, including plastids. The previous REMOVE conflated cytoplasm with cytosol. Retain this broad localization while retaining the separate challenge to GO:0005829 cytosol.	Correct but could be more specific. The enzyme operates in the chloroplast stroma (GO:0009570), which is the site of the Calvin cycle reactions. Stromal localization is supported by immunolocalization of the related cpFBPaseII and by the enzyme's pH-dependent regulation (active at stromal alkaline p	genes/9POAL/NCGR_LOCUS1270/NCGR_LOCUS1270-ai-review.yaml
shallower_than	UniProt subcellular location	9POAL	NCGR_LOCUS67308	GO:0005739	mitochondrion	ACCEPT	GO:0005743	mitochondrial inner membrane	ACCEPT	Correct localization for both alternative splice products of this locus.	Correct and well-supported localization for SDH2 as part of the inner membrane-associated Complex II.	genes/9POAL/NCGR_LOCUS67308/NCGR_LOCUS67308-ai-review.yaml
shallower_than	UniProt subcellular location	DESRO	K9J2R0	GO:0005886	plasma membrane	ACCEPT	GO:0016324	apical plasma membrane	ACCEPT	UniProt lists apical cell membrane and other membrane localizations.	UniProt lists apical cell membrane localization.	genes/DESRO/K9J2R0/K9J2R0-ai-review.yaml
shallower_than	UniProt subcellular location	DESRO	K9J2R0	GO:0005886	plasma membrane	ACCEPT	GO:0031258	lamellipodium membrane	ACCEPT	UniProt lists apical cell membrane and other membrane localizations.	UniProt subcellular location includes lamellipodium membrane.	genes/DESRO/K9J2R0/K9J2R0-ai-review.yaml
shallower_than	UniProt subcellular location	MISSI	MnSOD	GO:0005739	mitochondrion	KEEP_AS_NON_CORE	GO:0005759	mitochondrial matrix	ACCEPT	The broader mitochondrion term is true but less informative than the mitochondrial matrix annotation.	The matrix is the specific mitochondrial compartment supported by the UniProt entry.	genes/MISSI/MnSOD/MnSOD-ai-review.yaml
shallower_than	UniProt subcellular location	NICAT	NaODC_candidate_DCOR	GO:0005737	cytoplasm	KEEP_AS_NON_CORE	GO:0009507	chloroplast	KEEP_AS_NON_CORE	GO:0009507 chloroplast is a descendant of GO:0005737 cytoplasm (chloroplast is_a plastid, part_of cytoplasm), so the UniProt plastid assignment does not contradict the TreeGrafter cytoplasm call - it entails it. The protein is in any case a soluble class-II PLP-dependent decarboxylase (Pfam PF02784 	The location is supported, but it is less important than resolving the pathway-specialized ODC paralog.	genes/NICAT/NaODC_candidate_DCOR/NaODC_candidate_DCOR-ai-review.yaml
shallower_than	UniProt subcellular location	NICAT	NaODC_candidate_ODC	GO:0005737	cytoplasm	KEEP_AS_NON_CORE	GO:0009507	chloroplast	KEEP_AS_NON_CORE	GO:0009507 chloroplast is a descendant of GO:0005737 cytoplasm (chloroplast is_a plastid, part_of cytoplasm), so the UniProt plastid assignment does not contradict the TreeGrafter cytoplasm call - it entails it. The protein is in any case a soluble class-II PLP-dependent decarboxylase (Pfam PF02784 	The location is supported in UniProt, but the more important issue here is pathway membership and paralog ranking.	genes/NICAT/NaODC_candidate_ODC/NaODC_candidate_ODC-ai-review.yaml
shallower_than	UniProt subcellular location	OCTVU	DDO	GO:0005737	cytoplasm	KEEP_AS_NON_CORE	GO:0005782	peroxisomal matrix	ACCEPT	GO:0005737 cytoplasm is an ancestor of GO:0005782 peroxisomal matrix in the ontology (peroxisomal matrix is part_of peroxisome, part_of cytoplasm), so the TreeGrafter call is entailed by the more specific location rather than in conflict with it: DDO is a soluble monomeric FAD flavoenzyme with a C-t	Peroxisomal matrix localization is well-supported by the conserved SKL peroxisomal targeting signal at the C-terminus and by sequence similarity to mammalian orthologs known to localize to the peroxisome matrix.	genes/OCTVU/DDO/DDO-ai-review.yaml
shallower_than	UniProt subcellular location	OSCPE	TLN	GO:0005737	cytoplasm	ACCEPT	GO:0005938	cell cortex	ACCEPT	Correct, if general, for a soluble cytoskeletal adaptor.	Talins act at the membrane-cortex interface; general and plausible.	genes/OSCPE/TLN/TLN-ai-review.yaml
shallower_than	UniProt subcellular location	SALRS	couscous	GO:0005794	Golgi apparatus	UNDECIDED	GO:0000139	Golgi membrane	UNDECIDED	Same conflict as for Golgi membrane: a family-level expectation versus a single overexpressed-fusion observation that the authors regard as possibly artefactual. Kept undecided pending native localization (antibody staining or endogenous tagging with a Golgi marker).	The family default (Golgi, as for yeast Mnn2) conflicts with the one direct observation, which placed tagged Couscous outside the Golgi (possibly ER, untested). The authors themselves conclude localization is uncertain, and the N-terminal hydrophobic segment is ambiguous between a cleaved signal pep	genes/SALRS/couscous/couscous-ai-review.yaml
shallower_than	UniRule	PSEPK	ftsY	GO:0006605	protein targeting	MODIFY	GO:0006612	protein targeting to membrane	MODIFY	This parent term is correct but too broad. Replace it with GO:0006614, which captures the SRP-dependent cotranslational mechanism documented for FtsY.	The membrane-targeting statement is correct, but GO:0006614 provides the known SRP-dependent cotranslational mechanism and should replace this parent.	genes/PSEPK/ftsY/ftsY-ai-review.yaml
shallower_than	UniRule	PSEPK	nuoI	GO:0003954	NADH dehydrogenase activity	MODIFY	GO:0050136	NADH dehydrogenase (quinone) (non-electrogenic) activity	REMOVE	GO:0003954 (NADH + H+ + acceptor = NAD+ + reduced acceptor) is an is_a ancestor of GO:0008137 NADH dehydrogenase (ubiquinone) activity, the reaction catalysed by the assembled 13-subunit NDH-1 complex of which NuoI is an obligate component. NuoI carries two [4Fe-4S] clusters and no FMN or NADH-bindi	This term explicitly describes a non-electrogenic quinone reductase, whereas Nuo is the proton-translocating NDH-1 complex.	genes/PSEPK/nuoI/nuoI-ai-review.yaml
shallower_than	UniRule	PSEPK	recB	GO:0000725	recombinational repair	KEEP_AS_NON_CORE	GO:0000724	double-strand break repair via homologous recombination	ACCEPT	Accurate but more general than the specific DSB-via-HR term, which better represents the core process; retain as supporting/non-core.	Strongly supported by conserved RecBCD biology and by pseudomonad genetics (recB null mutants are UV/mitomycin C sensitive and accumulate fragmented chromosomal DNA); a core function.	genes/PSEPK/recB/recB-ai-review.yaml
shallower_than	UniRule	PSEPK	recC	GO:0006310	DNA recombination	ACCEPT	GO:0000724	double-strand break repair via homologous recombination	ACCEPT	P. aeruginosa and P. putida recBCD-like clones restore recombination proficiency, while the target record places RecC in the holoenzyme that prepares and loads recombinogenic DNA ends.	The target record assigns RecC to RecBCD-mediated recombinational repair, and deletion of recC disables DNA repair in the experimentally studied pseudomonad P. syringae.	genes/PSEPK/recC/recC-ai-review.yaml
shallower_than	UniRule	PSEPK	secD	GO:0015031	protein transport	KEEP_AS_NON_CORE	GO:0043952	protein transport by the Sec complex	ACCEPT	The over-annotation call is relaxed and the ancestor is retained as non-core. GO:0015031 protein transport is the directed movement of proteins into, out of or within a cell, which secD does as part of the SecDF accessory complex that uses the proton motive force to complete translocation after the 	This is the direct process assigned by the exact bacterial family mechanism.	genes/PSEPK/secD/secD-ai-review.yaml
shallower_than	UniRule	PSEPK	secD	GO:0015031	protein transport	KEEP_AS_NON_CORE	GO:0065002	intracellular protein transmembrane transport	ACCEPT	The over-annotation call is relaxed and the ancestor is retained as non-core. GO:0015031 protein transport is the directed movement of proteins into, out of or within a cell, which secD does as part of the SecDF accessory complex that uses the proton motive force to complete translocation after the 	The transmembrane-transport process is correct for the assembled SecDF accessory complex.	genes/PSEPK/secD/secD-ai-review.yaml
shallower_than	UniRule	PSEPK	secF	GO:0015031	protein transport	KEEP_AS_NON_CORE	GO:0043952	protein transport by the Sec complex	ACCEPT	The over-annotation call is relaxed and the ancestor is retained as non-core. GO:0015031 protein transport is the directed movement of proteins into, out of or within a cell, which secF does as part of the SecDF accessory complex that uses the proton motive force to complete translocation after the 	This is the direct process assigned by the exact bacterial family mechanism.	genes/PSEPK/secF/secF-ai-review.yaml
shallower_than	UniRule	PSEPK	secF	GO:0015031	protein transport	KEEP_AS_NON_CORE	GO:0065002	intracellular protein transmembrane transport	ACCEPT	The over-annotation call is relaxed and the ancestor is retained as non-core. GO:0015031 protein transport is the directed movement of proteins into, out of or within a cell, which secF does as part of the SecDF accessory complex that uses the proton motive force to complete translocation after the 	The transmembrane-transport process is correct for the assembled SecDF accessory complex.	genes/PSEPK/secF/secF-ai-review.yaml
shallower_than	combined IEA	9POAL	NCGR_LOCUS10166	GO:0005737	cytoplasm	ACCEPT	GO:0005789	endoplasmic reticulum membrane	UNDECIDED	Both plastids and the endoplasmic reticulum are cytoplasmic organelles. The previous reasoning wrongly treated cytoplasm as equivalent to cytosol and used unresolved organelle targeting to reject a broad TreeGrafter inference. The UniProt compartment/architecture assignment is electronic supporting 	Conserved hydrophobic segments support membrane association. Assignment specifically to ER membrane depends on the full gene product and targeting; chloroplast predictions alone do not refute it.	genes/9POAL/NCGR_LOCUS10166/NCGR_LOCUS10166-ai-review.yaml
shallower_than	combined IEA	9POAL	NCGR_LOCUS67308	GO:0009060	aerobic respiration	ACCEPT	GO:0006099	tricarboxylic acid cycle	ACCEPT	SDH2 is directly involved in aerobic respiration through its role in Complex II, which links the TCA cycle to the electron transport chain.	SDH2 is directly involved in the TCA cycle as a subunit of succinate dehydrogenase, which catalyzes the succinate-to-fumarate step.	genes/9POAL/NCGR_LOCUS67308/NCGR_LOCUS67308-ai-review.yaml
shallower_than	combined IEA	ACET2	celC	GO:0009251	glucan catabolic process	ACCEPT	GO:0030245	cellulose catabolic process	ACCEPT	This annotation is accurate. CelC breaks down cellulose, which is a glucan (polymer of glucose). The TreeGrafter annotation correctly infers this biological process from sequence homology to characterized cellulases.	This is the core biological process annotation for CelC. As an endoglucanase that cleaves internal bonds in cellulose chains, CelC directly participates in cellulose catabolism. UniProt explicitly annotates CelC for the cellulose degradation pathway (UniPathway:UPA00696). This annotation is supporte	genes/ACET2/celC/celC-ai-review.yaml
shallower_than	combined IEA	HETGA	Cd44	GO:0004888	transmembrane signaling receptor activity	ACCEPT	GO:0004896	cytokine receptor activity	KEEP_AS_NON_CORE	The TreeGrafter node assertion is confirmed by naked mole-rat data rather than merely inherited. Blocking CD44 on intact naked mole-rat cells raises saturation density and permits anchorage-independent growth, and the authors trace the signal through the cytoplasmic partner NF2/merlin, so the transm	The qualifier makes this a complex-level, not an autonomous, activity claim, which is exactly right for CD44 and is the reason it is retained rather than challenged. It is non-core because the evidence is a single human IDA study of the MIF-CD74-CD44 complex projected across species, and neither MIF	genes/HETGA/Cd44/Cd44-ai-review.yaml
shallower_than	combined IEA	HETGA	Ntrk1	GO:1990090	cellular response to nerve growth factor stimulus	ACCEPT	GO:0038180	nerve growth factor signaling pathway	ACCEPT	The term asks only that the cell change state in response to NGF, which naked mole-rat TrkA-expressing sensory neurons demonstrably do: they elaborate extensive neurites on NGF exposure. At the receptor level, NGF-driven phosphopeptide upregulation through the naked mole-rat intracellular domain was	This is the annotation the naked mole-rat phenotype most tempts a reviewer to negate, and it should not be negated. The pathway operates: naked mole-rat sensory neurons respond to NGF with neurite outgrowth, the cloned receptor sensitises TRPV1 to rat-equivalent levels at 1,000 ng/mL NGF, and NGF st	genes/HETGA/Ntrk1/Ntrk1-ai-review.yaml
shallower_than	combined IEA	METEA	glyA	GO:0046653	tetrahydrofolate metabolic process	KEEP_AS_NON_CORE	GO:0035999	tetrahydrofolate interconversion	ACCEPT			genes/METEA/glyA/glyA-ai-review.yaml
shallower_than	combined IEA	POLH7	AJ80_06654	GO:0016491	oxidoreductase activity	KEEP_AS_NON_CORE	GO:0050421	nitrite reductase (NO-forming) activity	ACCEPT	The oxidoreductase parent is consistent with nitrite reductase chemistry, but GO:0050421 is the informative function supported by the EC and family assignments.	The best-supported assertion is molecular activity, not organism-level pathway membership. UniProt assigns EC 1.7.2.1 and the sequence carries NO2-reductase_Cu/cupredoxin family signatures, making this a reasonable conserved-function inference. PTHR11709 is a broad multicopper oxidase family, so the	genes/POLH7/AJ80_06654/AJ80_06654-ai-review.yaml
shallower_than	combined IEA	PSEPK	PP_3157	GO:0042578	phosphoric ester hydrolase activity	KEEP_AS_NON_CORE	GO:0004401	histidinol-phosphatase activity	UNDECIDED	GO:0042578 phosphoric ester hydrolase activity is a verified ancestor of GO:0004401 histidinol-phosphatase activity, which this protein carries from InterPro IPR011809, EC 3.1.3.15 and UniRule, and whose reaction UniProt records as L-histidinol phosphate + H2O = L-histidinol + phosphate. The broad t	GO:0004401 matches EC 3.1.3.15, RHEA:14465, the UniProt product name, UniRule UR001996117, and the histidine-specific IPR011809 family. These are concordant computational and family-level assignments, but no direct PP_3157 substrate-specific assay establishes GO:0004401 in KT2440.	genes/PSEPK/PP_3157/PP_3157-ai-review.yaml
shallower_than	combined IEA	PSEPK	aceF	GO:0016407	acetyltransferase activity	KEEP_AS_NON_CORE	GO:0004742	dihydrolipoyllysine-residue acetyltransferase activity	ACCEPT	AceF is an acetyltransferase, but GO:0004742 captures the PDH-specific lipoyl-lysine acceptor and is the informative core molecular function.	UniProt assigns the substrate-specific EC 2.3.1.12 activity to Q88QZ6, and the OpenScientist report supports AceF as the lipoylated E2 core subunit of the AceE/AceF/LpdG PDH complex.	genes/PSEPK/aceF/aceF-ai-review.yaml
shallower_than	combined IEA	PSEPK	astE	GO:0016811	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides	KEEP_AS_NON_CORE	GO:0009017	succinylglutamate desuccinylase activity	ACCEPT	GO:0009017 is the informative substrate-specific child term.	The reviewed Q88EI7 record assigns EC 3.5.1.96 and RHEA:15169 with an AstE-specific HAMAP rule.	genes/PSEPK/astE/astE-ai-review.yaml
shallower_than	combined IEA	PSEPK	bcsA	GO:0016758	hexosyltransferase activity	MODIFY	GO:0016760	cellulose synthase (UDP-forming) activity	ACCEPT	UniProt and GOA assign the specific UDP-forming cellulose synthase activity, which is more informative than the generic hexosyltransferase parent.	UniProt describes BcsA as the catalytic subunit of cellulose synthase, maps EC 2.4.1.12/Rhea:19929, and GOA already contains the specific UDP-forming cellulose synthase term.	genes/PSEPK/bcsA/bcsA-ai-review.yaml
shallower_than	combined IEA	PSEPK	betA	GO:0016491	oxidoreductase activity	KEEP_AS_NON_CORE	GO:0008802	betaine-aldehyde dehydrogenase (NAD+) activity	UNDECIDED	Relaxed from MARK_AS_OVER_ANNOTATED on re-review. GO:0016491 is a true ancestor of the choline dehydrogenase activity that BetA is established to carry, and the more specific descendants (GO:0016614 and GO:0008812) are already present on other rows, so the parent is redundant but not an over-attribu	The GO row is an EC/Rhea-derived IEA from HAMAP MF_00750, so its support is family-level rather than organism-specific. Co-occurrence of the dedicated BetB enzyme is not evidence against BetA bifunctionality, but no target-specific biochemical assay establishes the second activity.	genes/PSEPK/betA/betA-ai-review.yaml
shallower_than	combined IEA	PSEPK	betA	GO:0016491	oxidoreductase activity	KEEP_AS_NON_CORE	GO:0008812	choline dehydrogenase activity	ACCEPT	Relaxed from MARK_AS_OVER_ANNOTATED on re-review. GO:0016491 is a true ancestor of the choline dehydrogenase activity that BetA is established to carry, and the more specific descendants (GO:0016614 and GO:0008812) are already present on other rows, so the parent is redundant but not an over-attribu	This is the primary core molecular function of BetA.	genes/PSEPK/betA/betA-ai-review.yaml
shallower_than	combined IEA	PSEPK	clsA	GO:0016020	membrane	KEEP_AS_NON_CORE	GO:0005886	plasma membrane	ACCEPT	Retain as non-core localization context alongside plasma membrane.	Cardiolipin synthases are membrane phospholipid enzymes.	genes/PSEPK/clsA/clsA-ai-review.yaml
shallower_than	combined IEA	PSEPK	clsB	GO:0016020	membrane	KEEP_AS_NON_CORE	GO:0005886	plasma membrane	ACCEPT	Retain as non-core localization context alongside plasma membrane.	Cardiolipin synthases are membrane phospholipid enzymes.	genes/PSEPK/clsB/clsB-ai-review.yaml
shallower_than	combined IEA	PSEPK	dnaA	GO:0006260	DNA replication	ACCEPT	GO:0006270	DNA replication initiation	ACCEPT	DnaA is essential for initiating chromosomal DNA replication.	DnaA forms the initiation complex and opens oriC before replisome loading.	genes/PSEPK/dnaA/dnaA-ai-review.yaml
shallower_than	combined IEA	PSEPK	dxs	GO:0016744	transketolase or transaldolase activity	KEEP_AS_NON_CORE	GO:0008661	1-deoxy-D-xylulose-5-phosphate synthase activity	ACCEPT	QuickGO places GO:0016744 on the is_a ancestor path of GO:0008661 1-deoxy-D-xylulose-5-phosphate synthase activity, which is annotated on another row and carries the core call. The ancestor describes transfer of an aldehyde or ketonic group between compounds, which is exactly the acyloin condensatio	UniProt assigns EC 2.2.1.7 and Rhea 12605 for condensation of pyruvate and glyceraldehyde 3-phosphate to DXP and carbon dioxide.	genes/PSEPK/dxs/dxs-ai-review.yaml
shallower_than	combined IEA	PSEPK	glpK	GO:0006071	glycerol metabolic process	KEEP_AS_NON_CORE	GO:0019563	glycerol catabolic process	ACCEPT			genes/PSEPK/glpK/glpK-ai-review.yaml
shallower_than	combined IEA	PSEPK	gpmI	GO:0005975	carbohydrate metabolic process	KEEP_AS_NON_CORE	GO:0006096	glycolytic process	ACCEPT	Retain as a supporting/non-core annotation rather than using it as the main functional summary.	This is a specific, biologically appropriate annotation for this gene product.	genes/PSEPK/gpmI/gpmI-ai-review.yaml
shallower_than	combined IEA	PSEPK	gshB	GO:0016879	ligase activity, forming carbon-nitrogen bonds	KEEP_AS_NON_CORE	GO:0004363	glutathione synthase activity	ACCEPT	GO:0004363 glutathione synthase activity is_a GO:0016879 in the current ontology, so this term is simply a true parent of the reaction GshB catalyses (gamma-L-glutamyl-L-cysteine + glycine + ATP, ATP-grasp C-N ligase chemistry; EC 6.3.2.3). Redundancy with the more specific term that another row alr	The exact Q88D35 record assigns EC 6.3.2.3 and ATP-dependent addition of glycine to gamma-L-glutamyl-L-cysteine.	genes/PSEPK/gshB/gshB-ai-review.yaml
shallower_than	combined IEA	PSEPK	guaD	GO:0019239	deaminase activity	KEEP_AS_NON_CORE	GO:0008892	guanine deaminase activity	ACCEPT	GO:0008892 guanine deaminase activity is_a GO:0019239 in the current ontology, so the broad term correctly describes the hydrolytic deamination (guanine + H2O = xanthine + NH4+, EC 3.5.4.3) assigned to Q88F18's guanine-deaminase family. Being less specific than the child term carried on another row 	The exact reaction, diagnostic InterPro family, and PANTHER node propagated from experimentally annotated orthologs converge on guanine deaminase activity. GOA names PTN002259155 in WITH/FROM, while the cached family PAINT slice independently records the term at IBD node PTN000138455. No direct enzy	genes/PSEPK/guaD/guaD-ai-review.yaml
shallower_than	combined IEA	PSEPK	guaD	GO:0046098	guanine metabolic process	KEEP_AS_NON_CORE	GO:0006147	guanine catabolic process	ACCEPT	GO:0006147 guanine catabolic process is_a GO:0046098 guanine metabolic process, so the propagated parent is true of GuaD's reaction; it is simply less informative about direction than the child term already carried by the UniRule row. Redundancy with a more specific sibling annotation is not grounds	This is the immediate biological process of the predicted guanine deaminase reaction.	genes/PSEPK/guaD/guaD-ai-review.yaml
shallower_than	combined IEA	PSEPK	moeB	GO:0016779	nucleotidyltransferase activity	ACCEPT	GO:0061605	molybdopterin-synthase adenylyltransferase activity	ACCEPT	ATP-dependent transfer of AMP to the terminal carboxylate of MoaD is catalytic nucleotidyl transfer. The specific molybdopterin-synthase adenylyltransferase term is already retained, and its broad catalytic ancestors remain correct. OpenScientist supports the classical MoeB architecture and conserve	UniProt supplies the MoaD C-terminal adenylylation reaction and EC 2.7.7.80.	genes/PSEPK/moeB/moeB-ai-review.yaml
shallower_than	combined IEA	PSEPK	mraY	GO:0044038	cell wall macromolecule biosynthetic process	KEEP_AS_NON_CORE	GO:0009252	peptidoglycan biosynthetic process	ACCEPT	GO:0044038 is a direct is_a ancestor of GO:0009252 peptidoglycan biosynthetic process, which MraY already carries, and its definition (formation of a macromolecule destined to form part of a cell wall) is satisfied by MraY's transfer of phospho-MurNAc-pentapeptide to undecaprenyl phosphate to form l	UniProt assigns MraY to the cell wall biogenesis / peptidoglycan biosynthesis pathway, and it initiates the lipid cycle of peptidoglycan synthesis.	genes/PSEPK/mraY/mraY-ai-review.yaml
shallower_than	combined IEA	PSEPK	mscL	GO:0006811	monoatomic ion transport	KEEP_AS_NON_CORE	GO:0034220	monoatomic ion transmembrane transport	ACCEPT	GO:0006811 is a direct is_a ancestor of GO:0034220 monoatomic ion transmembrane transport, which MscL already carries from UniRule, and its definition (directed movement of monoatomic ions by means of a transporter or pore) is exactly what a large-conductance stretch-gated pore does. Nothing in the 	MscL is a mechanosensitive membrane channel and the transmembrane process term is more specific than generic monoatomic ion transport.	genes/PSEPK/mscL/mscL-ai-review.yaml
shallower_than	combined IEA	PSEPK	murG	GO:0016757	glycosyltransferase activity	KEEP_AS_NON_CORE	GO:0016758	hexosyltransferase activity	MARK_AS_OVER_ANNOTATED	GO:0016757 is a direct is_a ancestor of GO:0050511 undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase activity, which MurG already carries, and UniProt describes the transfer of a GlcNAc moiety from UDP-GlcNAc to lipid I. The parent term is therefore simply true; per the	The target reaction is known at substrate level, so generic hexosyltransferase activity is redundant.	genes/PSEPK/murG/murG-ai-review.yaml
shallower_than	combined IEA	PSEPK	murG	GO:0016757	glycosyltransferase activity	KEEP_AS_NON_CORE	GO:0050511	undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase activity	MARK_AS_OVER_ANNOTATED	GO:0016757 is a direct is_a ancestor of GO:0050511 undecaprenyldiphospho-muramoylpentapeptide beta-N-acetylglucosaminyltransferase activity, which MurG already carries, and UniProt describes the transfer of a GlcNAc moiety from UDP-GlcNAc to lipid I. The parent term is therefore simply true; per the	GO:0051991 captures the exact DAP-containing lipid I substrate recorded for KT2440 and is preferred for the gene-level core function.	genes/PSEPK/murG/murG-ai-review.yaml
shallower_than	combined IEA	PSEPK	mutS	GO:0003690	double-stranded DNA binding	KEEP_AS_NON_CORE	GO:0030983	mismatched DNA binding	ACCEPT	GO:0003690 is a direct is_a ancestor of GO:0030983 mismatched DNA binding, which MutS already carries from UniRule/InterPro, and UniProt's mismatch-recognition function statement is consistent with binding duplex DNA. The parent is therefore true; redundancy with the more informative descendant is n	MutS is the mismatch-recognition component, unlike downstream MutL.	genes/PSEPK/mutS/mutS-ai-review.yaml
shallower_than	combined IEA	PSEPK	pnp	GO:0006401	RNA catabolic process	ACCEPT	GO:0006402	mRNA catabolic process	ACCEPT	Processive 3'-to-5' degradation of RNA is its defining biological role.	UniProt explicitly identifies mRNA degradation as its function.	genes/PSEPK/pnp/pnp-ai-review.yaml
shallower_than	combined IEA	PSEPK	purM	GO:0006164	purine nucleotide biosynthetic process	ACCEPT	GO:0006189	'de novo' IMP biosynthetic process	ACCEPT	FGAM-to-AIR cyclization is part of the route to IMP, a purine nucleotide. The broader process is correct and compatible with the more specific de novo IMP annotation; a duplicate narrower replacement is unnecessary.	This enzyme catalyzes a required reaction between PRPP and IMP.	genes/PSEPK/purM/purM-ai-review.yaml
shallower_than	combined IEA	PSEPK	pydB	GO:0016812	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in cyclic amides	KEEP_AS_NON_CORE	GO:0004157	dihydropyrimidinase activity	ACCEPT	Correct but less informative than GO:0004157.	This is the specific core molecular function of PydB.	genes/PSEPK/pydB/pydB-ai-review.yaml
shallower_than	combined IEA	PSEPK	pyrC	GO:0006221	pyrimidine nucleotide biosynthetic process	MARK_AS_OVER_ANNOTATED	GO:0044205	'de novo' UMP biosynthetic process	ACCEPT	Retain de novo UMP biosynthesis.	The reviewed record assigns step 3 of 3 from bicarbonate to dihydroorotate.	genes/PSEPK/pyrC/pyrC-ai-review.yaml
shallower_than	combined IEA	PSEPK	pyrD	GO:0009220	pyrimidine ribonucleotide biosynthetic process	TOO_GENERAL	GO:0044205	'de novo' UMP biosynthetic process	ACCEPT	Retain GO:0044205.	The reviewed record explicitly assigns the quinone-route pathway step.	genes/PSEPK/pyrD/pyrD-ai-review.yaml
shallower_than	combined IEA	PSEPK	queA	GO:0002099	tRNA wobble guanine modification	ACCEPT	GO:0008616	tRNA queuosine(34) biosynthetic process	ACCEPT	The reaction converts preQ1-tRNA at position 34 to epoxyqueuosine(34)-tRNA, so it directly participates in wobble guanine modification.	QueA converts preQ1-tRNA from Tgt into epoxyqueuosine-tRNA for QueG, directly linking the two flanking enzymatic steps.	genes/PSEPK/queA/queA-ai-review.yaml
shallower_than	combined IEA	PSEPK	rbsD	GO:0016866	intramolecular transferase activity	KEEP_AS_NON_CORE	GO:0062193	D-ribose pyranase activity	ACCEPT			genes/PSEPK/rbsD/rbsD-ai-review.yaml
shallower_than	combined IEA	PSEPK	rfbC	GO:0016854	racemase and epimerase activity	MODIFY	GO:0008830	dTDP-4-dehydrorhamnose 3,5-epimerase activity	ACCEPT	Replace with the substrate-specific dTDP-rhamnose epimerase term.	UniProt records EC 5.1.3.13 and the dTDP-4-dehydrorhamnose 3,5-epimerase reaction.	genes/PSEPK/rfbC/rfbC-ai-review.yaml
shallower_than	combined IEA	PSEPK	rlmE	GO:0008173	RNA methyltransferase activity	KEEP_AS_NON_CORE	GO:0008650	rRNA (uridine-2'-O-ribose)-methyltransferase activity	ACCEPT	"The over-annotation call is relaxed and the ancestor is retained as non-core. GO:0008173 is defined as transfer of a methyl group to a nucleoside residue in an RNA molecule, which is exactly what RlmE does (EC 2.1.1.166; UniProt ""Specifically methylates the uridine in position 2552 of 23S""). It is a"	UniProt assigns EC 2.1.1.166 and the Rhea reaction for uridine 2552 2'-O-ribose methylation in 23S rRNA. Falcon deep research independently confirms the SAM-dependent transfer of a methyl group to the 2'-O position of U2552 in 23S rRNA, generating Um2552.	genes/PSEPK/rlmE/rlmE-ai-review.yaml
shallower_than	combined IEA	PSEPK	rmlC	GO:0016854	racemase and epimerase activity	MODIFY	GO:0008830	dTDP-4-dehydrorhamnose 3,5-epimerase activity	ACCEPT	Replace with the substrate-specific RmlC activity.	UniProt records EC 5.1.3.13 and the Rhea reaction for the 3,5-epimerase step in dTDP-L-rhamnose biosynthesis.	genes/PSEPK/rmlC/rmlC-ai-review.yaml
shallower_than	combined IEA	PSEPK	sdhA	GO:0000104	succinate dehydrogenase activity	ACCEPT	GO:0008177	succinate dehydrogenase (quinone) activity	MARK_AS_OVER_ANNOTATED	Strongly supported by family/domain assignment (TIGR01816 sdhA_forward, Pfam FAD_binding_2, FRD/SDH subfamily), conserved active-site and FAD-binding residues, and UniProt EC 1.3.5.1. Consistent across all lines of evidence.	SdhA performs the FAD-dependent succinate-oxidation half-reaction, but quinone reduction requires the SdhB electron-transfer chain and SdhC/D membrane domain. The term is correct for the assembled SdhABCD complex and should be represented as a contribution for this subunit.	genes/PSEPK/sdhA/sdhA-ai-review.yaml
shallower_than	combined IEA	PSEPK	sdhD	GO:0009060	aerobic respiration	ACCEPT	GO:0006099	tricarboxylic acid cycle	ACCEPT	SdhD is part of membrane-bound succinate dehydrogenase/Complex II, coupling TCA-cycle succinate oxidation to aerobic respiratory electron transfer.	The SdhABCD complex catalyzes the succinate-to-fumarate step of the TCA cycle. SdhD is not the catalytic flavoprotein subunit, but it is part of the required membrane anchor/quinone-transfer domain of the same complex.	genes/PSEPK/sdhD/sdhD-ai-review.yaml
shallower_than	combined IEA	PSEPK	tyrS	GO:0043039	tRNA aminoacylation	KEEP_AS_NON_CORE	GO:0006418	tRNA aminoacylation for protein translation	MARK_AS_OVER_ANNOTATED	Relaxed from MARK_AS_OVER_ANNOTATED. GO:0043039 (tRNA charging) is a true is_a ancestor of GO:0006437 tyrosyl-tRNA aminoacylation, which this record already carries and which is accepted; the protein is a tyrosyl-tRNA synthetase and therefore genuinely performs tRNA charging. Per the audit rule that	This valid parent process is less informative than the separately present tyrosyl-tRNA aminoacylation annotation.	genes/PSEPK/tyrS/tyrS-ai-review.yaml
shallower_than	combined IEA	PSEPK	tyrS	GO:0043039	tRNA aminoacylation	KEEP_AS_NON_CORE	GO:0006437	tyrosyl-tRNA aminoacylation	ACCEPT	Relaxed from MARK_AS_OVER_ANNOTATED. GO:0043039 (tRNA charging) is a true is_a ancestor of GO:0006437 tyrosyl-tRNA aminoacylation, which this record already carries and which is accepted; the protein is a tyrosyl-tRNA synthetase and therefore genuinely performs tRNA charging. Per the audit rule that	The reviewed record specifies the matching aminoacyl-tRNA synthetase reaction; support is electronic/family-rule evidence rather than a direct KT2440 experiment.	genes/PSEPK/tyrS/tyrS-ai-review.yaml
shallower_than	combined IEA	PSEPK	ubiA	GO:0016740	transferase activity	KEEP_AS_NON_CORE	GO:0008412	4-hydroxybenzoate polyprenyltransferase activity	ACCEPT	Relaxed from MARK_AS_OVER_ANNOTATED. UbiA transfers an all-trans polyprenyl group to 4-hydroxybenzoate, so GO:0016740 transferase activity is a true root-level ancestor of the accepted GO:0008412 4-hydroxybenzoate polyprenyltransferase activity. A correct but very general parent is not an over-annot	UniProt assigns EC 2.5.1.39 and Rhea 27782 for octaprenylation of 4-hydroxybenzoate.	genes/PSEPK/ubiA/ubiA-ai-review.yaml
shallower_than	combined IEA	PSEPK	ubiA	GO:0016740	transferase activity	KEEP_AS_NON_CORE	GO:0016765	transferase activity, transferring alkyl or aryl (other than methyl) groups	MARK_AS_OVER_ANNOTATED	Relaxed from MARK_AS_OVER_ANNOTATED. UbiA transfers an all-trans polyprenyl group to 4-hydroxybenzoate, so GO:0016740 transferase activity is a true root-level ancestor of the accepted GO:0008412 4-hydroxybenzoate polyprenyltransferase activity. A correct but very general parent is not an over-annot	GO:0008412 identifies both the aromatic substrate and polyprenyl transfer.	genes/PSEPK/ubiA/ubiA-ai-review.yaml
shallower_than	combined IEA	PSEPK	ubiG	GO:0008168	methyltransferase activity	KEEP_AS_NON_CORE	GO:0010420	polyprenyldihydroxybenzoate methyltransferase activity	MARK_AS_OVER_ANNOTATED	Relaxed from MARK_AS_OVER_ANNOTATED. UbiG is a SAM-dependent O-methyltransferase, so GO:0008168 methyltransferase activity is a true ancestor of both accepted specific activities (GO:0102208 and GO:0061542). A correct general parent is not an over-annotation; it is kept as non-core because the two s	The reviewed UniProt record assigns two reactions on decarboxylated polyprenylphenol/ubiquinol intermediates, not a polyprenyldihydroxybenzoate methylation reaction. Because the GO term cites direct E. coli UbiG work, outright removal would overstate the negative evidence; it is retained as a non-ph	genes/PSEPK/ubiG/ubiG-ai-review.yaml
shallower_than	combined IEA	PSEPK	ubiG	GO:0008168	methyltransferase activity	KEEP_AS_NON_CORE	GO:0061542	3-demethylubiquinol 3-O-methyltransferase activity	ACCEPT	Relaxed from MARK_AS_OVER_ANNOTATED. UbiG is a SAM-dependent O-methyltransferase, so GO:0008168 methyltransferase activity is a true ancestor of both accepted specific activities (GO:0102208 and GO:0061542). A correct general parent is not an over-annotation; it is kept as non-core because the two s	UniProt assigns EC 2.1.1.64 and Rhea 44380 to this reaction.	genes/PSEPK/ubiG/ubiG-ai-review.yaml
shallower_than	combined IEA	PSEPK	ubiG	GO:0008168	methyltransferase activity	KEEP_AS_NON_CORE	GO:0102208	2-polyprenyl-6-hydroxyphenol methylase activity	ACCEPT	Relaxed from MARK_AS_OVER_ANNOTATED. UbiG is a SAM-dependent O-methyltransferase, so GO:0008168 methyltransferase activity is a true ancestor of both accepted specific activities (GO:0102208 and GO:0061542). A correct general parent is not an over-annotation; it is kept as non-core because the two s	UniProt assigns EC 2.1.1.222 and Rhea 31411 to this reaction.	genes/PSEPK/ubiG/ubiG-ai-review.yaml
shallower_than	combined IEA	PSEPK	uppS	GO:0045547	ditrans,polycis-polyprenyl diphosphate synthase [(2E,6E)-farnesyl diphosphate specific] activity	KEEP_AS_NON_CORE	GO:0008834	ditrans,polycis-undecaprenyl-diphosphate synthase [(2E,6E)-farnesyl-diphosphate specific] activity	ACCEPT	Relaxed from MARK_AS_OVER_ANNOTATED with a proposed replacement. QuickGO confirms GO:0008834 (the undecaprenyl-specific term this record already carries and accepts) is_a GO:0045547, so the flagged row is a true ancestor of the enzyme's actual reaction rather than a competing or less accurate claim.	The exact UniProt reaction produces di-trans,octa-cis-undecaprenyl diphosphate.	genes/PSEPK/uppS/uppS-ai-review.yaml
shallower_than	combined IEA	RHOPA	nirK2	GO:0016491	oxidoreductase activity	KEEP_AS_NON_CORE	GO:0050421	nitrite reductase (NO-forming) activity	ACCEPT	Oxidoreductase activity is a true parent for the nitrite reductase reaction, but GO:0050421 captures the specific molecular function and should be treated as the core activity.	This is the precise EC-supported activity for the predicted enzyme. UniProt assigns EC 1.7.2.1 and both NCBIfam and PANTHER place the sequence in conserved multicopper/copper nitrite reductase families. The broad PTHR11709 family is functionally diverse, so the specific activity is justified by EC 1	genes/RHOPA/nirK2/nirK2-ai-review.yaml
shallower_than	combined IEA	SACEN	eryBVII	GO:0016854	racemase and epimerase activity	ACCEPT	GO:0008830	dTDP-4-dehydrorhamnose 3,5-epimerase activity	ACCEPT	Accurate (general) molecular function.	Correct catalytic activity (EC 5.1.3.13). The 3,5-epimerase reaction is shared; the rhamnose naming reflects the canonical example, not a different activity.	genes/SACEN/eryBVII/eryBVII-ai-review.yaml
sole_source		9AVES	TAS1R3	GO:0033041	sweet taste receptor activity	ACCEPT				The GO:0033041 definition does not require the canonical T1R2-partner mechanism, only that the receptor combine with soluble sweet compounds to trigger a cellular response - which is exactly what was demonstrated for hummingbird TAS1R1-TAS1R3 (Calypte anna). Given the well-documented, phylogenetical		genes/9AVES/TAS1R3/TAS1R3-ai-review.yaml
sole_source		9POAL	NCGR_LOCUS10166	GO:0005829	cytosol	UNDECIDED				The sequence includes a plant HDH-like N-terminus and a hydrophobic ARV-like region. Neither predicted organelle targeting nor possible gene-model fusion proves exclusive localization. The exact TreeGrafter source placement and target processing require adjudication.		genes/9POAL/NCGR_LOCUS10166/NCGR_LOCUS10166-ai-review.yaml
sole_source		9POAL	NCGR_LOCUS1270	GO:0005829	cytosol	UNDECIDED				The predicted transit sequence, conserved redox-regulatory insertion and close chloroplast homologs strongly support stromal localization. They do not by themselves establish exclusive import or exclude a conditional cytosolic pool. The source PTN leaf maps to the closely matching chloroplast-associ		genes/9POAL/NCGR_LOCUS1270/NCGR_LOCUS1270-ai-review.yaml
sole_source		9POAL	NCGR_LOCUS1270	GO:0006002	fructose 6-phosphate metabolic process	ACCEPT				GO:0006002 covers chemical reactions involving F6P without requiring a cytosolic location. Chloroplast Calvin-cycle chemistry therefore satisfies the term. The previous review incorrectly treated absent pathway specificity as over-annotation.		genes/9POAL/NCGR_LOCUS1270/NCGR_LOCUS1270-ai-review.yaml
sole_source		9POAL	NCGR_LOCUS27674	GO:0005504	fatty acid binding	REMOVE				This annotation is an artifact of a chimeric gene model. The fatty acid binding function derives from the C-terminal CHI-fold/FAP domain (positions 555-650), which is a separate gene incorrectly fused with the N-terminal UMP-CMP kinase during genome annotation of M. lutarioriparius [PMID:33911077]. 		genes/9POAL/NCGR_LOCUS27674/NCGR_LOCUS27674-ai-review.yaml
sole_source		9POAL	NCGR_LOCUS67308	GO:0022904	respiratory electron transport chain	ACCEPT				Core biological process for SDH2. The electron transfer function of SDH2 is integral to the respiratory electron transport chain.		genes/9POAL/NCGR_LOCUS67308/NCGR_LOCUS67308-ai-review.yaml
sole_source		9PRIM	A0A8C9H4D2	GO:0007165	signal transduction	MARK_AS_OVER_ANNOTATED				OLFML2A is primarily an extracellular matrix-associated glycoprotein. Its influence on signaling pathways is indirect, mediated through ECM interactions, and has been demonstrated mainly in cancer models via perturbation studies. Annotating it to the broad term signal transduction overstates its rol		genes/9PRIM/A0A8C9H4D2/A0A8C9H4D2-ai-review.yaml
sole_source		ACET2	celC	GO:0005576	extracellular region	ACCEPT				Deep research supports extracellular localization. Non-cellulosomal hydrolytic enzymes in C. thermocellum function extracellularly in the milieu of plant biomass. While a signal peptide for CelC is expected for secretion, regulatory and operon studies explicitly classify CelC as non-cellulosomal, im		genes/ACET2/celC/celC-ai-review.yaml
sole_source		ACET2	celC	GO:0009986	cell surface	REMOVE				This annotation is incorrect for CelC. Deep research explicitly states that CelC is categorized as non-cellulosomal and acts as a free enzyme rather than a CipA-bound cellulosomal subunit. Regulatory and operon studies explicitly classify CelC as non-cellulosomal, implying absence of a dockerin modu		genes/ACET2/celC/celC-ai-review.yaml
sole_source		AERER	ermA	GO:0005829	cytosol	ACCEPT				The location is consistent with the protein type and existing UniProt/GOA evidence.		genes/AERER/ermA/ermA-ai-review.yaml
sole_source		AERME	mcr-3	GO:0009244	lipopolysaccharide core region biosynthetic process	MARK_AS_OVER_ANNOTATED				MCR proteins modify lipid A to confer polymyxin resistance; they are not core LPS oligosaccharide biosynthetic enzymes.		genes/AERME/mcr-3/mcr-3-ai-review.yaml
sole_source		AGKCO	fibrolase	GO:0005886	plasma membrane	REMOVE				Fibrolase is a secreted soluble enzyme that functions in the extracellular environment (blood plasma) after envenomation. It has no transmembrane domains or membrane-association motifs, and all functional studies show it acting as a soluble enzyme on soluble or fibrin-bound substrates. The UniProt e		genes/AGKCO/fibrolase/fibrolase-ai-review.yaml
sole_source		ASPRC	fogD	GO:0000140	acylglycerone-phosphate reductase (NADP+) activity	MODIFY				The focused OpenScientist report supports functional divergence from Ayr1: FogD retains the SDR fold and participates in flavoglaucin polyketide redox chemistry, while UniProt records EC 1.1.1.- for CH-OH donor/NAD(P) acceptor chemistry. FogD is only 39.5% identical to yeast Ayr1 and sits in the dis		genes/ASPRC/fogD/fogD-ai-review.yaml
sole_source		ASPRC	fogD	GO:0004806	triacylglycerol lipase activity	MARK_AS_OVER_ANNOTATED				PMID:24187129 validates triacylglycerol lipase activity for the Ayr1 source, so the source annotation is sound. The focused report found no FogD hydrolase assay and placed FogD in a distinct PTHR44169:SF3 secondary-metabolite SDR subfamily only 39.5% identical to Ayr1, making wholesale transfer of A		genes/ASPRC/fogD/fogD-ai-review.yaml
sole_source		ASPRC	fogD	GO:0005783	endoplasmic reticulum	KEEP_AS_NON_CORE				Ayr1 was experimentally localized to the ER, but the focused report found no FogD localization evidence and the demonstrated flavoglaucin-cluster role does not require this compartment. FogD is only 39.5% identical to Ayr1 and falls in the distinct PTHR44169:SF3 subfamily, so the existing row should		genes/ASPRC/fogD/fogD-ai-review.yaml
sole_source		ASPRC	fogD	GO:0005811	lipid droplet	KEEP_AS_NON_CORE				The Ayr1 source has experimentally supported lipid-droplet association, but the focused report found no target localization assay for FogD. A flavoglaucin biosynthetic role does not formally exclude a lipid-droplet pool, yet Ayr1's specific localization is not portable across 39.5% identity and the 		genes/ASPRC/fogD/fogD-ai-review.yaml
sole_source		ASPRC	fogD	GO:0006654	phosphatidic acid biosynthetic process	MARK_AS_OVER_ANNOTATED				Ayr1's phosphatidic-acid-pathway role is real, but it derives from a yeast primary lipid enzyme rather than a FogD-specific phenotype. PMID:32134669 and the PTHR44169:SF3 placement support flavoglaucin biosynthesis for FogD, and the focused report found no evidence that the target also participates 		genes/ASPRC/fogD/fogD-ai-review.yaml
sole_source		ASPRC	fogD	GO:0019433	triglyceride catabolic process	MARK_AS_OVER_ANNOTATED				Ayr1 demonstrates SDR reductase/lipase bifunctionality in the source family, but the focused report supports divergence of FogD's specific substrate scope across the distinct, 39.5%-identical PTHR44169:SF3 subfamily. No FogD-specific evidence places the flavoglaucin-cluster reductase in triglyceride		genes/ASPRC/fogD/fogD-ai-review.yaml
sole_source		BALMU	A0A8B8WEG2	GO:0005634	nucleus	KEEP_AS_NON_CORE				Nuclear localization is context-dependent (cell-cycle-phase specific) rather than the primary location where CDK16 carries out its main functions. The cytoplasm and plasma membrane are the predominant locations.		genes/BALMU/A0A8B8WEG2/A0A8B8WEG2-ai-review.yaml
sole_source		BALMU	A0A8B8WEG2	GO:0005737	cytoplasm	ACCEPT				Cytoplasmic localization is the predominant and best-characterized location for CDK16, supported by immunohistochemistry and cell fractionation studies.		genes/BALMU/A0A8B8WEG2/A0A8B8WEG2-ai-review.yaml
sole_source		BALMU	A0A8B8WEG2	GO:0006887	exocytosis	KEEP_AS_NON_CORE				Exocytosis is a legitimate biological process for CDK16, particularly in neurons, but it is a secondary consequence of CDK16's role in vesicular transport and cytoskeletal regulation rather than a core evolved function of the kinase.		genes/BALMU/A0A8B8WEG2/A0A8B8WEG2-ai-review.yaml
sole_source		BALMU	A0A8B8WEG2	GO:0008021	synaptic vesicle	UNDECIDED				The TreeGrafter annotation is plausible given CDK16's neuronal functions and involvement in vesicular transport, but the deep research literature primarily describes functional regulation of synaptic vesicle processes rather than direct physical localization of CDK16 to synaptic vesicles. Full-text 		genes/BALMU/A0A8B8WEG2/A0A8B8WEG2-ai-review.yaml
sole_source		BALMU	A0A8B8WEG2	GO:0031175	neuron projection development	KEEP_AS_NON_CORE				Neuron projection development is a legitimate biological process for CDK16, supported by experimental evidence in neuronal cell types. However, it represents a tissue-specific downstream effect rather than the core evolved function of this widely expressed kinase.		genes/BALMU/A0A8B8WEG2/A0A8B8WEG2-ai-review.yaml
sole_source		BETPN	Betv1	GO:0005634	nucleus	MARK_AS_OVER_ANNOTATED				Over-propagated with the ABA-receptor annotations; inconsistent with the cytoplasmic localization of Bet v 1.		genes/BETPN/Betv1/Betv1-ai-review.yaml
sole_source		BETPN	Betv2	GO:0005938	cell cortex	KEEP_AS_NON_CORE				Plausible cortical-actin localization; electronic, secondary to the cytoskeletal role.		genes/BETPN/Betv2/Betv2-ai-review.yaml
sole_source		BRUMA	cpi-2	GO:0005737	cytoplasm	REMOVE				Retained as REMOVE on re-review, on architectural grounds rather than on the absence of a target experiment. UniProt annotates a cleaved N-terminal signal peptide (FT SIGNAL 1..25) on the cpi-2 precursor and the mature protein is secreted; the characterized biology is inhibition of host cathepsins L		genes/BRUMA/cpi-2/cpi-2-ai-review.yaml
sole_source		BRUMA	cpi-2	GO:0031982	vesicle	KEEP_AS_NON_CORE						genes/BRUMA/cpi-2/cpi-2-ai-review.yaml
sole_source		CANLF	ALB	GO:0005737	cytoplasm	KEEP_AS_NON_CORE				Biosynthetic/transit localization; the functional compartment is extracellular plasma.		genes/CANLF/ALB/ALB-ai-review.yaml
sole_source		CAPO3	CoBra	GO:0000785	chromatin	ACCEPT				"A sequence-specific transcription factor shown by ChIP to occupy regulatory sites in its own organism is located at chromatin. The ChIP-qPCR covers 20 sites, and the antibody target is the ""CoBra"" of that study, which we map to A0A0D2VUC6 by inference [file:projects/ORIGINS_OF_MULTICELLULARITY/capsa"		genes/CAPO3/CoBra/CoBra-ai-review.yaml
sole_source		CAPO3	CoBra	GO:0001708	cell fate specification	REMOVE				GO defines cell fate specification as designating a cell to follow a developmental path. Capsaspora is unicellular, and no study links CoBra to the choice between its temporal life stages; Bra-motif sites are active in both the amoeboid and aggregative stages [PMID:27114036]. The Xenopus result show		genes/CAPO3/CoBra/CoBra-ai-review.yaml
sole_source		CAPO3	coHpo	GO:0005737	cytoplasm	ACCEPT				Hippo/MST kinases act in the cytoplasm to phosphorylate Warts/LATS, which in turn retains Yorkie in the cytoplasm. A cytoplasmic site of action for coHpo is consistent with its role in cytoplasmic sequestration of coYki in Capsaspora, and the term is broad enough not to over-claim. It remains a fami		genes/CAPO3/coHpo/coHpo-ai-review.yaml
sole_source		CAPO3	coITGB2	GO:0005178	integrin binding	KEEP_AS_NON_CORE				The claim is plausible from conserved motifs and from the presence of alpha partners, and it is not specific to multicellular animals, since it concerns heterodimer assembly rather than any animal ligand. The authors who described the repertoire state explicitly that heterodimerisation is assumed, n		genes/CAPO3/coITGB2/coITGB2-ai-review.yaml
sole_source		CAPO3	coITGB2	GO:0005925	focal adhesion	MARK_AS_OVER_ANNOTATED				Focal adhesions are a specific structure of animal cells, mature integrin adhesions at the ends of stress fibres. In Capsaspora the integrin and vinculin patches lie within filopodia, and the authors themselves describe this as an unexpected role for integrin adhesion within filopodia. They characte		genes/CAPO3/coITGB2/coITGB2-ai-review.yaml
sole_source		CAPO3	coITGB2	GO:0007160	cell-matrix adhesion	MODIFY				"The process is supported, but ""matrix"" implies an extracellular matrix that has not been defined for Capsaspora. The experiments measure attachment to a coated substrate, which is exactly what cell-substrate adhesion (GO:0031589), the parent of cell-matrix adhesion, describes. The integrin is the ad"		genes/CAPO3/coITGB2/coITGB2-ai-review.yaml
sole_source		CAPO3	coITGB2	GO:0007229	integrin-mediated signaling pathway	UNDECIDED				The pathway is plausible, since the signalling components are present and ligand-dependent changes in filopodia are observed. But those changes could equally reflect adhesion mechanics, and no signalling output has been tested. The 2010 authors also caution that scaffold proteins may have had other 		genes/CAPO3/coITGB2/coITGB2-ai-review.yaml
sole_source		CAPO3	coITGB2	GO:0009986	cell surface	KEEP_AS_NON_CORE				Correct for a type I transmembrane adhesion receptor and indirectly supported by the antibody-blocking experiment. It adds little beyond plasma membrane.		genes/CAPO3/coITGB2/coITGB2-ai-review.yaml
sole_source		CAPO3	coITGB2	GO:0016477	cell migration	UNDECIDED				Integrin traction is a plausible contributor to amoeboid crawling, but no data exist for Capsaspora. The process term should wait for a motility assay with the blocking antibody or a knockout.		genes/CAPO3/coITGB2/coITGB2-ai-review.yaml
sole_source		CAPO3	coITGB2	GO:0033627	cell adhesion mediated by integrin	ACCEPT				The term (attachment of a cell to another cell or to a substrate via an integrin) matches the experiment. The integrin is the adhesion receptor, so it does the work of the process. The domain-specific antibody result (ligand-binding domain blocks, stalk does not) argues against a non-specific steric		genes/CAPO3/coITGB2/coITGB2-ai-review.yaml
sole_source		CAPO3	coITGB2	GO:0098609	cell-cell adhesion	MARK_AS_OVER_ANNOTATED				In animals, integrin-dependent cell-cell adhesion comes from binding to counter-receptors on other cells (for example ICAM and VCAM on leukocytes and endothelium). These counter-receptors are animal innovations, and none has been identified in Capsaspora. The term reaches this protein only through a		genes/CAPO3/coITGB2/coITGB2-ai-review.yaml
sole_source		CAPO3	coWts	GO:0005856	cytoskeleton	MARK_AS_OVER_ANNOTATED				The cytoskeletal location is characteristic of the Rho-effector kinases of PTHR22988, and reaches coWts because of the family placement rather than anything known about Warts/LATS. coWts's MOB-binding region and C-terminal kinase domain identify it as a LATS kinase. Animal LATS kinases are cytoplasm		genes/CAPO3/coWts/coWts-ai-review.yaml
sole_source		CAPO3	coYki	GO:0003713	transcription coactivator activity	ACCEPT				The GO definition (activating transcription of specific genes by binding a DNA-binding transcription factor) matches what was shown: coYki binds the DNA-binding transcription factor coSd and the pair activates a target enhancer, and coYki alone does not activate transcription in the fly eye. The cro		genes/CAPO3/coYki/coYki-ai-review.yaml
sole_source		CAPO3	coYki	GO:0035329	hippo signaling	ACCEPT				Here the IEA is borne out experimentally in the organism itself. The term names the Yorkie/YAP effector in its definition, and it is not restricted to animals or tied to growth control. Its parents are signal-transduction terms, not multicellular or developmental processes. It is therefore not a TAX		genes/CAPO3/coYki/coYki-ai-review.yaml
sole_source		CAPO3	coYki	GO:0045944	positive regulation of transcription by RNA polymerase II	ACCEPT				This process follows directly from the coactivator activity. coYki does part of the work by bringing activation capacity to the TEAD-family factor coSd: coSd alone does not drive the targets, and the complex does. The Capsaspora RNA-seq shows coYki-dependent gene expression in vivo, but cannot separ		genes/CAPO3/coYki/coYki-ai-review.yaml
sole_source		CAUVC	fliI	GO:0046933	proton-transporting ATP synthase activity, rotational mechanism	REMOVE				The annotation is contradicted by the biology. FliI does not synthesize ATP or transport protons. Its ATPase is insensitive to F-type ATPase inhibitors, and proton flux in the flagellar export system runs through the export gate (a proton-protein antiporter involving FlhA), not through FliI. The tar		genes/CAUVC/fliI/fliI-ai-review.yaml
sole_source		CERSP	dorR	GO:0000156	phosphorelay response regulator activity	ACCEPT						genes/CERSP/dorR/dorR-ai-review.yaml
sole_source		CERSP	dorR	GO:0032993	protein-DNA complex	ACCEPT						genes/CERSP/dorR/dorR-ai-review.yaml
sole_source		CHRVO	Q7NUH2	GO:0006950	response to stress	UNDECIDED				While many MarR family regulators are involved in stress responses, this is not universal for the family. Without experimental evidence or knowledge of the specific regulon controlled by CV_2726, it is uncertain whether this particular MarR protein regulates stress-responsive genes. The TreeGrafter 		genes/CHRVO/Q7NUH2/Q7NUH2-ai-review.yaml
sole_source		COTJA	A0A8C2TBA7	GO:0005576	extracellular region	ACCEPT				"PAM exists in both membrane-bound and soluble forms. Soluble PAM forms generated through endoproteolytic processing are secreted into the extracellular space in active form. The deep research confirms ""Soluble PAM forms generated through endoproteolytic processing can be secreted into the extracellu"		genes/COTJA/A0A8C2TBA7/A0A8C2TBA7-ai-review.yaml
sole_source		CRIGR	HSPH1	GO:0005634	nucleus	KEEP_AS_NON_CORE				Nuclear localization is supported by literature on mammalian HSPH1 orthologs. The deep research review cites Chuang et al. 2024 as reporting constitutive cytoplasmic and nuclear localization. However, the primary functional compartment is the cytosol where the holdase and NEF activities operate. Kee		genes/CRIGR/HSPH1/HSPH1-ai-review.yaml
sole_source		CRIGR	HSPH1	GO:0006457	protein folding	KEEP_AS_NON_CORE				HSPH1 participates in the protein folding pathway by preventing aggregation and maintaining substrates in a folding-competent state for subsequent refolding by Hsc70/Hdj-1. The BP term 'protein folding' is broadly acceptable but HSPH1 is a holdase, not a foldase, so this is kept as non-core. Its dir		genes/CRIGR/HSPH1/HSPH1-ai-review.yaml
sole_source		CYLST	AmiC2	GO:0030288	outer membrane-bounded periplasmic space	ACCEPT				Consistent with a secreted amidase acting on periplasmic septal PG; not wrong, though less specific than the septal localization observed for the AmiC2 ortholog.		genes/CYLST/AmiC2/AmiC2-ai-review.yaml
sole_source		DESPS	nrfA	GO:0019645	anaerobic electron transport chain	ACCEPT				The reviewed UniProt record identifies NrfA as an ammonia-forming cytochrome c nitrite reductase, a periplasmic respiratory enzyme that consumes reduced cytochrome c during anaerobic nitrite reduction. Falcon supports the conserved NrfA reaction but did not recover DESPS-specific electron-partner ex		genes/DESPS/nrfA/nrfA-ai-review.yaml
sole_source		DESRO	K9IFT7	GO:0005615	extracellular space	ACCEPT				The 1–23 signal peptide and UniProt secretion assignment support the extracellular mature peptide. Extracellular region and extracellular space are compatible; a broad parent is not an erroneous location.		genes/DESRO/K9IFT7/K9IFT7-ai-review.yaml
sole_source		DESRO	K9IFT7	GO:0031731	CCR6 chemokine receptor binding	KEEP_AS_NON_CORE				The focused OpenScientist defensin report supports DEFB1-like placement well enough to keep the CCR6 TreeGrafter row, but found no direct assay of K9IFT7 or any bat defensin and emphasized that beta-defensin receptor usage varies. Treat the interaction as a low-confidence non-core molecular-function		genes/DESRO/K9IFT7/K9IFT7-ai-review.yaml
sole_source		DESRO	K9IIP0	GO:0005615	extracellular space	ACCEPT				Signal peptide, family behaviour, and orthologue annotation all agree. The LC-MS/MS detection was made on principal gland tissue, so strictly it is expression evidence rather than localisation evidence; it corroborates that the protein is made in quantity here, while the secreted localisation itself		genes/DESRO/K9IIP0/K9IIP0-ai-review.yaml
sole_source		DESRO	K9IIP0	GO:0050728	negative regulation of inflammatory response	ACCEPT				Well-supported family function with experimental backing in the human orthologue and an identified mechanism that depends on the Link module, which is intact in this protein. REMOVE is reserved for annotations that can be argued against on biological grounds; this one cannot.		genes/DESRO/K9IIP0/K9IIP0-ai-review.yaml
sole_source		DESRO	K9IJK6	GO:0014909	smooth muscle cell migration	MARK_AS_OVER_ANNOTATED				The focused OpenScientist report retains the secreted serine-protease/plasminogen-activation core but finds no positive evidence that compact salivary DSPA-gamma executes the downstream cellular smooth-muscle roles inherited from full-length mammalian tPA. K9IJK6 lacks the finger and EGF domains tha		genes/DESRO/K9IJK6/K9IJK6-ai-review.yaml
sole_source		DESRO	K9IJK6	GO:0048008	platelet-derived growth factor receptor signaling pathway	MARK_AS_OVER_ANNOTATED				The focused OpenScientist report retains the secreted serine-protease/plasminogen-activation core but finds no positive evidence that compact salivary DSPA-gamma executes inherited platelet-derived growth factor receptor signaling biology. K9IJK6 lacks full-length tPA exosites and acts in saliva rat		genes/DESRO/K9IJK6/K9IJK6-ai-review.yaml
sole_source		DESRO	K9IMD0	GO:0005769	early endosome	MARK_AS_OVER_ANNOTATED				The focused lactotransferrin report found no positive evidence for a membrane or endosomal draculin pool. Early-endosome localization is inherited from mammalian lactoferrin-receptor recycling, a context not established for the secreted salivary bat protein.		genes/DESRO/K9IMD0/K9IMD0-ai-review.yaml
sole_source		DESRO	K9IMD0	GO:0005886	plasma membrane	MARK_AS_OVER_ANNOTATED				The focused lactotransferrin report found no positive evidence for a membrane or endosomal draculin pool. Plasma-membrane localization is inherited from mammalian lactoferrin-receptor recycling, a context not established for the secreted salivary bat protein.		genes/DESRO/K9IMD0/K9IMD0-ai-review.yaml
sole_source		DESRO	K9IMD0	GO:0055037	recycling endosome	MARK_AS_OVER_ANNOTATED				The focused lactotransferrin report found no positive evidence for a membrane or endosomal draculin pool. Recycling-endosome localization is inherited from mammalian lactoferrin-receptor recycling, a context not established for the secreted salivary bat protein.		genes/DESRO/K9IMD0/K9IMD0-ai-review.yaml
sole_source		DESRO	K9IWC0	GO:0006182	cGMP biosynthetic process	ACCEPT				Correct for a natriuretic peptide of any subtype. Accepted with the receptor identity corrected in the summary rather than modified, since the GO term itself does not name a receptor.		genes/DESRO/K9IWC0/K9IWC0-ai-review.yaml
sole_source		DESRO	K9IWC0	GO:0007168	receptor guanylyl cyclase signaling pathway	ACCEPT				Directly supported. This is the signalling pathway the peptide initiates.		genes/DESRO/K9IWC0/K9IWC0-ai-review.yaml
sole_source		DESRO	K9IWR0	GO:0043123	positive regulation of canonical NF-kappaB signal transduction	ACCEPT				Relaxed from MARK_AS_OVER_ANNOTATED on re-review. The previous rejection rested only on the absence of a Desmodus-specific experiment, which is not evidence against a supported phylogenetic inference. The protein carries the complete TNF-domain architecture (Pfam PF00229; InterPro IPR002960 TNF_beta		genes/DESRO/K9IWR0/K9IWR0-ai-review.yaml
sole_source		DESRO	K9IWR0	GO:2001238	positive regulation of extrinsic apoptotic signaling pathway	ACCEPT				Relaxed from MARK_AS_OVER_ANNOTATED on re-review. The earlier rejection cited only the lack of a Desmodus-specific assay. The target has the full TNF ligand architecture and subfamily assignment, and the cytotoxic, TNFR1-mediated activity of lymphotoxin-alpha is the basis of the term; positive regul		genes/DESRO/K9IWR0/K9IWR0-ai-review.yaml
sole_source		DESRO	K9J287	GO:0003677	DNA binding	KEEP_AS_NON_CORE				Relaxed from MARK_AS_OVER_ANNOTATED on re-review. The previous rejection gave only the absence of a direct binding assay, which is not evidence against the propagation. Binding DNA is entailed by the DNase I activity accepted elsewhere in this review, so the term is true rather than over-attributed;		genes/DESRO/K9J287/K9J287-ai-review.yaml
sole_source		DESRO	K9J287	GO:0005634	nucleus	REMOVE				UniProt subcellular location indicates endoplasmic reticulum, not nucleus.		genes/DESRO/K9J287/K9J287-ai-review.yaml
sole_source		DESVH	Q72DS9	GO:0005886	plasma membrane	ACCEPT				Multiple lines of evidence support plasma membrane localization. Phobius prediction of 6 TM helices, InterPro domains including transmembrane di-heme cytochromes (Gene3D 1.20.950.20), and literature explicitly describing Qmo as membrane-bound. This is a core localization for QmoC function.		genes/DESVH/Q72DS9/Q72DS9-ai-review.yaml
sole_source		DESVH	Q72DT2	GO:0005886	plasma membrane	ACCEPT				PMID:23842468 reports AprA and AprB together with Qmo subunits in membrane preparations from the exact strain, supported by reciprocal affinity purification. This establishes more than a predicted electron-transfer partnership. GO:0005886 includes the phospholipid bilayer and associated proteins; it		genes/DESVH/Q72DT2/Q72DT2-ai-review.yaml
sole_source		DESVH	Q72DT2	GO:0009055	electron transfer activity	ACCEPT				Live QuickGO rechecked on 2026-09-23 defines directed electron movement between molecular entities and explicitly includes redox transformations in enzymatic metabolic reactions. It does not restrict GO:0009055 to a separate electron-transport carrier. In AprAB, AprB supplies the Fe-S relay while Ap		genes/DESVH/Q72DT2/Q72DT2-ai-review.yaml
sole_source		DESVH	Q72DT2	GO:0009061	anaerobic respiration	MODIFY				While anaerobic respiration is technically correct, the more specific term GO:0019420 (dissimilatory sulfate reduction) precisely captures AprA's biological role. AprA catalyzes a key step in this pathway where APS is reduced to sulfite.		genes/DESVH/Q72DT2/Q72DT2-ai-review.yaml
sole_source		DESVH	Q72DT2	GO:0050660	flavin adenine dinucleotide binding	ACCEPT				FAD binding is well-established for AprA based on domain architecture (FAD-binding_2 domain) and functional characterization. The FAD cofactor is central to the catalytic mechanism of APS reduction.		genes/DESVH/Q72DT2/Q72DT2-ai-review.yaml
sole_source		DOROP	ADAR2	GO:0003726	double-stranded RNA adenosine deaminase activity	ACCEPT				This is the defining catalytic activity of sqADAR2 and the most important molecular function annotation. It has been demonstrated directly using recombinant enzyme on multiple substrates, with quantitative activity data. The term is at exactly the right level of specificity.		genes/DOROP/ADAR2/ADAR2-ai-review.yaml
sole_source		DOROP	ADAR2	GO:0006382	adenosine to inosine editing	ACCEPT				A-to-I editing is the defining biological process for sqADAR2. This is supported by extensive direct evidence from multiple studies using recombinant protein assays and transcriptome-wide editing profiling. The term is at exactly the right level of specificity.		genes/DOROP/ADAR2/ADAR2-ai-review.yaml
sole_source		DORPE	AP180	GO:0000149	SNARE binding	UNDECIDED				No direct evidence for SNARE binding by squid AP180. However, the ANTH domain of AP180/CALM family members binds directly to the SNARE motif of VAMP2/synaptobrevin, and this interaction is conserved from yeast to mammals. AP180-knockout mice show greatly reduced VAMP2 in synaptic vesicles, and yeast		genes/DORPE/AP180/AP180-ai-review.yaml
sole_source		DORPE	AP180	GO:0006900	vesicle budding from membrane	KEEP_AS_NON_CORE				Vesicle budding from membrane is a valid but very general description of AP180 function. The protein's role is specifically in clathrin-mediated vesicle budding at the synapse. More specific terms (GO:0048268 clathrin coat assembly, GO:0048488 synaptic vesicle endocytosis) capture the core function 		genes/DORPE/AP180/AP180-ai-review.yaml
sole_source		DORPE	cpx	GO:0043195	terminal bouton	ACCEPT				Terminal bouton localization is consistent with the known function of complexin at presynaptic terminals. The squid giant synapse experiments directly demonstrate complexin activity at the presynaptic terminal. While the squid giant synapse is not a classical bouton, the TreeGrafter inference from m		genes/DORPE/cpx/cpx-ai-review.yaml
sole_source		DROVI	B4MAQ2	GO:0003723	RNA binding	ACCEPT				RNA binding is a genuine molecular function of Exportin-5 proteins, which directly contact structured RNA cargo. The term is somewhat broad but accurately reflects the protein's activity.		genes/DROVI/B4MAQ2/B4MAQ2-ai-review.yaml
sole_source		DROVI	B4MAQ2	GO:0005634	nucleus	ACCEPT				Nuclear localization is a fundamental aspect of exportin function, as these receptors must be present in the nucleus to bind cargo and RanGTP before translocation through the nuclear pore.		genes/DROVI/B4MAQ2/B4MAQ2-ai-review.yaml
sole_source		DROVI	B4MAQ2	GO:0005737	cytoplasm	ACCEPT				Cytoplasmic presence is intrinsic to the exportin transport cycle, where cargo is released and the receptor is recycled back to the nucleus.		genes/DROVI/B4MAQ2/B4MAQ2-ai-review.yaml
sole_source		DROVI	B4MAQ2	GO:0006405	RNA export from nucleus	ACCEPT				RNA nuclear export is the central biological process for Exportin-5 proteins, directly supported by the domain architecture and Drosophila Exportin-5 literature showing export of pre-miRNAs and tRNAs.		genes/DROVI/B4MAQ2/B4MAQ2-ai-review.yaml
sole_source		DROVI	B4MAQ2	GO:0042565	RNA nuclear export complex	ACCEPT				The RNA nuclear export complex is the functional assembly through which Exportin-5 performs its transport activity, supported by extensive biochemical and structural evidence from the exportin-5 literature.		genes/DROVI/B4MAQ2/B4MAQ2-ai-review.yaml
sole_source		ECOLX	mcr-1	GO:0009244	lipopolysaccharide core region biosynthetic process	MARK_AS_OVER_ANNOTATED				Mechanistically inaccurate over-propagation: a lipid A phosphoethanolamine transferase is binned under 'LPS core region biosynthetic process'. The accurate process is captured by the NEW 'response to antibiotic' annotation below; the molecular event is lipid A modification, not core biosynthesis.		genes/ECOLX/mcr-1/mcr-1-ai-review.yaml
sole_source		ECOLX	mcr2	GO:0009244	lipopolysaccharide core region biosynthetic process	MARK_AS_OVER_ANNOTATED				MCR proteins modify lipid A to confer polymyxin resistance; they are not core LPS oligosaccharide biosynthetic enzymes.		genes/ECOLX/mcr2/mcr2-ai-review.yaml
sole_source		FELCA	ALB	GO:0005737	cytoplasm	KEEP_AS_NON_CORE				Biosynthetic/transit localization; the functional compartment is extracellular plasma.		genes/FELCA/ALB/ALB-ai-review.yaml
sole_source		FISTH	AmiC1	GO:0030288	outer membrane-bounded periplasmic space	ACCEPT						genes/FISTH/AmiC1/AmiC1-ai-review.yaml
sole_source		FISTH	AmiC2	GO:0030288	outer membrane-bounded periplasmic space	ACCEPT				Consistent with a secreted amidase acting on periplasmic septal PG; not wrong, though less specific than the septal localization observed for the AmiC2 ortholog.		genes/FISTH/AmiC2/AmiC2-ai-review.yaml
sole_source		FUSNU	pepV	GO:0006526	L-arginine biosynthetic process	REMOVE				The M20A family (PTHR43808) is broad and contains multiple functionally distinct subfamilies, including PepV dipeptidases, ArgE/acetylornithine deacetylase, and DapE. TreeGrafter placed A0A133P372 on the acetylornithine-deacetylase node, but the PepV-specific CDD/TIGRFAM/InterPro signatures and the 		genes/FUSNU/pepV/pepV-ai-review.yaml
sole_source		GADMO	A0A8C5FPT8	GO:0005096	GTPase activator activity	UNDECIDED				The deep research clearly establishes that mammalian TBC1D14 does not function as a GAP for RAB11, its primary binding partner. However, GAP activity toward other Rab substrates has not been tested and cannot be excluded. The TreeGrafter inference from the TBC domain is a reasonable default but may 		genes/GADMO/A0A8C5FPT8/A0A8C5FPT8-ai-review.yaml
sole_source		HELPJ	fliI	GO:0046933	proton-transporting ATP synthase activity, rotational mechanism	REMOVE				The term requires ATP synthesis from ADP and Pi driven by rotary proton transport through a membrane Fo sector. FliI is a soluble ATP-consuming export ATPase: its activity is insensitive to F-type ATPase inhibitors, it has no Fo partner, and in the flagellar export system protons are conducted by th		genes/HELPJ/fliI/fliI-ai-review.yaml
sole_source		HETGA	Cd44	GO:0006954	inflammatory response	KEEP_AS_NON_CORE				The phylogenetic placement is sound and CD44's inflammatory role is deeply conserved, so there is no positive argument for removal. But naked mole-rat immunology is atypical - their immune cell populations lack natural killer cells and they are not broadly disease-resistant - and none of the naked m		genes/HETGA/Cd44/Cd44-ai-review.yaml
sole_source		HETGA	Cgas	GO:0002218	activation of innate immune response	ACCEPT				Innate immune activation is the inherited signaling role of cGAMP production upstream of STING; target repair-specialization evidence does not negate that separate core signaling branch. The curated ancestral cGAS inference is supported by the intact catalytic triad, zinc thumb and nucleotide-bindin		genes/HETGA/Cgas/Cgas-ai-review.yaml
sole_source		HETGA	Cgas	GO:0002230	positive regulation of defense response to virus by host	ACCEPT				The antiviral-defense regulation term concerns inherited cGAMP-STING immune signaling, not the target-specific homologous-recombination phenotype. The curated ancestral cGAS inference is supported by the intact catalytic triad, zinc thumb and nucleotide-binding machinery in A0AAX6RS70 and mammalian 		genes/HETGA/Cgas/Cgas-ai-review.yaml
sole_source		HETGA	Cgas	GO:0003682	chromatin binding	ACCEPT				This is the one molecular function for which there is explicit naked-mole-rat evidence. The primary study reports that the four species-specific substitutions make cGAS retain chromatin longer after DNA damage, and refers to the resulting state as prolonged chromatin binding. The structural basis is		genes/HETGA/Cgas/Cgas-ai-review.yaml
sole_source		HETGA	Cgas	GO:0003690	double-stranded DNA binding	ACCEPT				cGAS reads B-form double-stranded DNA through a zinc thumb and a set of basic DNA-binding surfaces. Residue transfer from human cGAS shows the zinc thumb intact (H390/C396/C397/C404 to H422/C428/C429/C436) and the C-terminal DNA-binding region 384-407 at 62.5% identity, i.e. ordinary orthologue-leve		genes/HETGA/Cgas/Cgas-ai-review.yaml
sole_source		HETGA	Cgas	GO:0005634	nucleus	ACCEPT				The entire naked-mole-rat phenotype is a nuclear one — retention on chromatin after DNA damage, promotion of the FANCI-RAD50 interaction, and RAD50 recruitment to damage sites. A protein cannot do that without a nuclear pool. This is therefore not merely a propagated localization but one corroborate		genes/HETGA/Cgas/Cgas-ai-review.yaml
sole_source		HETGA	Cgas	GO:0005829	cytosol	ACCEPT				Cytosolic localization is the best-established property of cGAS in mammals, and the Euteleostomi node carries it on experimental grounding from both human CGAS and mouse Cgas. Nothing in the naked-mole-rat work excludes a cytosolic pool: what changes in this species is how long the protein stays on 		genes/HETGA/Cgas/Cgas-ai-review.yaml
sole_source		HETGA	Cgas	GO:0006974	DNA damage response	ACCEPT				The propagated term is confirmed in the target species. cGAS in the naked mole-rat changes its behaviour specifically upon DNA damage — it is retained on chromatin instead of being extracted — and that change feeds directly into repair-factor recruitment. The term is broad, but here breadth is appro		genes/HETGA/Cgas/Cgas-ai-review.yaml
sole_source		HETGA	Cgas	GO:0032481	positive regulation of type I interferon production	ACCEPT				Type I interferon production is regulated downstream of the conserved cGAMP-STING branch; this is retained as a phylogenetic inference, not asserted as a direct naked-mole-rat cytokine assay. The curated ancestral cGAS inference is supported by the intact catalytic triad, zinc thumb and nucleotide-b		genes/HETGA/Cgas/Cgas-ai-review.yaml
sole_source		HETGA	Cgas	GO:0035861	site of double-strand break	ACCEPT				"The naked-mole-rat abstract does not use the phrase ""site of double-strand break"", so the direct localization claim is one step beyond what it literally states. But it does say that cGAS is retained on chromatin specifically upon DNA damage and that this facilitates RAD50 recruitment to damage sites"		genes/HETGA/Cgas/Cgas-ai-review.yaml
sole_source		HETGA	Cgas	GO:0038001	paracrine signaling	ACCEPT				GO:0038001 specifies transmission through intercellular fluid. Primary PMID:33768207 establishes export of freely soluble cGAMP and effects on recipient immune cells; this is the relevant paracrine comparator, whereas the gap-junction route in PMID:24077100 alone would not meet that definition. cGAS		genes/HETGA/Cgas/Cgas-ai-review.yaml
sole_source		HETGA	Cgas	GO:0061501	2',3'-cyclic GMP-AMP synthase activity	ACCEPT				This term comes from a different and much deeper node than the rest of the set — PTN000838114 at taxon:6072 (Eumetazoa), seeded by eight members spanning fly cGLRs, zebrafish, mouse and human — and the naked mole rat is well inside it. Since no naked-mole-rat enzymology exists, the propagation was c		genes/HETGA/Cgas/Cgas-ai-review.yaml
sole_source		HETGA	Cgas	GO:0071360	cellular response to exogenous dsRNA	MODIFY				The focused OpenScientist donor audit found that the four mouse experimental sources behind GO:0071360 test cytosolic DNA, DNA virus, dsDNA binding, or dsDNA-dependent cGAS activation, not exogenous dsRNA or poly(I:C)-driven cGAS signaling. The defect is a dsRNA/dsDNA term-selection error in the don		genes/HETGA/Cgas/Cgas-ai-review.yaml
sole_source		HETGA	Cgas	GO:2000042	negative regulation of double-strand break repair via homologous recombination	REMOVE				This is the one propagated term with direct, species-specific evidence against it. The primary study states that naked-mole-rat cGAS lacks the suppressive function that the human and mouse orthologs have in homologous recombination repair, and attributes the difference to four amino acids fixed duri		genes/HETGA/Cgas/Cgas-ai-review.yaml
sole_source		HETGA	Ntrk1	GO:0010976	positive regulation of neuron projection development	ACCEPT				Most annotations on this protein are untested electronic projections; this one is not. Park et al. cultured naked mole-rat dorsal root ganglion neurons and showed that in the absence of NGF they elaborate very few neurites, whereas with 500 ng/mL NGF the same TrkA-positive cells elaborate extensive 		genes/HETGA/Ntrk1/Ntrk1-ai-review.yaml
sole_source		HETGA	Ntrk1	GO:0030424	axon	KEEP_AS_NON_CORE				TrkA in sensory and sympathetic neurons is internalised at axon terminals and retrogradely transported in signalling endosomes, which is the basis for the TreeGrafter projection from PTN000699860. In the naked mole-rat, TrkA-positive dorsal root ganglion neurons certainly exist and project axons in 		genes/HETGA/Ntrk1/Ntrk1-ai-review.yaml
sole_source		HETGA	Ntrk1	GO:0043121	neurotrophin binding	ACCEPT				The naked mole-rat ectodomain has diverged, including the juxtamembrane NGF-binding region, which raises the obvious question of whether ligand binding is compromised. Omerbasic et al. tested precisely this: a chimera carrying the rat extracellular domain with the naked mole-rat transmembrane and ki		genes/HETGA/Ntrk1/Ntrk1-ai-review.yaml
sole_source		HETGA	Ntrk1	GO:0043235	signaling receptor complex	ACCEPT				Receptor tyrosine kinases are annotated part_of a receptor complex because the signalling unit is a dimer, not a monomer; TrkA additionally associates with the co-receptor p75NTR in the characterised orthologues. For the naked mole-rat protein the relevant direct observation is that the receptor bea		genes/HETGA/Ntrk1/Ntrk1-ai-review.yaml
sole_source		HETGA	Ntrk1	GO:0051897	positive regulation of phosphatidylinositol 3-kinase/protein kinase B signal transduction	KEEP_AS_NON_CORE				The PANTHER node assertion rests on the characterised orthologues, where TrkA autophosphorylation recruits PI3K through IRS proteins and sustained AKT activation underlies NGF-dependent survival. The naked mole-rat measurements did not touch this branch: the SILAC phosphoproteomics and westerns quan		genes/HETGA/Ntrk1/Ntrk1-ai-review.yaml
sole_source		HETGA	Scn9a	GO:0019228	neuronal action potential	ACCEPT				This is the process term the naked-mole-rat literature actually argues about. The published mechanism is that acid prevents action potential initiation in this species by blocking this channel, which presupposes that the channel drives action potential initiation in the first place. Neither the proj		genes/HETGA/Scn9a/Scn9a-ai-review.yaml
sole_source		HETGA	Scn9a	GO:0086010	membrane depolarization during action potential	ACCEPT				Correct, specific, and the process on which the entire naked-mole-rat acid phenotype turns: when the variant channel is proton-blocked, the depolarization that would initiate the action potential does not occur, which is why acid silences rather than excites these neurons.		genes/HETGA/Scn9a/Scn9a-ai-review.yaml
sole_source		HETGA	Tac1	GO:0006954	inflammatory response	KEEP_AS_NON_CORE				This is the one row where the naked-mole-rat literature legitimately changes the curation call, and it changes it to non-core rather than to REMOVE. Two facts pull in opposite directions and both must be respected. On one side, the peptidergic inflammatory arm is explicitly described as hypofunction		genes/HETGA/Tac1/Tac1-ai-review.yaml
sole_source		HETGA	Tac1	GO:0031835	substance P receptor binding	ACCEPT				This is the annotation that the naked-mole-rats-lack-substance-P framing would tempt a reviewer to remove, and removing it would be wrong. The claim in the literature is about where the peptide is made, not about what it is: substance P occupies positions 58-68 of this precursor as RPKPQQFFGLM, with		genes/HETGA/Tac1/Tac1-ai-review.yaml
sole_source		HYPJE	IRE1	GO:0070059	intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress	MARK_AS_OVER_ANNOTATED				The focused fungal IRE1 report found no evidence that Trichoderma IRE1 drives the mammalian IRE1-TRAF2-ASK1/JNK apoptotic arm. The direct target paper supports adaptive UPR signaling through kinase autophosphorylation and HAC1 processing, while the apoptotic branch derives from mammalian SF17 IRE1 e		genes/HYPJE/IRE1/IRE1-ai-review.yaml
sole_source		MACFA	A0A2K5UJ34	GO:0032474	otolith morphogenesis	MARK_AS_OVER_ANNOTATED				Otoliths are fish-specific structures. Macaques have otoconia, not otoliths. The TreeGrafter transfer from zebrafish propagated a taxon-inappropriate term. While the gene may be involved in inner ear development in mammals, this specific term should not be applied to a primate protein.		genes/MACFA/A0A2K5UJ34/A0A2K5UJ34-ai-review.yaml
sole_source		MACFA	A0A2K5UJ34	GO:0060271	cilium assembly	ACCEPT				Cilium assembly is a conserved process across metazoans. TTC39C ciliary localization has been experimentally validated in C. elegans, the zebrafish ortholog has IMP evidence for cilium-dependent developmental processes, and TPR domain proteins commonly function as ciliary scaffolds. The IEA TreeGraf		genes/MACFA/A0A2K5UJ34/A0A2K5UJ34-ai-review.yaml
sole_source		METEA	ackA	GO:0006083	acetate metabolic process	ACCEPT						genes/METEA/ackA/ackA-ai-review.yaml
sole_source		METEA	fumC	GO:0006108	malate metabolic process	ACCEPT						genes/METEA/fumC/fumC-ai-review.yaml
sole_source		METEA	gck	GO:0005737	cytoplasm	ACCEPT						genes/METEA/gck/gck-ai-review.yaml
sole_source		METEA	gcvH	GO:0005737	cytoplasm	ACCEPT				Localization to the cytoplasm is the most defensible annotation for a bacterial glycine cleavage system H protein; the GCS and associated one-carbon transformations are soluble central-metabolic processes.		genes/METEA/gcvH/gcvH-ai-review.yaml
sole_source		METEA	gcvH	GO:0009249	protein lipoylation	ACCEPT				GcvH carries the canonical biotin/lipoyl-binding fold with a conserved lipoylated lysine (Lys-58); lipoylation of this acceptor is well supported across bacteria and is essential for carrier function.		genes/METEA/gcvH/gcvH-ai-review.yaml
sole_source		METEA	gcvP	GO:0005829	cytosol	ACCEPT				Cytosolic localization is consistent with the bacterial glycine cleavage system, which operates as a soluble multi-protein complex in the cytosol rather than membrane-bound or secreted.		genes/METEA/gcvP/gcvP-ai-review.yaml
sole_source		METEA	gcvP	GO:0005960	glycine cleavage complex	ACCEPT				GcvP is a defining subunit of the four-protein glycine cleavage complex (P, T, H, L); the complex is the structure within which its catalytic function is exercised.		genes/METEA/gcvP/gcvP-ai-review.yaml
sole_source		METEA	gcvP	GO:0016594	glycine binding	ACCEPT				Glycine binding is an integral part of the P-protein catalytic cycle, with glycine documented as the specific substrate. Substrate binding is a meaningful molecular function annotation supporting the catalytic activity.		genes/METEA/gcvP/gcvP-ai-review.yaml
sole_source		METEA	gcvP	GO:0030170	pyridoxal phosphate binding	ACCEPT				PLP is the essential prosthetic group of the P-protein and is required for glycine binding and decarboxylation; the covalent attachment at Lys-699 (UniProt) and PLP-dependence of the reaction are well supported.		genes/METEA/gcvP/gcvP-ai-review.yaml
sole_source		METEA	mdcD	GO:0006633	fatty acid biosynthetic process	REMOVE				MdcD acts in the malonate-degradation complex with a specialized MdcC carrier. It does not provide the malonyl-CoA-building reaction of acetyl-CoA carboxylase. The distinct substrate-carrier and target neighborhood, rather than simple absence of a native assay, argue against this inherited pathway a		genes/METEA/mdcD/mdcD-ai-review.yaml
sole_source		METEA	mdcD	GO:2001295	malonyl-CoA biosynthetic process	REMOVE				The characterized homologous complex decarboxylates malonyl groups on specialized MdcC and regenerates acetyl-MdcC. It does not synthesize malonyl-CoA. The target MdcD-specific family and mdcA/C/E neighborhood support that pathway distinction.		genes/METEA/mdcD/mdcD-ai-review.yaml
sole_source		METEA	mluR	GO:0016989	sigma factor antagonist activity	ACCEPT						genes/METEA/mluR/mluR-ai-review.yaml
sole_source		METEA	mxbM	GO:0000156	phosphorelay response regulator activity	ACCEPT						genes/METEA/mxbM/mxbM-ai-review.yaml
sole_source		METEA	mxbM	GO:0005829	cytosol	ACCEPT						genes/METEA/mxbM/mxbM-ai-review.yaml
sole_source		METEA	mxbM	GO:0032993	protein-DNA complex	KEEP_AS_NON_CORE						genes/METEA/mxbM/mxbM-ai-review.yaml
sole_source		METEA	sucB	GO:0005829	cytosol	ACCEPT				Appropriate cellular localization for a bacterial TCA cycle enzyme. Bacteria lack membrane-bound organelles, so the OGDH complex operates in the cytosol. The TreeGrafter annotation is consistent with expected bacterial cell biology.		genes/METEA/sucB/sucB-ai-review.yaml
sole_source		METTP	gatC	GO:0070681	glutaminyl-tRNAGln biosynthesis via transamidation	ACCEPT						genes/METTP/gatC/gatC-ai-review.yaml
sole_source		MISSI	DHS	GO:0005737	cytoplasm	ACCEPT				The UniProt entry and TreeGrafter GOA row both place this deoxyhypusine synthase in the cytoplasm.		genes/MISSI/DHS/DHS-ai-review.yaml
sole_source		MISSI	DHS	GO:0034038	deoxyhypusine synthase activity	ACCEPT				The protein is named deoxyhypusine synthase, has the DHS family/domain assignment, and the GOA/UniProt cross-reference supports this activity.		genes/MISSI/DHS/DHS-ai-review.yaml
sole_source		MYTGA	A0A8B6GS20	GO:0005737	cytoplasm	ACCEPT						genes/MYTGA/A0A8B6GS20/A0A8B6GS20-ai-review.yaml
sole_source		MYTGA	A0A8B6GS20	GO:0010507	negative regulation of autophagy	MARK_AS_OVER_ANNOTATED				MTMR9 does not directly regulate autophagy. Its role is indirect, through modulation of active MTMR partners. The evidence for a specifically negative regulatory role is weak; some data suggest the opposite direction.		genes/MYTGA/A0A8B6GS20/A0A8B6GS20-ai-review.yaml
sole_source		MYTGA	A0A8B6GS20	GO:0019903	protein phosphatase binding	ACCEPT						genes/MYTGA/A0A8B6GS20/A0A8B6GS20-ai-review.yaml
sole_source		MYTGA	A0A8B6GS20	GO:0046856	phosphatidylinositol dephosphorylation	MODIFY				MTMR9 cannot catalyze phosphatidylinositol dephosphorylation due to absence of the catalytic cysteine. Its role is regulatory, modulating the activity of active MTMR partners. GO:0060304 (regulation of phosphatidylinositol dephosphorylation) better captures this function.		genes/MYTGA/A0A8B6GS20/A0A8B6GS20-ai-review.yaml
sole_source		NICAT	NaPMT1.1	GO:0005829	cytosol	KEEP_AS_NON_CORE				The available evidence reviewed here strongly supports catalytic role, pathway placement, and root induction. The cytosol term is reasonable but not central enough to elevate as a core conclusion in this pass.		genes/NICAT/NaPMT1.1/NaPMT1.1-ai-review.yaml
sole_source		NICAT	NaPMT1.1	GO:0008295	spermidine biosynthetic process	REMOVE				Spermidine is not a product of PMT1. The enzyme's output is N-methylputrescine (EC 2.1.1.53), the first committed pyrrolidine-branch intermediate of nicotine biosynthesis, and UniProt places the protein in the nicotine pathway rather than in polyamine biosynthesis. Making spermidine requires the ami		genes/NICAT/NaPMT1.1/NaPMT1.1-ai-review.yaml
sole_source		NICAT	NaPMT1.2	GO:0005829	cytosol	KEEP_AS_NON_CORE				Retain the localization as a reasonable non-core inference while prioritizing the better-supported catalytic and pathway assignments.		genes/NICAT/NaPMT1.2/NaPMT1.2-ai-review.yaml
sole_source		NICAT	NaPMT1.2	GO:0008295	spermidine biosynthetic process	REMOVE				Spermidine is not a product of PMT2. The enzyme yields N-methylputrescine (EC 2.1.1.53), committing putrescine to the pyrrolidine branch of nicotine biosynthesis, and UniProt assigns the protein to the nicotine pathway rather than to polyamine biosynthesis. Spermidine formation needs the aminopropyl		genes/NICAT/NaPMT1.2/NaPMT1.2-ai-review.yaml
sole_source		NICAT	NaPMT3	GO:0005829	cytosol	ACCEPT				The TreeGrafter localization is compatible with the PMT family and there is no target-specific evidence of a different compartment. Less detailed study of PMT3 than PMT1 does not make the same enzymatic location non-core.		genes/NICAT/NaPMT3/NaPMT3-ai-review.yaml
sole_source		NICAT	NaPMT3	GO:0008295	spermidine biosynthetic process	REMOVE				PMT3 channels putrescine into alkaloid biosynthesis rather than spermidine biosynthesis.		genes/NICAT/NaPMT3/NaPMT3-ai-review.yaml
sole_source		NICAT	NaQPT2_candidate_QPT_0	GO:0005737	cytoplasm	KEEP_AS_NON_CORE				Retain the location as reasonable contextual information while focusing on catalytic chemistry and paralog resolution.		genes/NICAT/NaQPT2_candidate_QPT_0/NaQPT2_candidate_QPT_0-ai-review.yaml
sole_source		NICAT	NaQPT2_candidate_QPT_0	GO:0034213	quinolinate catabolic process	ACCEPT				QPT converts quinolinate into nicotinate mononucleotide and therefore participates directly in quinolinate consumption.		genes/NICAT/NaQPT2_candidate_QPT_0/NaQPT2_candidate_QPT_0-ai-review.yaml
sole_source		NICAT	NaQPT2_candidate_QPT_1	GO:0005737	cytoplasm	KEEP_AS_NON_CORE				This location is plausible for QPT chemistry, but the important unresolved issue is whether QPT_1 is the pathway-specialized paralog.		genes/NICAT/NaQPT2_candidate_QPT_1/NaQPT2_candidate_QPT_1-ai-review.yaml
sole_source		NICAT	NaQPT2_candidate_QPT_1	GO:0034213	quinolinate catabolic process	ACCEPT				QPT chemistry consumes quinolinate and therefore belongs in quinolinate catabolism.		genes/NICAT/NaQPT2_candidate_QPT_1/NaQPT2_candidate_QPT_1-ai-review.yaml
sole_source		NOSP7	AmiC1	GO:0030288	outer membrane-bounded periplasmic space	ACCEPT						genes/NOSP7/AmiC1/AmiC1-ai-review.yaml
sole_source		NOSP7	AmiC2	GO:0030288	outer membrane-bounded periplasmic space	ACCEPT				Consistent with a secreted amidase acting on periplasmic septal PG; not wrong, though less specific than the septal localization observed experimentally.		genes/NOSP7/AmiC2/AmiC2-ai-review.yaml
sole_source		NOSS1	AmiC1	GO:0030288	outer membrane-bounded periplasmic space	MODIFY						genes/NOSS1/AmiC1/AmiC1-ai-review.yaml
sole_source		NOSS1	AmiC2	GO:0030288	outer membrane-bounded periplasmic space	ACCEPT				Consistent with a secreted amidase acting on periplasmic septal PG; not wrong, though less specific than the septal localization observed experimentally.		genes/NOSS1/AmiC2/AmiC2-ai-review.yaml
sole_source		NOVAD	Saro_0802	GO:0016121	carotene catabolic process	MODIFY				Replace with GO:0046272 (stilbene catabolic process), matching the demonstrated stilbene-cleavage activity. Same TreeGrafter over-propagation as the carotenoid MF term.		genes/NOVAD/Saro_0802/Saro_0802-ai-review.yaml
sole_source		NOVAD	Saro_2809	GO:0016121	carotene catabolic process	MODIFY				Replace with GO:0046272 (stilbene catabolic process). Same TreeGrafter over-propagation as the carotenoid MF term.		genes/NOVAD/Saro_2809/Saro_2809-ai-review.yaml
sole_source		OCTVU	CTR1	GO:0032870	cellular response to hormone stimulus	KEEP_AS_NON_CORE				While cephalotocin is a neuropeptide with hormone-like properties, this term is somewhat imprecise. The annotation from TreeGrafter reflects the broader OT/VP superfamily classification. It is not wrong but is not the most informative term for this receptor's function. The core function is better ca		genes/OCTVU/CTR1/CTR1-ai-review.yaml
sole_source		OCTVU	CTR1	GO:0042277	peptide binding	MODIFY				"The term ""peptide binding"" is too generic for a GPCR that specifically binds cephalotocin and activates intracellular signaling. More informative terms such as neuropeptide receptor activity (GO:0008188) better capture the actual molecular function. Peptide binding fails to distinguish a signaling r"		genes/OCTVU/CTR1/CTR1-ai-review.yaml
sole_source		OCTVU	CTR2	GO:0032870	cellular response to hormone stimulus	KEEP_AS_NON_CORE				Cephalotocin has properties of both a neuropeptide and a neurohormone. The TreeGrafter annotation is broadly reasonable given CTR2 is a peripheral tissue receptor for a neuropeptide hormone. However, this term is not the most informative; the core function is better captured by neuropeptide receptor		genes/OCTVU/CTR2/CTR2-ai-review.yaml
sole_source		OCTVU	CTR2	GO:0042277	peptide binding	MODIFY				"The term ""peptide binding"" is too generic for a GPCR that specifically binds cephalotocin and activates intracellular signaling. GO:0008188 (neuropeptide receptor activity) better captures the actual molecular function. Peptide binding fails to distinguish a signaling receptor from a passive binding"		genes/OCTVU/CTR2/CTR2-ai-review.yaml
sole_source		OCTVU	OCTS1	GO:0004364	glutathione transferase activity	MARK_AS_OVER_ANNOTATED				Retain MARK_AS_OVER_ANNOTATED for propagation of an ancestral detoxifying GST function to a structural lens protein. Residual in-vitro catalysis is real and is not erased by this decision; its physiological importance for OCTS1 has not been demonstrated. The OctS4 study supports the family mechanism		genes/OCTVU/OCTS1/OCTS1-ai-review.yaml
sole_source		OCTVU	OCTS1	GO:0006749	glutathione metabolic process	MARK_AS_OVER_ANNOTATED				Retain the challenge to a physiological glutathione-metabolism assignment: the evidence supports a structural lens role and conserved GSH interaction, but does not establish appreciable OCTS1-specific glutathione turnover in vivo. The reported residual catalysis and homolog experiments are acknowled		genes/OCTVU/OCTS1/OCTS1-ai-review.yaml
sole_source		OCTVU	OPR	GO:0032870	cellular response to hormone stimulus	MODIFY				While octopressin can be considered a hormonal peptide, the more precise biological process is neuropeptide signaling. OPR mediates the physiological effects of octopressin in both nervous system and peripheral tissues. GO:0007218 (neuropeptide signaling pathway) is a more informative and specific t		genes/OCTVU/OPR/OPR-ai-review.yaml
sole_source		OCTVU	OPR	GO:0042277	peptide binding	MODIFY				"Peptide binding alone does not capture the receptor signaling function of OPR. The appropriate MF annotation is GO:0008188 (neuropeptide receptor activity), which encompasses both the binding of the neuropeptide ligand and the initiation of signaling. Simple ""peptide binding"" is uninformative for a "		genes/OCTVU/OPR/OPR-ai-review.yaml
sole_source		OSCPE	TLN	GO:0005886	plasma membrane	ACCEPT				Consistent with the conserved FERM head (membrane- and integrin-binding) in TLN. Not tested in sponge.		genes/OSCPE/TLN/TLN-ai-review.yaml
sole_source		OSCPE	TLN	GO:0030036	actin cytoskeleton organization	KEEP_AS_NON_CORE				Talin anchors actin filaments at adhesions and so contributes to actin organization, but this is a consequence of its adaptor role rather than its core function; untested in sponge.		genes/OSCPE/TLN/TLN-ai-review.yaml
sole_source		PSEPK	PP_0094	GO:0004713	protein tyrosine kinase activity	REMOVE				Opposite reaction direction, not a coarse term. GO:0004713 is a transferase activity - transfer of the gamma phosphate of ATP onto a protein tyrosine residue - whereas PP_0094 is a 216-residue haloacid dehalogenase (HAD) superfamily hydrolase (Pfam PF13419 HAD_2, InterPro IPR023214 HAD_sf) with the 		genes/PSEPK/PP_0094/PP_0094-ai-review.yaml
sole_source		PSEPK	PP_0094	GO:0005829	cytosol	KEEP_AS_NON_CORE				The protein lacks features of a secreted or membrane enzyme; localization is supporting context rather than the core functional annotation.		genes/PSEPK/PP_0094/PP_0094-ai-review.yaml
sole_source		PSEPK	PP_0301	GO:0047617	fatty acyl-CoA hydrolase activity	MODIFY				PP_0301 is the conserved carnitine-locus ortholog of experimentally characterized P. aeruginosa CdhB Q9HTH9. That protein catalyzes RHEA:45716, hydrolysis of N,N,N-trimethylglycyl-CoA to glycine betaine and CoA. The family-derived fatty-acyl substrate label is misleading.		genes/PSEPK/PP_0301/PP_0301-ai-review.yaml
sole_source		PSEPK	PP_0312	GO:0033539	fatty acid beta-oxidation using acyl-CoA dehydrogenase	MARK_AS_OVER_ANNOTATED				The term names a specific partnership - beta-oxidation in which an acyl-CoA dehydrogenase is the electron donor - and PP_0312's syntenic partner is the DgcAB dimethylglycine dehydrogenase system rather than an acyl-CoA dehydrogenase; the analogous four-gene locus is genetically required for dimethyl		genes/PSEPK/PP_0312/PP_0312-ai-review.yaml
sole_source		PSEPK	PP_0416	GO:0005829	cytosol	KEEP_AS_NON_CORE				UniProt and GOA do not indicate a membrane or periplasmic localization; the catalytic role is more informative than the generic cytosol annotation.		genes/PSEPK/PP_0416/PP_0416-ai-review.yaml
sole_source		PSEPK	PP_0416	GO:0006281	DNA repair	KEEP_AS_NON_CORE				UniProt/HAMAP explicitly frames phosphoglycolate phosphatase as dissimilating 2-phosphoglycolate formed during repair of oxidative DNA lesions, so the process should not be removed even though the enzyme's direct molecular function is phosphatase activity.		genes/PSEPK/PP_0416/PP_0416-ai-review.yaml
sole_source		PSEPK	PP_0500	GO:0005829	cytosol	ACCEPT				TreeGrafter assigns cytosol, consistent with soluble PP_0500.		genes/PSEPK/PP_0500/PP_0500-ai-review.yaml
sole_source		PSEPK	PP_0892	GO:0016020	membrane	ACCEPT				The PLD-family cardiolipin synthase-like assignment is consistent with a membrane enzyme.		genes/PSEPK/PP_0892/PP_0892-ai-review.yaml
sole_source		PSEPK	PP_0982	GO:0015920	lipopolysaccharide transport	ACCEPT				This is a biological-process assignment to a pathway participant, not a claim of ATPase activity.		genes/PSEPK/PP_0982/PP_0982-ai-review.yaml
sole_source		PSEPK	PP_0983	GO:0015920	lipopolysaccharide transport	ACCEPT				This is a biological-process assignment to a pathway participant, not a claim of ATPase activity.		genes/PSEPK/PP_0983/PP_0983-ai-review.yaml
sole_source		PSEPK	PP_1084	GO:0033554	cellular response to stress	KEEP_AS_NON_CORE				GO:0033554 is defined as any process changing the state or activity of a cell as a result of a stimulus indicating the organism is under stress, which is what PpPrx does: UniProt records a thiol-specific peroxidase that plays a role in cell protection against oxidative stress, and the same PANTHER n		genes/PSEPK/PP_1084/PP_1084-ai-review.yaml
sole_source		PSEPK	PP_1084	GO:0042744	hydrogen peroxide catabolic process	ACCEPT				The UniProt function states that the enzyme reduces hydrogen peroxide to water, and KT2440 experiments directly assayed PP_1084/PpPrx against H2O2.		genes/PSEPK/PP_1084/PP_1084-ai-review.yaml
sole_source		PSEPK	PP_1084	GO:0045454	cell redox homeostasis	KEEP_AS_NON_CORE				Retain as a supported non-core process because peroxide reduction contributes to redox balance.		genes/PSEPK/PP_1084/PP_1084-ai-review.yaml
sole_source		PSEPK	PP_1255	GO:0005737	cytoplasm	KEEP_AS_NON_CORE				The localization is compatible with a soluble enzyme in the hydroxyproline-utilization locus, but it is a TreeGrafter inference and does not define the protein's substrate-specific role.		genes/PSEPK/PP_1255/PP_1255-ai-review.yaml
sole_source		PSEPK	PP_1703	GO:0016020	membrane	REMOVE				The Q88M71 UniProt record contains neither a SIGNAL feature nor a TRANSMEM feature. Its first annotated domain is the Mo/W-bisMGD-type 4Fe-4S region beginning at residue 3, leaving no N-terminal export peptide or transmembrane anchor. The electronic Periplasm and Signal keywords are therefore contra		genes/PSEPK/PP_1703/PP_1703-ai-review.yaml
sole_source		PSEPK	PP_1907	GO:0005829	cytosol	KEEP_AS_NON_CORE				The protein is small and soluble, and OpenScientist found no signal peptide or transmembrane evidence; localization is supporting context rather than the core molecular function.		genes/PSEPK/PP_1907/PP_1907-ai-review.yaml
sole_source		PSEPK	PP_1907	GO:0006281	DNA repair	KEEP_AS_NON_CORE				The inferred role is hydrolysis of 2-phosphoglycolate, a metabolite that can arise during repair of oxidatively damaged 3'-phosphoglycolate DNA ends. PP_1907 is not itself a DNA repair enzyme, so the process annotation is retained only as non-core context.		genes/PSEPK/PP_1907/PP_1907-ai-review.yaml
sole_source		PSEPK	PP_2213	GO:0004321	fatty-acyl-CoA synthase activity	MODIFY				Replace or supplement this broad term with GO:0015645 (fatty acid ligase activity) based on the UniProt family and reaction evidence.		genes/PSEPK/PP_2213/PP_2213-ai-review.yaml
sole_source		PSEPK	PP_2213	GO:0006633	fatty acid biosynthetic process	KEEP_AS_NON_CORE				Retain as a supporting/non-core annotation rather than using it as the main functional summary.		genes/PSEPK/PP_2213/PP_2213-ai-review.yaml
sole_source		PSEPK	PP_2213	GO:0006637	acyl-CoA metabolic process	ACCEPT				This is a specific, biologically appropriate annotation for this gene product.		genes/PSEPK/PP_2213/PP_2213-ai-review.yaml
sole_source		PSEPK	PP_2213	GO:0015645	fatty acid ligase activity	ACCEPT				This is a specific, biologically appropriate annotation for this gene product.		genes/PSEPK/PP_2213/PP_2213-ai-review.yaml
sole_source		PSEPK	PP_2320	GO:0005576	extracellular region	MODIFY				In a Gram-negative bacterium, the periplasm is the precise compartment for an enzyme acting on the sacculus beneath the outer membrane.		genes/PSEPK/PP_2320/PP_2320-ai-review.yaml
sole_source		PSEPK	PP_2325	GO:0005737	cytoplasm	ACCEPT				Q88KG5 has a soluble Rossmann-like/ApbA architecture and no signal peptide or transmembrane segment.		genes/PSEPK/PP_2325/PP_2325-ai-review.yaml
sole_source		PSEPK	PP_2528	GO:0005737	cytoplasm	ACCEPT				The protein has soluble PLP-dependent Cys/Met-metabolism domains and no evidence for membrane or secreted localization.		genes/PSEPK/PP_2528/PP_2528-ai-review.yaml
sole_source		PSEPK	PP_2608	GO:0005829	cytosol	ACCEPT				The localization is a reasonable phylogenetic inference and is not contradicted by the structural or sequence evidence.		genes/PSEPK/PP_2608/PP_2608-ai-review.yaml
sole_source		PSEPK	PP_2608	GO:0009423	chorismate biosynthetic process	REMOVE				RifI2 has atypically low shikimate activity and NAD(+) preference, and the study does not establish a physiological role in chorismate biosynthesis. P. putida also encodes multiple canonical AroE-family candidates (PP_0074, PP_2406, PP_3002, PP_3768), so the whole-pathway assignment is an unsupporte		genes/PSEPK/PP_2608/PP_2608-ai-review.yaml
sole_source		PSEPK	PP_2608	GO:0019632	shikimate metabolic process	MARK_AS_OVER_ANNOTATED				"Not removed, because this review accepts GO:0052734 shikimate 3-dehydrogenase (NAD+) activity as the core molecular function, and GO:0019632 is the direction-neutral process restatement of acting on shikimate (""chemical reactions and pathways involving shikimate"") - it carries none of the chorismate"		genes/PSEPK/PP_2608/PP_2608-ai-review.yaml
sole_source		PSEPK	PP_2608	GO:0050661	NADP binding	MODIFY				NADP binding is a family-propagated cofactor assignment contradicted by the directly characterized cofactor preference and the NAD(+)-bound 4K28 structure. Replace it with NAD binding.		genes/PSEPK/PP_2608/PP_2608-ai-review.yaml
sole_source		PSEPK	PP_2998	GO:0005737	cytoplasm	ACCEPT				Q88IK1 has a soluble two-domain Rossmann-like/ApbA architecture and no signal peptide or transmembrane segment.		genes/PSEPK/PP_2998/PP_2998-ai-review.yaml
sole_source		PSEPK	PP_3117	GO:0006281	DNA repair	MODIFY				ImuA is an accessory component of the mutagenic DnaE2 damage-tolerance pathway rather than a canonical repair enzyme.		genes/PSEPK/PP_3117/PP_3117-ai-review.yaml
sole_source		PSEPK	PP_3303	GO:0005829	cytosol	ACCEPT				PP_3303 acts on soluble ACP-bound substrates and has no membrane-targeting features.		genes/PSEPK/PP_3303/PP_3303-ai-review.yaml
sole_source		PSEPK	PP_3394	GO:0006552	L-leucine catabolic process	REMOVE				The focused DRE-TIM report found that MvaB/PP_3540, not PP_3394, is the ortholog of the experimentally verified P. aeruginosa LiuE. PP_3394 has neither ortholog-level identity to LiuE nor a leucine/terpene-degradation neighborhood, so this electronic leucine-catabolism row is a paralog over-transfer		genes/PSEPK/PP_3394/PP_3394-ai-review.yaml
sole_source		PSEPK	PP_3394	GO:0046951	ketone body biosynthetic process	REMOVE				The bacterial leucine/terpene terminal reaction is catabolic rather than ketone-body biosynthesis, and the computational PP_3394/MvaB discriminator assigns that HMG-CoA-lyase chemistry to MvaB/PP_3540. PP_3394 itself still lacks a direct assay or mutant phenotype, but the ARBA whole-pathway process 		genes/PSEPK/PP_3394/PP_3394-ai-review.yaml
sole_source		PSEPK	PP_3768	GO:0005829	cytosol	ACCEPT				The protein lacks membrane or secretion features and belongs to a soluble metabolic enzyme family.		genes/PSEPK/PP_3768/PP_3768-ai-review.yaml
sole_source		PSEPK	PP_3768	GO:0009423	chorismate biosynthetic process	ACCEPT				This is reasonable pathway context for a shikimate-dehydrogenase-like protein. PP_3768 remains a weak module-satisfying candidate because KT2440 has several more canonical aroE paralogs and this entry lacks direct biochemical or genetic evidence, but the chorismate-pathway annotation itself is appro		genes/PSEPK/PP_3768/PP_3768-ai-review.yaml
sole_source		PSEPK	PP_3768	GO:0019632	shikimate metabolic process	KEEP_AS_NON_CORE				Retain as broader process context while noting that PP_3768's precise physiological role remains unresolved.		genes/PSEPK/PP_3768/PP_3768-ai-review.yaml
sole_source		PSEPK	PP_3768	GO:0050661	NADP binding	ACCEPT				Cofactor-binding inference is supported by conserved domain architecture and is integral to the predicted oxidoreductase activity.		genes/PSEPK/PP_3768/PP_3768-ai-review.yaml
sole_source		PSEPK	PP_4379	GO:0044550	secondary metabolite biosynthetic process	MARK_AS_OVER_ANNOTATED				The TreeGrafter term does not identify a specific secondary-metabolite pathway for PP_4379. Direct KT2440 evidence instead establishes a core fatty-acid chain-initiation role. Because its acyl products could feed specialized metabolites, the broad process is treated as over-annotated rather than def		genes/PSEPK/PP_4379/PP_4379-ai-review.yaml
sole_source		PSEPK	PP_4545	GO:0044550	secondary metabolite biosynthetic process	MARK_AS_OVER_ANNOTATED				The direct KT2440 study establishes a core fatty-acid initiation role. It does not establish a specific physiological role in secondary-metabolite biosynthesis, so the broad TreeGrafter process assignment is likely over-propagated from KAS-III family membership.		genes/PSEPK/PP_4545/PP_4545-ai-review.yaml
sole_source		PSEPK	PP_4594	GO:0004123	cystathionine gamma-lyase activity	UNDECIDED				GOA/PANTHER assign cystathionine gamma-lyase activity, while UniProt's submitted protein name says cystathionine gamma-synthase. A blinded OpenScientist control run found the term partially supported - the protein is a catalytically intact gamma-subfamily enzyme (not a pseudo-enzyme, not a beta-lyas		genes/PSEPK/PP_4594/PP_4594-ai-review.yaml
sole_source		PSEPK	PP_4594	GO:0005737	cytoplasm	ACCEPT				The GOA cytoplasm annotation fits the soluble Cys/Met PLP-dependent enzyme family.		genes/PSEPK/PP_4594/PP_4594-ai-review.yaml
sole_source		PSEPK	PP_4594	GO:0016846	carbon-sulfur lyase activity	KEEP_AS_NON_CORE				A PLP-dependent cystathionine gamma-lyase/synthase-family enzyme is expected to be a carbon-sulfur lyase or related C-S transfer enzyme, but the exact physiological activity remains unresolved. This broad term holds if PP_4594 is a gamma-lyase (cystathionine or methionine gamma-lyase, both EC 4.4.1.		genes/PSEPK/PP_4594/PP_4594-ai-review.yaml
sole_source		PSEPK	PP_4638	GO:0005829	cytosol	ACCEPT				PP_4638 lacks signal peptide and transmembrane features; this location does not imply acceptance of the transferred MTHFR reaction.		genes/PSEPK/PP_4638/PP_4638-ai-review.yaml
sole_source		PSEPK	PP_4638	GO:0071949	FAD binding	ACCEPT				The N-terminal region matches an FAD-linked oxidoreductase/MTHFR catalytic fold, and PAINT propagates FAD binding from experimentally characterized MetF at the conserved family node.		genes/PSEPK/PP_4638/PP_4638-ai-review.yaml
sole_source		PSEPK	PP_5298	GO:0005829	cytosol	KEEP_AS_NON_CORE				Retain this generic TreeGrafter location outside the core summary.		genes/PSEPK/PP_5298/PP_5298-ai-review.yaml
sole_source		PSEPK	PP_5298	GO:0006598	polyamine catabolic process	MODIFY				The substrate is specifically a putrescine-derived intermediate, so replace this generic polyamine parent with GO:0009447.		genes/PSEPK/PP_5298/PP_5298-ai-review.yaml
sole_source		PSEPK	aceF	GO:0005737	cytoplasm	ACCEPT				UniProt records cytoplasm for Q88QZ6, consistent with a soluble bacterial PDH complex rather than a membrane or secreted enzyme.		genes/PSEPK/aceF/aceF-ai-review.yaml
sole_source		PSEPK	aceF	GO:0031405	lipoic acid binding	KEEP_AS_NON_CORE				Q88QZ6 carries covalently bound lipoate on two lipoyl domains; this is required for substrate channeling but is represented as non-core relative to the exact acetyltransferase activity.		genes/PSEPK/aceF/aceF-ai-review.yaml
sole_source		PSEPK	aceK	GO:0016208	AMP binding	ACCEPT				The E. coli AceK structure shows AMP at an interdomain allosteric site controlling the opposing catalytic activities. This provides positive family-level support for the TreeGrafter inference to the conserved P. putida AceK. An unmeasured target-specific binding constant is not sufficient reason to 		genes/PSEPK/aceK/aceK-ai-review.yaml
sole_source		PSEPK	acoA	GO:0006086	pyruvate decarboxylation to acetyl-CoA	REMOVE				The PTN002264059 process propagation follows the generic E1 fold rather than substrate specificity. Gene identity, operon context, and the PpG2 locus study support acetoin catabolism; the correct process is added as a separate NEW annotation below.		genes/PSEPK/acoA/acoA-ai-review.yaml
sole_source		PSEPK	acpP	GO:0000035	acyl binding	KEEP_AS_NON_CORE				Acyl binding is inherent to AcpP, while carrier activity captures transfer between enzymes.		genes/PSEPK/acpP/acpP-ai-review.yaml
sole_source		PSEPK	acpP	GO:0009245	lipid A biosynthetic process	KEEP_AS_NON_CORE				Lipid A synthesis consumes hydroxyacyl-ACP produced by FAS-II. This is a valid downstream carrier role but secondary to AcpP's central fatty-acid-synthesis function.		genes/PSEPK/acpP/acpP-ai-review.yaml
sole_source		PSEPK	acsA1	GO:0005829	cytosol	ACCEPT				This is a specific, biologically appropriate annotation for this gene product.		genes/PSEPK/acsA1/acsA1-ai-review.yaml
sole_source		PSEPK	acsA2	GO:0005829	cytosol	ACCEPT				This is a specific, biologically appropriate annotation for this gene product.		genes/PSEPK/acsA2/acsA2-ai-review.yaml
sole_source		PSEPK	ahcY	GO:0033353	L-methionine cycle	ACCEPT				SAH hydrolysis connects SAM-dependent methylation to homocysteine remethylation. This is the direct AhcY implementation of the bacterial methionine cycle.		genes/PSEPK/ahcY/ahcY-ai-review.yaml
sole_source		PSEPK	ahpC	GO:0033554	cellular response to stress	ACCEPT				The general stress-response annotation is supported by the direct antioxidant mechanism and OxyR-associated response. Broadness alone does not turn that response into a non-core function.		genes/PSEPK/ahpC/ahpC-ai-review.yaml
sole_source		PSEPK	ahpC	GO:0042744	hydrogen peroxide catabolic process	ACCEPT				Hydrogen peroxide is among the substrates explicitly listed in the UniProt reaction/function annotation. Activity toward additional organic hydroperoxides does not invalidate the specific H2O2 catabolic process or require generalizing it.		genes/PSEPK/ahpC/ahpC-ai-review.yaml
sole_source		PSEPK	ahpC	GO:0045454	cell redox homeostasis	ACCEPT				Peroxide reduction directly limits oxidative burden as part of the antioxidant system. This is a supported broad process, not merely an unrelated phenotype.		genes/PSEPK/ahpC/ahpC-ai-review.yaml
sole_source		PSEPK	alaS	GO:0002161	aminoacyl-tRNA deacylase activity	ACCEPT				Editing is supported by TreeGrafter and the Thr/Ala-tRNA synthetase editing-domain assignment, but is not directly demonstrated for KT2440 AlaS.		genes/PSEPK/alaS/alaS-ai-review.yaml
sole_source		PSEPK	alaS	GO:0045892	negative regulation of DNA-templated transcription	UNDECIDED				The TreeGrafter propagation is not contradicted by AlaRS catalysis, but the local record provides no target-specific regulatory evidence.		genes/PSEPK/alaS/alaS-ai-review.yaml
sole_source		PSEPK	alg8	GO:0030213	hyaluronan biosynthetic process	REMOVE				Alg8 polymerizes GDP-mannuronate into the alginate precursor mannuronan. Hyaluronan instead contains alternating glucuronic acid and N-acetylglucosamine. The rejection rests on substrate specificity, not a claim that hyaluronan synthesis is restricted to vertebrates.		genes/PSEPK/alg8/alg8-ai-review.yaml
sole_source		PSEPK	alg8	GO:0050501	hyaluronan synthase activity	REMOVE				Q88NC5 polymerizes mannuronate in alginate biosynthesis, whereas this annotation specifies hyaluronan. The PTHR22913:SF12 label says mannuronan synthase but its member export mixes Alg8, HasA, and NodC, so it cannot establish substrate specificity by itself; GO:0047643 is the correct target-specific		genes/PSEPK/alg8/alg8-ai-review.yaml
sole_source		PSEPK	alg8	GO:0085029	extracellular matrix assembly	KEEP_AS_NON_CORE				GO:0085029 covers aggregation, arrangement and bonding of extracellular matrix. Alg8 performs polymer assembly rather than merely being a substrate of the process. PMID:17601783 links alginate to biofilm architecture under water limitation in P. putida mt-2; this supports conditional matrix function		genes/PSEPK/alg8/alg8-ai-review.yaml
sole_source		PSEPK	alr	GO:0005829	cytosol	REMOVE				Remove the phylogenetic cytosol transfer because Q88GJ9 has a cleaved N-terminal signal peptide and experimentally detected periplasmic activity. The fractionation study did not exclude all cytoplasmic activity, so this decision is based on the positive targeting evidence.		genes/PSEPK/alr/alr-ai-review.yaml
sole_source		PSEPK	alr	GO:0030632	D-alanine biosynthetic process	MARK_AS_OVER_ANNOTATED				Relaxed from REMOVE on re-review: the term is over-attributed rather than chemically impossible. Q88GJ9 is a broad-specificity amino-acid racemase that does act on alanine in vitro (measured KM 12.62 mM and kcat 7.33 s-1 with L-alanine), so it can form D-alanine; what the evidence refutes is a physi		genes/PSEPK/alr/alr-ai-review.yaml
sole_source		PSEPK	amaC	GO:0005829	cytosol	ACCEPT				Cytosolic localization is appropriate for aromatic amino acid transamination in bacterial metabolism.		genes/PSEPK/amaC/amaC-ai-review.yaml
sole_source		PSEPK	amaC	GO:0042802	identical protein binding	KEEP_AS_NON_CORE				Relaxed from MARK_AS_OVER_ANNOTATED on re-review. UniProt records AmaC as a homodimer (SUBUNIT, ARBA00011738), and class-I PLP-dependent aminotransferases are obligate homodimers with the active site formed across the subunit interface, so identical protein binding is true rather than an over-attrib		genes/PSEPK/amaC/amaC-ai-review.yaml
sole_source		PSEPK	ampD	GO:0009254	peptidoglycan turnover	ACCEPT				The target belongs to the AmpD-specific subfamily, and the P. putida pathway model explicitly includes cytoplasmic AmpD processing.		genes/PSEPK/ampD/ampD-ai-review.yaml
sole_source		PSEPK	argD	GO:0042802	identical protein binding	KEEP_AS_NON_CORE				"Relaxed from MARK_AS_OVER_ANNOTATED on re-review. The UniProt entry asserts ""SUBUNIT: Homodimer"" under HAMAP-Rule MF_01107, and class-III PLP-dependent aminotransferases form their active sites across the dimer interface, so self-association is a real property of the protein and the term is true. It"		genes/PSEPK/argD/argD-ai-review.yaml
sole_source		PSEPK	argG	GO:0000050	urea cycle	REMOVE				GO:0000050, GO:0004055, and GO:0006526 are co-asserted at the same untaxon-restricted PAINT node, PTN000172504, so this decision does not challenge the node based on its seed list. The biological mismatch is specific to KT2440: its proteome metadata contains ArgG but no protein annotated as arginase		genes/PSEPK/argG/argG-ai-review.yaml
sole_source		PSEPK	argJ	GO:0006592	L-ornithine biosynthetic process	ACCEPT				The EC 2.3.1.35 transacetylation reaction produces ornithine in the cyclic route.		genes/PSEPK/argJ/argJ-ai-review.yaml
sole_source		PSEPK	aroC	GO:0005829	cytosol	KEEP_AS_NON_CORE						genes/PSEPK/aroC/aroC-ai-review.yaml
sole_source		PSEPK	aroC	GO:0010181	FMN binding	ACCEPT						genes/PSEPK/aroC/aroC-ai-review.yaml
sole_source		PSEPK	aroE	GO:0005829	cytosol	ACCEPT				Appropriate compartment for a soluble biosynthetic dehydrogenase; consistent with the TreeGrafter inference and with the absence of membrane-targeting or secretion signals in the sequence.		genes/PSEPK/aroE/aroE-ai-review.yaml
sole_source		PSEPK	aroE__Q88IJ7	GO:0005829	cytosol	ACCEPT				The sequence lacks membrane or secretion features and the inferred cytosolic localization is appropriate for a shikimate-pathway enzyme.		genes/PSEPK/aroE__Q88IJ7/aroE__Q88IJ7-ai-review.yaml
sole_source		PSEPK	aroE__Q88K85	GO:0005829	cytosol	ACCEPT				The sequence lacks membrane or secretion features and the inferred cytosolic localization is appropriate for a shikimate-pathway enzyme.		genes/PSEPK/aroE__Q88K85/aroE__Q88K85-ai-review.yaml
sole_source		PSEPK	aroE__Q88K85	GO:0019632	shikimate metabolic process	KEEP_AS_NON_CORE				This is biologically true but less precise than chorismate biosynthetic process for the anabolic role captured here.		genes/PSEPK/aroE__Q88K85/aroE__Q88K85-ai-review.yaml
sole_source		PSEPK	aroE__Q88K85	GO:0050661	NADP binding	ACCEPT				Cofactor binding is intrinsic to the annotated oxidoreductase reaction and is supported by sequence/domain evidence.		genes/PSEPK/aroE__Q88K85/aroE__Q88K85-ai-review.yaml
sole_source		PSEPK	aroE__Q88RQ5	GO:0005829	cytosol	ACCEPT				The sequence lacks membrane or secretion features and the inferred cytosolic localization is appropriate for a shikimate-pathway enzyme.		genes/PSEPK/aroE__Q88RQ5/aroE__Q88RQ5-ai-review.yaml
sole_source		PSEPK	aroF-I	GO:0005737	cytoplasm	ACCEPT				Cytoplasmic localization is appropriate for a bacterial shikimate-pathway enzyme and no secretion or membrane features are indicated.		genes/PSEPK/aroF-I/aroF-I-ai-review.yaml
sole_source		PSEPK	aroF-II	GO:0005737	cytoplasm	ACCEPT				Cytoplasmic localization is appropriate for a bacterial shikimate-pathway enzyme and no secretion or membrane features are indicated.		genes/PSEPK/aroF-II/aroF-II-ai-review.yaml
sole_source		PSEPK	aroQ-III	GO:0019631	quinate catabolic process	MARK_AS_OVER_ANNOTATED				The catabolic process term is an over-propagation from a family-level phylogenetic grouping. The protein's verified role is biosynthetic (chorismate biosynthesis); there is no organism-specific evidence that PP_3003 rather than another paralog functions in quinate catabolism, and that role is normal		genes/PSEPK/aroQ-III/aroQ-III-ai-review.yaml
sole_source		PSEPK	aroQ1	GO:0019631	quinate catabolic process	MARK_AS_OVER_ANNOTATED				This TreeGrafter process propagation may be biologically plausible at the pathway-family level, but it is not paralog-specific. The core supported role of aroQ1 is the dehydroquinate dehydratase step feeding chorismate biosynthesis.		genes/PSEPK/aroQ1/aroQ1-ai-review.yaml
sole_source		PSEPK	aroQ2	GO:0019631	quinate catabolic process	MARK_AS_OVER_ANNOTATED				This TreeGrafter process propagation may be biologically plausible at the pathway-family level, but it is not paralog-specific. The core supported role of aroQ2 is the dehydroquinate dehydratase step feeding chorismate biosynthesis.		genes/PSEPK/aroQ2/aroQ2-ai-review.yaml
sole_source		PSEPK	aruC	GO:0042802	identical protein binding	MARK_AS_OVER_ANNOTATED				Rejection confirmed on re-review. Unlike the sibling aminotransferases argD and amaC, the Q88QW2 UniProt entry carries no SUBUNIT statement at all, so there is no assertion of self-association for this protein beyond the family-level propagation; class-III PLP aminotransferases are commonly dimeric,		genes/PSEPK/aruC/aruC-ai-review.yaml
sole_source		PSEPK	benB	GO:0019380	3-phenylpropionate catabolic process	REMOVE				Re-review: the rejection stands. BenB is the beta subunit of the benABC benzoate 1,2-dioxygenase of the chromosomal ben locus, and the KT2440 pathway literature maps ben genes to benzoate catabolism, not to the hca 3-phenylpropionate route. GO:0019380 names a different substrate rather than a coarse		genes/PSEPK/benB/benB-ai-review.yaml
sole_source		PSEPK	benD	GO:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	MODIFY				BenD is not merely a generic CH-OH oxidoreductase. Its substrate and reaction are specifically the benzoate cis-diol to catechol conversion step.		genes/PSEPK/benD/benD-ai-review.yaml
sole_source		PSEPK	benD	GO:0030497	fatty acid elongation	REMOVE				The annotation is a family-based overpropagation from a broad SDR lineage and is not compatible with the benzoate-to-catechol function supported by gene context and enzyme naming.		genes/PSEPK/benD/benD-ai-review.yaml
sole_source		PSEPK	betA	GO:0016020	membrane	ACCEPT				Retain as a valid cellular-component annotation.		genes/PSEPK/betA/betA-ai-review.yaml
sole_source		PSEPK	betC	GO:0005737	cytoplasm	KEEP_AS_NON_CORE				The TreeGrafter annotation is not contradicted by the target sequence or pathway context, but location is ancillary to the catalytic function.		genes/PSEPK/betC/betC-ai-review.yaml
sole_source		PSEPK	cbcW	GO:0015871	choline transport	ACCEPT				Characterized Pseudomonas CbcWV cores transport choline with CbcX.		genes/PSEPK/cbcW/cbcW-ai-review.yaml
sole_source		PSEPK	ccmB	GO:1903607	cytochrome c biosynthetic process	ACCEPT				This is the appropriately specific core process for the CcmAB membrane subunit.		genes/PSEPK/ccmB/ccmB-ai-review.yaml
sole_source		PSEPK	ccmD	GO:1903607	cytochrome c biosynthetic process	ACCEPT				This is the appropriately specific core process.		genes/PSEPK/ccmD/ccmD-ai-review.yaml
sole_source		PSEPK	chrR	GO:0005829	cytosol	KEEP_AS_NON_CORE				Retain as non-core cellular component.		genes/PSEPK/chrR/chrR-ai-review.yaml
sole_source		PSEPK	chrR	GO:0010181	FMN binding	KEEP_AS_NON_CORE				Retain as a non-core cofactor annotation.		genes/PSEPK/chrR/chrR-ai-review.yaml
sole_source		PSEPK	clpV	GO:0005737	cytoplasm	KEEP_AS_NON_CORE				Cytoplasmic localization is compatible with sheath disassembly but is contextual rather than ClpV1's core molecular function.		genes/PSEPK/clpV/clpV-ai-review.yaml
sole_source		PSEPK	clpV	GO:0034605	cellular response to heat	REMOVE				The ClpV-specific domain and K1 locus establish T6SS sheath recycling rather than a heat-shock role.		genes/PSEPK/clpV/clpV-ai-review.yaml
sole_source		PSEPK	clpX	GO:0009376	HslUV protease complex	MODIFY				The HslUV protease complex is a different protease (HslU/HslV); ClpX is a component of the ClpX-ClpP complex. The cellular component should be corrected to the endopeptidase Clp complex.		genes/PSEPK/clpX/clpX-ai-review.yaml
sole_source		PSEPK	clpX	GO:0051301	cell division	KEEP_AS_NON_CORE				Cell division is an indirect, pleiotropic effect of ClpXP-mediated proteolysis of regulators, not the core molecular/biological function of ClpX. Retain as non-core.		genes/PSEPK/clpX/clpX-ai-review.yaml
sole_source		PSEPK	colR	GO:0000156	phosphorelay response regulator activity	ACCEPT				The annotation matches both domain architecture and organism-specific genetics. It captures the core response-regulator activity of the protein.		genes/PSEPK/colR/colR-ai-review.yaml
sole_source		PSEPK	colR	GO:0005829	cytosol	KEEP_AS_NON_CORE				The annotation is not wrong, but the core biology is promoter engagement and regulon control rather than generic residence in the cytosol.		genes/PSEPK/colR/colR-ai-review.yaml
sole_source		PSEPK	cycH	GO:0005886	plasma membrane	ACCEPT				Family architecture and characterized orthologs support a membrane-associated role without requiring a specific substrate-presentation mechanism.		genes/PSEPK/cycH/cycH-ai-review.yaml
sole_source		PSEPK	dacB	GO:0000270	peptidoglycan metabolic process	ACCEPT				Both established PBP4 reactions remodel the peptide component of the sacculus.		genes/PSEPK/dacB/dacB-ai-review.yaml
sole_source		PSEPK	dadX	GO:0005829	cytosol	ACCEPT				TreeGrafter supplies the annotation, and the mature protein record lacks the signal peptide that distinguishes the periplasmic KT2440 Alr/BSR. No direct fractionation experiment for DadX was identified.		genes/PSEPK/dadX/dadX-ai-review.yaml
sole_source		PSEPK	dapE	GO:0006526	L-arginine biosynthetic process	REMOVE				Q88MP5 has the DapE-specific reaction, pathway assignment, and NCBIfam:TIGR01246 signature.		genes/PSEPK/dapE/dapE-ai-review.yaml
sole_source		PSEPK	davD	GO:0005829	cytosol	KEEP_AS_NON_CORE				Cytosol is consistent with a soluble bacterial metabolic enzyme, but the annotation is electronic and no direct localization evidence was found. It therefore should not define the curated core function.		genes/PSEPK/davD/davD-ai-review.yaml
sole_source		PSEPK	davT	GO:0042802	identical protein binding	KEEP_AS_NON_CORE				Class-III (fold-type I) PLP-dependent aminotransferases assemble as homodimers with the active sites formed at the subunit interface, and DavT carries the full diagnostic complement of that family (Aminotran_3 domain IPR005814, PLP-attachment site IPR049704, bacterial 4-aminobutyrate-aminotransferas		genes/PSEPK/davT/davT-ai-review.yaml
sole_source		PSEPK	dfp	GO:0071513	phosphopantothenoylcysteine decarboxylase complex	ACCEPT				GO:0071513 is defined by the complex's decarboxylase reaction rather than a fixed subunit architecture. Full-length bacterial CoaBC family members form oligomeric complexes whose CoaC regions catalyze this reaction; direct structural work shows a dodecameric fused CoaBC assembly.		genes/PSEPK/dfp/dfp-ai-review.yaml
sole_source		PSEPK	dgcB	GO:0005886	plasma membrane	ACCEPT				UniProt maps five transmembrane segments between residues 6 and 179.		genes/PSEPK/dgcB/dgcB-ai-review.yaml
sole_source		PSEPK	dnaA	GO:0005886	plasma membrane	KEEP_AS_NON_CORE				The reviewed UniProt record supports phospholipid interaction, while DnaA's primary action is at oriC in the cytoplasm/nucleoid.		genes/PSEPK/dnaA/dnaA-ai-review.yaml
sole_source		PSEPK	dnaB	GO:0005829	cytosol	ACCEPT				DnaB operates at chromosome-replication forks in the cytosol/nucleoid.		genes/PSEPK/dnaB/dnaB-ai-review.yaml
sole_source		PSEPK	dnaG	GO:0005737	cytoplasm	ACCEPT				DnaG acts at chromosome-replication forks in the bacterial cytoplasm.		genes/PSEPK/dnaG/dnaG-ai-review.yaml
sole_source		PSEPK	dnaQ	GO:0005829	cytosol	ACCEPT				DnaQ acts in the cytosolic chromosome-replication machinery.		genes/PSEPK/dnaQ/dnaQ-ai-review.yaml
sole_source		PSEPK	dxs	GO:0005829	cytosol	KEEP_AS_NON_CORE				The localization does not describe the catalytic role and is retained as non-core context.		genes/PSEPK/dxs/dxs-ai-review.yaml
sole_source		PSEPK	ech	GO:0008300	isoprenoid catabolic process	MODIFY				Ech acts on aromatic hydroxycinnamoyl-CoA thioesters in ferulate catabolism, not on isoprenoids.		genes/PSEPK/ech/ech-ai-review.yaml
sole_source		PSEPK	edd	GO:0005829	cytosol	KEEP_AS_NON_CORE				Cytosolic localization is compatible with the known organization of sugar catabolism in KT2440, but the main biological value of this review is the enzyme activity and ED-pathway assignment.		genes/PSEPK/edd/edd-ai-review.yaml
sole_source		PSEPK	eutB	GO:0005829	cytosol	ACCEPT				This is consistent with a soluble EutB/EutC enzyme, although it does not by itself exclude regulated microcompartment encapsulation.		genes/PSEPK/eutB/eutB-ai-review.yaml
sole_source		PSEPK	exbB	GO:0017038	protein import	MARK_AS_OVER_ANNOTATED				The 'protein import' definition (targeting/directed movement of proteins into a cell or organelle) does not capture ExbB's PMF-coupled energization of small-nutrient uptake; this is an electronic over-propagation.		genes/PSEPK/exbB/exbB-ai-review.yaml
sole_source		PSEPK	fabD	GO:0005829	cytosol	ACCEPT				FabD acts on soluble CoA and ACP substrates and lacks membrane-targeting features.		genes/PSEPK/fabD/fabD-ai-review.yaml
sole_source		PSEPK	fabD	GO:0006633	fatty acid biosynthetic process	ACCEPT				The FabD reaction supplies the two-carbon donor used by FAS-II condensing enzymes.		genes/PSEPK/fabD/fabD-ai-review.yaml
sole_source		PSEPK	fabF	GO:0005829	cytosol	KEEP_AS_NON_CORE				Retain the localization annotation without using it to define the core function because direct localization evidence for KT2440 FabF is unavailable.		genes/PSEPK/fabF/fabF-ai-review.yaml
sole_source		PSEPK	fadA__Q88L01	GO:0010124	phenylacetate catabolic process	REMOVE				KT2440 catabolizes phenylacetate through a dedicated paa operon whose thiolase step is already filled by paaJ (Q88HS3, PP_3280, EC 2.3.1.174), with the flanking steps covered by paaH (Q88HS1, PP_3282) and paaF (Q88HR9, PP_3284), while Q88L01 is assigned to the FadA-specific PANTHER subfamily PTHR438		genes/PSEPK/fadA__Q88L01/fadA__Q88L01-ai-review.yaml
sole_source		PSEPK	fadE	GO:0005737	cytoplasm	UNDECIDED				No direct localization evidence is available, and the membrane-associated topology prediction makes an unqualified cytoplasm annotation uncertain.		genes/PSEPK/fadE/fadE-ai-review.yaml
sole_source		PSEPK	fau	GO:0009396	folic acid-containing compound biosynthetic process	KEEP_AS_NON_CORE				GO:0009396 includes formation of substituted folate carrier states and is supported at PTN000601268. GO:0035999 and GO:0030272 provide the more informative core process and molecular function.		genes/PSEPK/fau/fau-ai-review.yaml
sole_source		PSEPK	fau	GO:0035999	tetrahydrofolate interconversion	ACCEPT				This process term is specific to the reaction's role and avoids assigning Fau to upstream folate synthesis or downstream one-carbon consumers.		genes/PSEPK/fau/fau-ai-review.yaml
sole_source		PSEPK	fbp	GO:0006002	fructose 6-phosphate metabolic process	KEEP_AS_NON_CORE				The term correctly reflects the reaction product but is a general substrate/product metabolism term, secondary to the specific gluconeogenesis process.		genes/PSEPK/fbp/fbp-ai-review.yaml
sole_source		PSEPK	fbp	GO:0030388	fructose 1,6-bisphosphate metabolic process	KEEP_AS_NON_CORE				The term correctly reflects the reaction substrate but is a general substrate metabolism term, secondary to the specific gluconeogenesis process.		genes/PSEPK/fbp/fbp-ai-review.yaml
sole_source		PSEPK	fcs	GO:0006631	fatty acid metabolic process	MODIFY				Fcs acts on ferulate, a hydroxycinnamic (aromatic) acid, not a fatty acid, and the supporting molecular function is feruloyl-CoA synthetase activity for hydroxycinnamate catabolism rather than fatty acid metabolism. The enzyme is the committed entry step of the ferulate/hydroxycinnamate catabolic fu		genes/PSEPK/fcs/fcs-ai-review.yaml
sole_source		PSEPK	fcs	GO:0031956	medium-chain fatty acid-CoA ligase activity	MODIFY				Although Fcs is correctly placed in the AMP-binding/acyl-CoA synthetase superfamily, the medium-chain fatty acid-CoA ligase term (GO:0031956) does not describe its substrate. Fcs activates ferulate (and other hydroxycinnamates) to their CoA thioesters; the precise, EC-supported term trans-feruloyl-C		genes/PSEPK/fcs/fcs-ai-review.yaml
sole_source		PSEPK	fdx	GO:0005829	cytosol	KEEP_AS_NON_CORE				The location is plausible but not defining and lacks direct KT2440 localization evidence.		genes/PSEPK/fdx/fdx-ai-review.yaml
sole_source		PSEPK	flgE	GO:0005829	cytosol	REMOVE				FlgE is an exported axial subunit. UniProt gives its subcellular location as the bacterial flagellum basal body, and the assembly literature places the protein outside the cytoplasm, travelling through the central channel of the growing structure and polymerizing at the distal end of the rod; its te		genes/PSEPK/flgE/flgE-ai-review.yaml
sole_source		PSEPK	fliD	GO:0071973	bacterial-type flagellum-dependent cell motility	KEEP_AS_NON_CORE				Correct downstream process; filament assembly is the direct role.		genes/PSEPK/fliD/fliD-ai-review.yaml
sole_source		PSEPK	fliI	GO:0046933	proton-transporting ATP synthase activity, rotational mechanism	REMOVE				Phylogenetic transfer across homologous ATPase families produced a contradicted molecular-function assignment.		genes/PSEPK/fliI/fliI-ai-review.yaml
sole_source		PSEPK	fmt	GO:0005829	cytosol	KEEP_AS_NON_CORE				TreeGrafter places Fmt in the cytosol, consistent with a soluble bacterial tRNA-modification enzyme.		genes/PSEPK/fmt/fmt-ai-review.yaml
sole_source		PSEPK	folD1	GO:0005829	cytosol	ACCEPT				The localization is computational rather than experimentally measured in KT2440, but it is biologically appropriate for this soluble central metabolic enzyme.		genes/PSEPK/folD1/folD1-ai-review.yaml
sole_source		PSEPK	fpr-I	GO:0034599	cellular response to oxidative stress	UNDECIDED				Fpr proteins can participate in oxidative-stress physiology, but the TreeGrafter assignment is not direct evidence that Q88MD5 has this role.		genes/PSEPK/fpr-I/fpr-I-ai-review.yaml
sole_source		PSEPK	fpr-I	GO:0042167	heme catabolic process	UNDECIDED				The family can supply heme oxygenase, but this TreeGrafter process is not independently established for Q88MD5.		genes/PSEPK/fpr-I/fpr-I-ai-review.yaml
sole_source		PSEPK	frmA	GO:0005829	cytosol	KEEP_AS_NON_CORE				Retain the localization annotation, but do not use it to define the enzyme's core function without direct localization evidence in KT2440.		genes/PSEPK/frmA/frmA-ai-review.yaml
sole_source		PSEPK	frmC	GO:0005829	cytosol	KEEP_AS_NON_CORE				The localization is compatible with a soluble-metabolite hydrolase but lacks direct localization evidence in KT2440, so it should not define the core function.		genes/PSEPK/frmC/frmC-ai-review.yaml
sole_source		PSEPK	fruA	GO:0090563	protein-phosphocysteine-sugar phosphotransferase activity	KEEP_AS_NON_CORE				This is a genuine mechanistic EIIB sub-step within the single net FruA transport-phosphorylation reaction represented by core term GO:0022877, not a second independent core function.		genes/PSEPK/fruA/fruA-ai-review.yaml
sole_source		PSEPK	fruK	GO:0005829	cytosol	ACCEPT				Biologically coherent leaf-level location for the core FruK activity.		genes/PSEPK/fruK/fruK-ai-review.yaml
sole_source		PSEPK	ftsY	GO:0005047	signal recognition particle binding	ACCEPT				This annotation accurately describes one of the core molecular functions of FtsY. Receptor engagement of SRP-RNC is the defining interaction that precedes transfer of the RNC to Sec.		genes/PSEPK/ftsY/ftsY-ai-review.yaml
sole_source		PSEPK	fumC	GO:0006108	malate metabolic process	KEEP_AS_NON_CORE				Accurate given malate is directly produced/consumed, but a broad parent process relative to the TCA cycle. Retained as supporting, non-core.		genes/PSEPK/fumC/fumC-ai-review.yaml
sole_source		PSEPK	fur	GO:0008270	zinc ion binding	MODIFY				Fur is an iron sensor; its regulatory cofactor is Fe(II) (Mn(II) used as a surrogate in vitro), and UniProt annotates Fe cation binding sites (residues 86, 88, 107, 124). Ferrous iron binding more accurately reflects the iron-sensing function than the family-propagated zinc ion binding. If a structu		genes/PSEPK/fur/fur-ai-review.yaml
sole_source		PSEPK	fur	GO:1900376	regulation of secondary metabolite biosynthetic process	KEEP_AS_NON_CORE				Plausible and consistent with Fur control of siderophore (a secondary metabolite) biosynthesis, but it is a general grouping term. The specific GO:1900705 captures the salient process; retained as non-core context rather than as a core function.		genes/PSEPK/fur/fur-ai-review.yaml
sole_source		PSEPK	fur	GO:1900705	negative regulation of siderophore biosynthetic process	ACCEPT				Core, biologically specific process for Fur consistent with its repressor role and the pseudomonad iron-acquisition literature.		genes/PSEPK/fur/fur-ai-review.yaml
sole_source		PSEPK	gabD-II	GO:0009450	GABA catabolic process	UNDECIDED				No KT2440 phenotype or direct enzyme assay ties Q88EN2 to GABA catabolism; the competing ectoine-catabolic interpretation must be resolved experimentally.		genes/PSEPK/gabD-II/gabD-II-ai-review.yaml
sole_source		PSEPK	galB	GO:0016811	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides	REMOVE				GalB is a hydratase/lyase-class enzyme acting in gallate degradation, not a hydrolase acting on linear amide C-N bonds. The specific GO:0047584 hydratase term should be retained.		genes/PSEPK/galB/galB-ai-review.yaml
sole_source		PSEPK	galR	GO:0005829	cytosol	ACCEPT				GalR is a soluble bacterial transcriptional regulator, and the TreeGrafter cytosol annotation is consistent with the core regulatory role.		genes/PSEPK/galR/galR-ai-review.yaml
sole_source		PSEPK	garD	GO:0019698	D-galacturonate catabolic process	KEEP_AS_NON_CORE				P. putida KT2440 Udh converts D-galacturonate to D-galactarate, which is then consumed by GarD. The annotation is therefore biologically valid, although the direct D-galactarate entry reaction is the more informative core role of GarD.		genes/PSEPK/garD/garD-ai-review.yaml
sole_source		PSEPK	gcl	GO:0005948	acetolactate synthase complex	REMOVE				Gcl is annotated and described as glyoxylate carboligase, not as an acetolactate synthase complex subunit.		genes/PSEPK/gcl/gcl-ai-review.yaml
sole_source		PSEPK	gcl	GO:0009099	L-valine biosynthetic process	REMOVE				The gene product is glyoxylate carboligase in glyoxylate catabolism, not acetolactate synthase or a valine-biosynthetic enzyme.		genes/PSEPK/gcl/gcl-ai-review.yaml
sole_source		PSEPK	gcl	GO:0050660	flavin adenine dinucleotide binding	KEEP_AS_NON_CORE				OpenScientist and family evidence support Gcl as a ThDP/TPP-family enzyme with FAD binding; FAD is retained as cofactor context rather than treated as the core function.		genes/PSEPK/gcl/gcl-ai-review.yaml
sole_source		PSEPK	gcvH1	GO:0005737	cytoplasm	KEEP_AS_NON_CORE				The H protein is a soluble component of the cytoplasmic glycine cleavage system, with no signal peptide or transmembrane segment, so the TreeGrafter cytoplasm call is true. Redundancy with the more specific cytosol annotation, which is itself kept as non-core, is not grounds for rejection; the locat		genes/PSEPK/gcvH1/gcvH1-ai-review.yaml
sole_source		PSEPK	gcvH1	GO:0005829	cytosol	KEEP_AS_NON_CORE				Retain the more specific of the two generic location annotations outside the core summary.		genes/PSEPK/gcvH1/gcvH1-ai-review.yaml
sole_source		PSEPK	gcvH1	GO:0009249	protein lipoylation	UNDECIDED				Participation in a biological process does not require catalysis, and GcvH proteins can be obligatory intermediates in bacterial lipoyl relays. The covalent carrier state is certain, but available KT2440 evidence does not distinguish an active relay role from being only a LipA/LipB substrate.		genes/PSEPK/gcvH1/gcvH1-ai-review.yaml
sole_source		PSEPK	gcvH2	GO:0005737	cytoplasm	KEEP_AS_NON_CORE				The H protein is a soluble component of the cytoplasmic glycine cleavage system, with no signal peptide or transmembrane segment, so the TreeGrafter cytoplasm call is true. Redundancy with the more specific cytosol annotation, which is itself kept as non-core, is not grounds for rejection; the locat		genes/PSEPK/gcvH2/gcvH2-ai-review.yaml
sole_source		PSEPK	gcvH2	GO:0005829	cytosol	KEEP_AS_NON_CORE				Retain the more specific of the two generic location annotations outside the core summary.		genes/PSEPK/gcvH2/gcvH2-ai-review.yaml
sole_source		PSEPK	gcvH2	GO:0009249	protein lipoylation	UNDECIDED				Participation in a biological process does not require catalysis, and GcvH proteins can be obligatory intermediates in bacterial lipoyl relays. The covalent carrier state is certain, but available KT2440 evidence does not distinguish an active relay role from being only a LipA/LipB substrate.		genes/PSEPK/gcvH2/gcvH2-ai-review.yaml
sole_source		PSEPK	gcvP1	GO:0005829	cytosol	KEEP_AS_NON_CORE				This generic TreeGrafter location is retained outside the core functional summary.		genes/PSEPK/gcvP1/gcvP1-ai-review.yaml
sole_source		PSEPK	gcvP1	GO:0005960	glycine cleavage complex	ACCEPT				The reviewed UniProt record explicitly identifies P, H, T, and L proteins as system components.		genes/PSEPK/gcvP1/gcvP1-ai-review.yaml
sole_source		PSEPK	gcvP1	GO:0016594	glycine binding	KEEP_AS_NON_CORE				Glycine binding is a true substrate interaction, while GO:0004375 remains the informative core catalytic term.		genes/PSEPK/gcvP1/gcvP1-ai-review.yaml
sole_source		PSEPK	gcvP1	GO:0030170	pyridoxal phosphate binding	KEEP_AS_NON_CORE				UniProt records PLP dependence; the catalytic activity remains the core molecular function.		genes/PSEPK/gcvP1/gcvP1-ai-review.yaml
sole_source		PSEPK	gcvP2	GO:0005829	cytosol	KEEP_AS_NON_CORE				This generic TreeGrafter location is retained outside the core functional summary.		genes/PSEPK/gcvP2/gcvP2-ai-review.yaml
sole_source		PSEPK	gcvP2	GO:0005960	glycine cleavage complex	ACCEPT				The reviewed UniProt record explicitly identifies P, H, T, and L proteins as system components.		genes/PSEPK/gcvP2/gcvP2-ai-review.yaml
sole_source		PSEPK	gcvP2	GO:0016594	glycine binding	KEEP_AS_NON_CORE				Glycine binding is a true substrate interaction, while GO:0004375 remains the informative core catalytic term.		genes/PSEPK/gcvP2/gcvP2-ai-review.yaml
sole_source		PSEPK	gcvP2	GO:0030170	pyridoxal phosphate binding	KEEP_AS_NON_CORE				UniProt records PLP dependence; the catalytic activity remains the core molecular function.		genes/PSEPK/gcvP2/gcvP2-ai-review.yaml
sole_source		PSEPK	gcvT	GO:0005829	cytosol	KEEP_AS_NON_CORE				This generic TreeGrafter location is retained outside the core functional summary.		genes/PSEPK/gcvT/gcvT-ai-review.yaml
sole_source		PSEPK	gdhA	GO:0005829	cytosol	ACCEPT						genes/PSEPK/gdhA/gdhA-ai-review.yaml
sole_source		PSEPK	glgB	GO:0005737	cytoplasm	KEEP_AS_NON_CORE				GlgB is a soluble monomeric GH13 branching enzyme with no signal peptide or transmembrane segment, acting on intracellular alpha-glucan, so the TreeGrafter cytoplasm call is true. Redundancy with the more specific cytosol annotation, which is itself kept as non-core, is not grounds for rejection; th		genes/PSEPK/glgB/glgB-ai-review.yaml
sole_source		PSEPK	glgB	GO:0005829	cytosol	KEEP_AS_NON_CORE				The location is computational but biologically appropriate and is the more precise of the two existing compartment annotations.		genes/PSEPK/glgB/glgB-ai-review.yaml
sole_source		PSEPK	glgP	GO:0005737	cytoplasm	KEEP_AS_NON_CORE				The TreeGrafter location is biologically plausible but is not a defining catalytic property and lacks direct localization evidence in KT2440.		genes/PSEPK/glgP/glgP-ai-review.yaml
sole_source		PSEPK	glnA	GO:0016020	membrane	REMOVE				GO:0016020 is defined as a lipid bilayer with the proteins embedded in or attached to it. Q88CY3 has no transmembrane feature and no signal peptide in UniProt, which gives its subcellular location as cytoplasm; the protein is a soluble dodecamer of two stacked hexameric rings with catalytic sites at		genes/PSEPK/glnA/glnA-ai-review.yaml
sole_source		PSEPK	glnK	GO:0005829	cytosol	ACCEPT				Consistent with PII-family biology; no contradicting evidence.		genes/PSEPK/glnK/glnK-ai-review.yaml
sole_source		PSEPK	groES	GO:0046872	metal ion binding	REMOVE				Q88DS3 is a 10 kDa Cpn10 beta-barrel (Pfam PF00166, InterPro IPR020818) that works as a heptameric ring capping GroEL; UniProt records no BINDING site, no metal cofactor and no ligand for this protein, and the co-chaperonin cycle is driven by the GroEL ATPase rather than by any cofactor of GroES its		genes/PSEPK/groES/groES-ai-review.yaml
sole_source		PSEPK	groES	GO:0051087	protein-folding chaperone binding	ACCEPT						genes/PSEPK/groES/groES-ai-review.yaml
sole_source		PSEPK	gshA	GO:0005829	cytosol	KEEP_AS_NON_CORE				The TreeGrafter location is compatible with the soluble enzyme, but localization is not the defining function and is not independently established for Q88R90.		genes/PSEPK/gshA/gshA-ai-review.yaml
sole_source		PSEPK	gshA	GO:0046872	metal ion binding	KEEP_AS_NON_CORE				Metal dependence is a supporting catalytic feature rather than the substrate-specific molecular function, and the exact Q88R90 record does not state a metal preference.		genes/PSEPK/gshA/gshA-ai-review.yaml
sole_source		PSEPK	gshB	GO:0005737	cytoplasm	KEEP_AS_NON_CORE				The TreeGrafter location is compatible with the soluble enzyme, but localization is not the defining function and is not independently established for Q88D35.		genes/PSEPK/gshB/gshB-ai-review.yaml
sole_source		PSEPK	gspE	GO:0005886	plasma membrane	ACCEPT				The conserved GspE family assignment and T2SS complex membership support plasma-membrane association without implying that GspE is an integral membrane protein.		genes/PSEPK/gspE/gspE-ai-review.yaml
sole_source		PSEPK	gspE	GO:0015627	type II protein secretion system complex	ACCEPT				UniProt, InterPro, and PANTHER consistently identify Q88P06 as a GspE-family T2SS ATPase.		genes/PSEPK/gspE/gspE-ai-review.yaml
sole_source		PSEPK	gspE	GO:0015628	protein secretion by the type II secretion system	ACCEPT				This is the specific biological process performed by the GspE ATPase in the assembled machine.		genes/PSEPK/gspE/gspE-ai-review.yaml
sole_source		PSEPK	gspE	GO:0016887	ATP hydrolysis activity	ACCEPT				Q88P06 carries the P-loop NTPase and T2SS GspE domains, and TreeGrafter assigns ATP hydrolysis activity to the exact GspE lineage.		genes/PSEPK/gspE/gspE-ai-review.yaml
sole_source		PSEPK	guaD	GO:0005829	cytosol	KEEP_AS_NON_CORE				A cytosolic location is compatible with purine-base metabolism, but it is an inferred family-level localization and does not define the enzyme's core function.		genes/PSEPK/guaD/guaD-ai-review.yaml
sole_source		PSEPK	gyrA	GO:0009330	DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) complex	ACCEPT						genes/PSEPK/gyrA/gyrA-ai-review.yaml
sole_source		PSEPK	hemB	GO:0005829	cytosol	ACCEPT				No signal peptide or transmembrane segment is predicted, and UniProt retains the TreeGrafter cytosol cross-reference.		genes/PSEPK/hemB/hemB-ai-review.yaml
sole_source		PSEPK	hemBB	GO:0005829	cytosol	ACCEPT				No signal peptide or transmembrane segment is predicted, and UniProt retains the TreeGrafter cytosol cross-reference.		genes/PSEPK/hemBB/hemBB-ai-review.yaml
sole_source		PSEPK	hfq	GO:0005829	cytosol	ACCEPT				Localization is inferred from function rather than KT2440-specific imaging, but cytosolic localization is well established for Hfq across bacteria and is consistent with its post-transcriptional regulatory role.		genes/PSEPK/hfq/hfq-ai-review.yaml
sole_source		PSEPK	hfq	GO:0043487	regulation of RNA stability	ACCEPT				Regulation of RNA stability is a well-documented function of Hfq and is specifically supported in P. putida KT2440 (Hfq increases CrcZ stability).		genes/PSEPK/hfq/hfq-ai-review.yaml
sole_source		PSEPK	hfq	GO:0045974	regulation of translation, ncRNA-mediated	ACCEPT				This term precisely captures Hfq's core biological role as an sRNA-mediated post-transcriptional regulator of translation, strongly supported by Pseudomonas literature.		genes/PSEPK/hfq/hfq-ai-review.yaml
sole_source		PSEPK	hisA	GO:0000162	L-tryptophan biosynthetic process	REMOVE				Q88R42 has the HisA-specific activity and is assigned only to the histidine pathway by the reviewed UniProt record. KT2440 has a distinct reviewed TrpF protein, Q88LE0, that catalyzes the phosphoribosylanthranilate isomerase reaction in L-tryptophan biosynthesis. No evidence supports a PriA-like bif		genes/PSEPK/hisA/hisA-ai-review.yaml
sole_source		PSEPK	hisD	GO:0005737	cytoplasm	KEEP_AS_NON_CORE				Cytoplasm is the appropriate bacterial compartment annotation, but localization is supporting context rather than the defining function.		genes/PSEPK/hisD/hisD-ai-review.yaml
sole_source		PSEPK	hisD	GO:0005829	cytosol	KEEP_AS_NON_CORE				HisD is a soluble NAD-dependent dehydrogenase with no transmembrane segment or signal peptide, and UniProt places the histidine-biosynthesis enzymes in the cytoplasm; in a bacterium without organelles the cytosol is where that soluble pool resides, so the term is true rather than an over-annotation.		genes/PSEPK/hisD/hisD-ai-review.yaml
sole_source		PSEPK	hldE	GO:0005829	cytosol	KEEP_AS_NON_CORE				The TreeGrafter location is plausible but does not define HldE function.		genes/PSEPK/hldE/hldE-ai-review.yaml
sole_source		PSEPK	hmgA	GO:0005737	cytoplasm	KEEP_AS_NON_CORE				Retain as a non-core cellular-component annotation.		genes/PSEPK/hmgA/hmgA-ai-review.yaml
sole_source		PSEPK	hmgB	GO:1902000	homogentisate catabolic process	ACCEPT				HmgB is one of the three experimentally identified enzymes of the P. putida central homogentisate-catabolic pathway.		genes/PSEPK/hmgB/hmgB-ai-review.yaml
sole_source		PSEPK	hmgC	GO:0006749	glutathione metabolic process	MARK_AS_OVER_ANNOTATED				Glutathione is a catalytic cofactor for maleylacetoacetate isomerization; that cofactor requirement does not make HmgC part of glutathione biosynthesis, degradation, or homeostasis. Its established biological process is homogentisate catabolism.		genes/PSEPK/hmgC/hmgC-ai-review.yaml
sole_source		PSEPK	hmp	GO:0046210	nitric oxide catabolic process	ACCEPT				Correct and specific biological process directly reflecting the documented NO detoxification function.		genes/PSEPK/hmp/hmp-ai-review.yaml
sole_source		PSEPK	hscB	GO:1990230	iron-sulfur cluster transfer complex	ACCEPT				This complex membership captures the specialized chaperone cycle without implying generic protein folding.		genes/PSEPK/hscB/hscB-ai-review.yaml
sole_source		PSEPK	hutF	GO:0005829	cytosol	KEEP_AS_NON_CORE				TreeGrafter predicts cytosol, but no target-specific localization experiment is available and localization is secondary to the reaction.		genes/PSEPK/hutF/hutF-ai-review.yaml
sole_source		PSEPK	hyi	GO:0046487	glyoxylate metabolic process	ACCEPT				Hyi connects hydroxypyruvate to the tartronate-semialdehyde intermediate used in glyoxylate metabolism.		genes/PSEPK/hyi/hyi-ai-review.yaml
sole_source		PSEPK	ilvA-I	GO:0003941	L-serine ammonia-lyase activity	KEEP_AS_NON_CORE				Direct recombinant enzyme studies demonstrate L-serine use by biosynthetic IlvA homologs (PMID:30226377, Mycobacterium smegmatis; PMID:30327426, Salmonella enterica). The target retains the biosynthetic Ser/Thr-dehydratase catalytic architecture, supporting the TreeGrafter molecular-activity inferen		genes/PSEPK/ilvA-I/ilvA-I-ai-review.yaml
sole_source		PSEPK	ilvA-II	GO:0003941	L-serine ammonia-lyase activity	KEEP_AS_NON_CORE				Direct recombinant enzyme studies demonstrate L-serine use by biosynthetic IlvA homologs (PMID:30226377, Mycobacterium smegmatis; PMID:30327426, Salmonella enterica). The target retains the biosynthetic Ser/Thr-dehydratase catalytic architecture, supporting the TreeGrafter molecular-activity inferen		genes/PSEPK/ilvA-II/ilvA-II-ai-review.yaml
sole_source		PSEPK	ilvC	GO:0005829	cytosol	KEEP_AS_NON_CORE				The TreeGrafter cytosol annotation is consistent with a soluble bacterial biosynthetic enzyme but should remain non-core. Falcon deep research supports cytosolic localization by homology, noting no KT2440-specific localization experiment was retrieved.		genes/PSEPK/ilvC/ilvC-ai-review.yaml
sole_source		PSEPK	ilvD	GO:0005829	cytosol	KEEP_AS_NON_CORE				The location is TreeGrafter-propagated and compatible with pathway chemistry, but the UniProt record provides no independent localization statement and location is not the defining function.		genes/PSEPK/ilvD/ilvD-ai-review.yaml
sole_source		PSEPK	ilvI	GO:0005948	acetolactate synthase complex	KEEP_AS_NON_CORE				Complex membership is correct but secondary to the enzyme activity.		genes/PSEPK/ilvI/ilvI-ai-review.yaml
sole_source		PSEPK	infC	GO:0016020	membrane	REMOVE				The exact target record assigns IF-3 to the cytoplasm and contains no signal peptide, transmembrane segment, or membrane-localization statement; the membrane transfer conflicts with the characterized soluble 30S role. The graft position explains the error: Q88K26's PANTHER family PTHR10938 matches s		genes/PSEPK/infC/infC-ai-review.yaml
sole_source		PSEPK	iscA	GO:0005737	cytoplasm	KEEP_AS_NON_CORE				Plausible location, but not a defining activity and not directly measured in KT2440.		genes/PSEPK/iscA/iscA-ai-review.yaml
sole_source		PSEPK	iscA	GO:0005829	cytosol	KEEP_AS_NON_CORE				The location is plausible but not defining and is not directly measured in KT2440.		genes/PSEPK/iscA/iscA-ai-review.yaml
sole_source		PSEPK	ivd	GO:0006552	L-leucine catabolic process	ACCEPT				Ivd converts leucine-derived 3-methylbutanoyl-CoA to 3-methylcrotonyl-CoA.		genes/PSEPK/ivd/ivd-ai-review.yaml
sole_source		PSEPK	katA	GO:0005737	cytoplasm	ACCEPT				There is no indication of secretion or membrane anchoring in the UniProt record, and cytoplasmic localization is compatible with the known role of catalases in intracellular peroxide defense.		genes/PSEPK/katA/katA-ai-review.yaml
sole_source		PSEPK	katG	GO:0005829	cytosol	KEEP_AS_NON_CORE				Catalase-peroxidases are typically soluble cytoplasmic enzymes, so the prediction is biologically plausible, but the annotation is electronic only and the cellular location is not the core defining feature of the gene.		genes/PSEPK/katG/katG-ai-review.yaml
sole_source		PSEPK	katG	GO:0042744	hydrogen peroxide catabolic process	ACCEPT				Both UniProt catalytic-activity reactions consume hydrogen peroxide, making H2O2 catabolism the most direct process-level description of this enzyme's role.		genes/PSEPK/katG/katG-ai-review.yaml
sole_source		PSEPK	kdpE	GO:0000156	phosphorelay response regulator activity	ACCEPT						genes/PSEPK/kdpE/kdpE-ai-review.yaml
sole_source		PSEPK	kdpE	GO:0032993	protein-DNA complex	KEEP_AS_NON_CORE						genes/PSEPK/kdpE/kdpE-ai-review.yaml
sole_source		PSEPK	kdsC	GO:0008781	N-acylneuraminate cytidylyltransferase activity	REMOVE				Q88P96 carries EC 3.1.3.45 and the KdsC-family signature. The cytidylyltransferase activity is a paralog transfer within the mixed CMAS/KdsC PANTHER family.		genes/PSEPK/kdsC/kdsC-ai-review.yaml
sole_source		PSEPK	ligA	GO:0005829	cytosol	ACCEPT				LigA acts on chromosomal DNA in the cytosol/nucleoid and has no secretion or membrane-targeting features.		genes/PSEPK/ligA/ligA-ai-review.yaml
sole_source		PSEPK	liuC	GO:0008300	isoprenoid catabolic process	REMOVE				P. putida KT2440 lacks the acyclic-terpene utilization context and was experimentally unable to grow on acyclic terpenes, while retaining leucine and isovalerate utilization.		genes/PSEPK/liuC/liuC-ai-review.yaml
sole_source		PSEPK	lolC	GO:0044874	lipoprotein localization to outer membrane	ACCEPT						genes/PSEPK/lolC/lolC-ai-review.yaml
sole_source		PSEPK	lolD	GO:0022857	transmembrane transporter activity	MODIFY				The previous rejection rested on LolD being a peripheral nucleotide- binding subunit rather than the membrane-spanning component, but GO annotates ABC ATPase subunits with transporter activity as a matter of convention: the characterised E. coli ortholog LolD (P75957) carries GO:0022857 by IBA from 		genes/PSEPK/lolD/lolD-ai-review.yaml
sole_source		PSEPK	lolD	GO:0055085	transmembrane transport	REMOVE				GO:0055085 requires movement across a membrane, whereas LolCDE mechanically extrudes lipid-anchored cargo from the membrane surface into the periplasm.		genes/PSEPK/lolD/lolD-ai-review.yaml
sole_source		PSEPK	lolE	GO:0044874	lipoprotein localization to outer membrane	ACCEPT						genes/PSEPK/lolE/lolE-ai-review.yaml
sole_source		PSEPK	lpd	GO:0006103	2-oxoglutarate metabolic process	KEEP_AS_NON_CORE				Retain the TreeGrafter process call as non-core context because Lpd has compatible E3 chemistry, while the available KT2440 evidence does not establish which physiological client complex uses this paralog.		genes/PSEPK/lpd/lpd-ai-review.yaml
sole_source		PSEPK	lpdG	GO:0006103	2-oxoglutarate metabolic process	ACCEPT				The TreeGrafter call agrees with conserved lpdG/LPD-glc function and the adjacent sucA/sucB complex genes.		genes/PSEPK/lpdG/lpdG-ai-review.yaml
sole_source		PSEPK	lpdV	GO:0006103	2-oxoglutarate metabolic process	REMOVE				The TreeGrafter process call crosses P. putida E3 paralogs; LPD-val is experimentally distinguished from LPD-glc and is encoded in the KT2440 bkd operon.		genes/PSEPK/lpdV/lpdV-ai-review.yaml
sole_source		PSEPK	lptA	GO:0009279	cell outer membrane	MARK_AS_OVER_ANNOTATED				Contact with LptD at the outer membrane does not establish stable outer-membrane localization.		genes/PSEPK/lptA/lptA-ai-review.yaml
sole_source		PSEPK	lptA	GO:0017089	glycolipid transfer activity	MODIFY				The generic glycolipid term is correct but under-specific for a dedicated LPS carrier. GO:0140332 is defined as removing a lipopolysaccharide from the outer leaflet of a donor membrane, carrying it through the aqueous phase in a hydrophobic pocket, and delivering it to an acceptor membrane, which is		genes/PSEPK/lptA/lptA-ai-review.yaml
sole_source		PSEPK	lptC	GO:0017089	glycolipid transfer activity	MARK_AS_OVER_ANNOTATED				The broad MF adds no useful information beyond lipopolysaccharide transfer activity.		genes/PSEPK/lptC/lptC-ai-review.yaml
sole_source		PSEPK	lptC	GO:0030288	outer membrane-bounded periplasmic space	ACCEPT				Periplasmic localization is integral to transfer from LptBFG to LptA.		genes/PSEPK/lptC/lptC-ai-review.yaml
sole_source		PSEPK	lptD	GO:1990351	transporter complex	ACCEPT				Complex membership is supported by the conserved LptD family and its interaction with LptE.		genes/PSEPK/lptD/lptD-ai-review.yaml
sole_source		PSEPK	lptE	GO:0001530	lipopolysaccharide binding	ACCEPT				LPS binding is supported by the LptE family assignment and UniProt functional description.		genes/PSEPK/lptE/lptE-ai-review.yaml
sole_source		PSEPK	lptE	GO:0015920	lipopolysaccharide transport	ACCEPT				The term is a biological-process annotation and does not imply that LptE alone transports LPS.		genes/PSEPK/lptE/lptE-ai-review.yaml
sole_source		PSEPK	lptE	GO:1990351	transporter complex	ACCEPT				Conserved LptDE complex membership is supported by the LptE family assignment.		genes/PSEPK/lptE/lptE-ai-review.yaml
sole_source		PSEPK	mazG	GO:0006203	dGTP catabolic process	ACCEPT				Q88MB7 is assigned to the same tandem-domain PANTHER subfamily as biochemically characterized E. coli MazG. The latter accommodates all eight canonical ribo- and deoxyribonucleoside triphosphates, supporting the TreeGrafter dGTP-catabolism transfer.		genes/PSEPK/mazG/mazG-ai-review.yaml
sole_source		PSEPK	mazG	GO:0046047	TTP catabolic process	MARK_AS_OVER_ANNOTATED				GO:0046047 is defined for ribosylthymine triphosphate, a nucleotide that is not a normal constituent of the bacterial nucleotide pool; the physiologically relevant thymidine species is dTTP, which GO:0046076 already records on Q88MB7 from the same PANTHER node. The rejection is softened from REMOVE 		genes/PSEPK/mazG/mazG-ai-review.yaml
sole_source		PSEPK	mazG	GO:0046052	UTP catabolic process	ACCEPT				Q88MB7 has the canonical tandem MazG architecture, and the characterized E. coli family member hydrolyzes all canonical nucleoside triphosphates, including UTP.		genes/PSEPK/mazG/mazG-ai-review.yaml
sole_source		PSEPK	mazG	GO:0046061	dATP catabolic process	ACCEPT				The exact MazG subfamily and tandem-domain architecture support transfer of the canonical deoxyribonucleoside-triphosphate substrate range.		genes/PSEPK/mazG/mazG-ai-review.yaml
sole_source		PSEPK	mazG	GO:0046076	dTTP catabolic process	ACCEPT				The exact MazG subfamily and tandem-domain architecture support transfer of the canonical deoxyribonucleoside-triphosphate substrate range. This is the appropriate thymidine-nucleotide process term for the canonical deoxyribonucleotide substrate.		genes/PSEPK/mazG/mazG-ai-review.yaml
sole_source		PSEPK	mazG	GO:0046081	dUTP catabolic process	ACCEPT				The exact MazG subfamily and tandem-domain architecture support transfer of the canonical deoxyribonucleoside-triphosphate substrate range.		genes/PSEPK/mazG/mazG-ai-review.yaml
sole_source		PSEPK	mccB	GO:0006552	L-leucine catabolic process	ACCEPT				The MCC reaction follows Ivd in the conserved liu gene cluster.		genes/PSEPK/mccB/mccB-ai-review.yaml
sole_source		PSEPK	mccB	GO:1905202	methylcrotonoyl-CoA carboxylase complex	ACCEPT				MccB is the beta subunit of methylcrotonyl-CoA carboxylase.		genes/PSEPK/mccB/mccB-ai-review.yaml
sole_source		PSEPK	mdh	GO:0006089	lactate metabolic process	REMOVE				This process annotation derives from the same incorrect LDH-superfamily grafting as GO:0004459. The enzyme acts on malate/oxaloacetate in the TCA cycle, not on lactate. Over-propagated electronic inference, appropriate to remove. The correct process is tricarboxylic acid cycle (GO:0006099), captured		genes/PSEPK/mdh/mdh-ai-review.yaml
sole_source		PSEPK	metB	GO:0005737	cytoplasm	ACCEPT				The GOA cytoplasm annotation fits the soluble Cys/Met PLP-dependent enzyme family.		genes/PSEPK/metB/metB-ai-review.yaml
sole_source		PSEPK	metF	GO:0071949	FAD binding	ACCEPT				Q88D51 has the full FAD-linked oxidoreductase/MTHFR architecture, and PANTHER PAINT propagates FAD binding from experimentally supported E. coli MetF at the conserved family node.		genes/PSEPK/metF/metF-ai-review.yaml
sole_source		PSEPK	metH	GO:0005829	cytosol	ACCEPT				MetH is a soluble cytosolic enzyme catalyzing homocysteine methylation in amino-acid biosynthesis.		genes/PSEPK/metH/metH-ai-review.yaml
sole_source		PSEPK	metH	GO:0050667	homocysteine metabolic process	MODIFY				MetH consumes homocysteine to make methionine in the de novo methionine biosynthesis pathway; L-methionine biosynthetic process is the better process term.		genes/PSEPK/metH/metH-ai-review.yaml
sole_source		PSEPK	metXS	GO:0009092	L-homoserine metabolic process	KEEP_AS_NON_CORE				MetXS uses L-homoserine as substrate, but the biologically informative pathway context is activation of homoserine for L-methionine biosynthesis.		genes/PSEPK/metXS/metXS-ai-review.yaml
sole_source		PSEPK	metZ	GO:0005737	cytoplasm	ACCEPT				MetZ lacks membrane or secretion features and is annotated as a cytoplasmic PLP-dependent enzyme.		genes/PSEPK/metZ/metZ-ai-review.yaml
sole_source		PSEPK	mfd	GO:0003678	DNA helicase activity	MODIFY				Replace the TreeGrafter helicase inference with the experimentally grounded DNA translocase activity.		genes/PSEPK/mfd/mfd-ai-review.yaml
sole_source		PSEPK	mlaD	GO:0005543	phospholipid binding	ACCEPT				Q88P92 contains the diagnostic MlaD/MCE domain and a single N-terminal membrane anchor; structural work on orthologs places phospholipid binding at the periplasm-facing MlaD ring.		genes/PSEPK/mlaD/mlaD-ai-review.yaml
sole_source		PSEPK	moaB-I	GO:0005829	cytosol	KEEP_AS_NON_CORE				Q88L15 lacks membrane/export features and is adjacent to cytosolic moeA.		genes/PSEPK/moaB-I/moaB-I-ai-review.yaml
sole_source		PSEPK	moaB-II	GO:0005829	cytosol	KEEP_AS_NON_CORE				Q88E67 lacks membrane/export features and occurs in a soluble cofactor-biosynthesis neighborhood.		genes/PSEPK/moaB-II/moaB-II-ai-review.yaml
sole_source		PSEPK	moaD	GO:1990133	molybdopterin adenylyltransferase complex	ACCEPT				MoeB-family proteins form a 2:2 complex with MoaD while adenylating its C-terminal glycine.		genes/PSEPK/moaD/moaD-ai-review.yaml
sole_source		PSEPK	moeA	GO:0005737	cytoplasm	KEEP_AS_NON_CORE				Cytosol is_a part of the cytoplasm, so the broader term is true of Q88L14, a soluble enzyme with no membrane-targeting features that acts in the cytoplasmic molybdenum-cofactor pathway. Redundancy with the cytosol row on the same PANTHER node is not an over-annotation; both are retained as non-core 		genes/PSEPK/moeA/moeA-ai-review.yaml
sole_source		PSEPK	moeA	GO:0005829	cytosol	KEEP_AS_NON_CORE				The molybdate-insertion reaction occurs in the soluble cofactor biosynthetic pathway.		genes/PSEPK/moeA/moeA-ai-review.yaml
sole_source		PSEPK	moeB	GO:0005737	cytoplasm	ACCEPT				MoeB operates with soluble MoaD in the cytoplasmic molybdenum-cofactor pathway. Cytoplasm and cytosol are compatible core localizations; redundancy does not establish over-annotation.		genes/PSEPK/moeB/moeB-ai-review.yaml
sole_source		PSEPK	moeB	GO:0005829	cytosol	ACCEPT				MoeB operates with soluble MoaD in the cytoplasmic molybdenum-cofactor pathway. Cytoplasm and cytosol are compatible core localizations; redundancy does not establish over-annotation.		genes/PSEPK/moeB/moeB-ai-review.yaml
sole_source		PSEPK	mraY	GO:0071555	cell wall organization	KEEP_AS_NON_CORE				Assembly of the peptidoglycan sacculus is a genuine downstream consequence of MraY's lipid I synthesis, and UniProt files the protein under cell wall biogenesis/degradation, so the term is true rather than wrong. It is kept as non-core because MraY's direct activity is the substrate-level transferas		genes/PSEPK/mraY/mraY-ai-review.yaml
sole_source		PSEPK	mrcA	GO:0030288	outer membrane-bounded periplasmic space	ACCEPT				The localization is well-supported by the protein architecture: PBP1A has an N-terminal membrane anchor with the GT and TP catalytic domains extending into the periplasm where they act on lipid II and the nascent peptidoglycan layer.		genes/PSEPK/mrcA/mrcA-ai-review.yaml
sole_source		PSEPK	mupP	GO:0005829	cytosol	ACCEPT				Full-text fractionation analysis directly tested the PP_1764 deletion mutant and detected recycling intermediates in its cytosolic fraction.		genes/PSEPK/mupP/mupP-ai-review.yaml
sole_source		PSEPK	mupP	GO:0006281	DNA repair	REMOVE				The rejection stands on positive grounds rather than on the propagation alone: MupP is a 223-residue HAD-superfamily (CbbY/CbbZ/Gph/YieH family, MupP subfamily) sugar-phosphate phosphatase with a biochemically determined reaction (EC 3.1.3.105, MurNAc-6P + H2O = MurNAc + phosphate, Km 310 uM) and a 		genes/PSEPK/mupP/mupP-ai-review.yaml
sole_source		PSEPK	murB	GO:0071555	cell wall organization	KEEP_AS_NON_CORE				MurB supports cell-wall organization through peptidoglycan synthesis, but GO:0009252 describes its direct pathway role more precisely.		genes/PSEPK/murB/murB-ai-review.yaml
sole_source		PSEPK	murJ	GO:0034204	lipid translocation	ACCEPT				GO:0034204 is defined as the translocation, or flipping, of lipid molecules from one monolayer of a membrane bilayer to the opposite monolayer, which is precisely the MurJ flippase reaction described by UniProt: transport of lipid-linked peptidoglycan precursors from the inner to the outer leaflet o		genes/PSEPK/murJ/murJ-ai-review.yaml
sole_source		PSEPK	mutS	GO:0005829	cytosol	ACCEPT				Consistent with the reviewed protein record and chromosomal DNA substrate.		genes/PSEPK/mutS/mutS-ai-review.yaml
sole_source		PSEPK	mvaB	GO:0006552	L-leucine catabolic process	ACCEPT				The HMG-CoA lyase reaction consumes the product of LiuC.		genes/PSEPK/mvaB/mvaB-ai-review.yaml
sole_source		PSEPK	mvaB	GO:0046951	ketone body biosynthetic process	MARK_AS_OVER_ANNOTATED				The GO:0046951 definition describes formation of the ketone bodies acetoacetate, D-3-hydroxybutyrate or acetone, a coordinated ketogenic programme whose physiological output is an exported fuel. MvaB's chemistry produces acetoacetate, so the term is not false at the reaction level, but the pathway c		genes/PSEPK/mvaB/mvaB-ai-review.yaml
sole_source		PSEPK	nadC	GO:0005737	cytoplasm	ACCEPT				The cytoplasmic assignment is consistent with the soluble de novo pathway.		genes/PSEPK/nadC/nadC-ai-review.yaml
sole_source		PSEPK	nadC	GO:0034213	quinolinate catabolic process	KEEP_AS_NON_CORE				NadC consumes quinolinate, so the term is not false. Its physiological role here is constructive NAD+ biosynthesis rather than a separate quinolinate-degradation pathway, making GO:0009435 the core process.		genes/PSEPK/nadC/nadC-ai-review.yaml
sole_source		PSEPK	nicD	GO:0016020	membrane	REMOVE				The curated UniProt entry describes a soluble enzymatic role in nicotinate degradation and has no subcellular-location or transmembrane evidence supporting membrane localization. Falcon deep research confirms NicD is best annotated as cytosolic, assayed in soluble crude extracts, with no membrane se		genes/PSEPK/nicD/nicD-ai-review.yaml
sole_source		PSEPK	nicR	GO:0006950	response to stress	REMOVE				Remove this broad phylogenetic (TreeGrafter) process annotation as unsupported for NicR. Falcon deep research found no stress-response role; all experimental evidence places NicR specifically as a repressor in the aerobic nicotinate catabolic pathway, and the MarR-family assignment does not by itsel		genes/PSEPK/nicR/nicR-ai-review.yaml
sole_source		PSEPK	nuoA	GO:0030964	NADH dehydrogenase complex	ACCEPT				NuoA is the small membrane-interface subunit of respiratory complex I; its target GOA and UniProt records support the NADH dehydrogenase complex assignment.		genes/PSEPK/nuoA/nuoA-ai-review.yaml
sole_source		PSEPK	nuoB	GO:0009060	aerobic respiration	KEEP_AS_NON_CORE				Complex I supports aerobic respiration, but this broad process is not subunit-specific.		genes/PSEPK/nuoB/nuoB-ai-review.yaml
sole_source		PSEPK	nuoB	GO:0015990	electron transport coupled proton transport	ACCEPT				NuoB is the 4Fe-4S quinone-site subunit of respiratory complex I; its target GOA and UniProt records support the electron transport coupled proton transport assignment.		genes/PSEPK/nuoB/nuoB-ai-review.yaml
sole_source		PSEPK	nuoB	GO:0045271	respiratory chain complex I	ACCEPT				NuoB is the 4Fe-4S quinone-site subunit of respiratory complex I; its target GOA and UniProt records support the respiratory chain complex I assignment.		genes/PSEPK/nuoB/nuoB-ai-review.yaml
sole_source		PSEPK	nuoH	GO:0003954	NADH dehydrogenase activity	MODIFY				GO:0003954 (NADH + H+ + acceptor = NAD+ + reduced acceptor) is an is_a ancestor of GO:0008137 NADH dehydrogenase (ubiquinone) activity, the reaction catalysed by the assembled 13-subunit NDH-1 complex of which NuoH is an obligate component. NuoH is an 8-TM integral membrane subunit of the membrane s		genes/PSEPK/nuoH/nuoH-ai-review.yaml
sole_source		PSEPK	nuoH	GO:0009060	aerobic respiration	KEEP_AS_NON_CORE				Complex I supports aerobic respiration, but this broad process is not subunit-specific.		genes/PSEPK/nuoH/nuoH-ai-review.yaml
sole_source		PSEPK	nuoI	GO:0009060	aerobic respiration	KEEP_AS_NON_CORE				Complex I supports aerobic respiration, but this broad process is not subunit-specific.		genes/PSEPK/nuoI/nuoI-ai-review.yaml
sole_source		PSEPK	nuoK	GO:0030964	NADH dehydrogenase complex	ACCEPT				NuoK is the small proximal membrane subunit of respiratory complex I; its target GOA and UniProt records support the NADH dehydrogenase complex assignment.		genes/PSEPK/nuoK/nuoK-ai-review.yaml
sole_source		PSEPK	nuoL	GO:0015990	electron transport coupled proton transport	ACCEPT				NuoL is the antiporter-like proton-pump subunit of respiratory complex I; its target GOA and UniProt records support the electron transport coupled proton transport assignment.		genes/PSEPK/nuoL/nuoL-ai-review.yaml
sole_source		PSEPK	nuoM	GO:0015990	electron transport coupled proton transport	ACCEPT				NuoM is the antiporter-like proton-pump subunit of respiratory complex I; its target GOA and UniProt records support the electron transport coupled proton transport assignment.		genes/PSEPK/nuoM/nuoM-ai-review.yaml
sole_source		PSEPK	nuoM	GO:0048039	ubiquinone binding	REMOVE				GO:0048039 ubiquinone binding is defined as binding to ubiquinone. In complex I the quinone-binding cavity is formed at the peripheral-arm/membrane-arm junction by NuoB, NuoD and NuoH; NuoM is a 14-TM antiporter-like subunit (UniProt Q88FG6: 'Multi-pass membrane protein') at the distal end of the me		genes/PSEPK/nuoM/nuoM-ai-review.yaml
sole_source		PSEPK	oxyR	GO:0032993	protein-DNA complex	ACCEPT				Consistent with the demonstrated sequence-specific DNA binding. Reasonable cellular-component annotation for a DNA-binding regulator, though non-core.		genes/PSEPK/oxyR/oxyR-ai-review.yaml
sole_source		PSEPK	paaA	GO:0005829	cytosol	ACCEPT				PaaA is a non-membrane oxygenase subunit in a cytosolic CoA-ester pathway.		genes/PSEPK/paaA/paaA-ai-review.yaml
sole_source		PSEPK	paaC	GO:0005829	cytosol	ACCEPT				PaaC is a non-membrane oxygenase subunit in a cytosolic CoA-ester pathway.		genes/PSEPK/paaC/paaC-ai-review.yaml
sole_source		PSEPK	paaE	GO:0050660	flavin adenine dinucleotide binding	KEEP_AS_NON_CORE				PaaE is assigned an FAD cofactor, while oxidoreductase function is core.		genes/PSEPK/paaE/paaE-ai-review.yaml
sole_source		PSEPK	paaF	GO:0006635	fatty acid beta-oxidation	MARK_AS_OVER_ANNOTATED				"The rejection is retained on substrate grounds, not merely because the source is a family transfer. GO:0006635 is defined as the process that ""results in the complete oxidation of a long-chain fatty acid"" through successive two-carbon shortenings. PaaF is encoded inside the phenylacetate (paa) catab"		genes/PSEPK/paaF/paaF-ai-review.yaml
sole_source		PSEPK	paaJ	GO:0006635	fatty acid beta-oxidation	MARK_AS_OVER_ANNOTATED				"The rejection is retained on substrate grounds, not merely because the source is a thiolase-family transfer. GO:0006635 is defined as the process that ""results in the complete oxidation of a long-chain fatty acid"", whereas PaaJ is the 3-oxoadipyl-CoA/3-oxo-5,6-dehydrosuberyl-CoA thiolase of the paa "		genes/PSEPK/paaJ/paaJ-ai-review.yaml
sole_source		PSEPK	paaJ	GO:0010124	phenylacetate catabolic process	ACCEPT				The assigned bifunctional name includes the 3-oxo-5,6-dehydrosuberyl-CoA intermediate of phenylacetate catabolism.		genes/PSEPK/paaJ/paaJ-ai-review.yaml
sole_source		PSEPK	pabA	GO:0000162	L-tryptophan biosynthetic process	ACCEPT				"Correct process annotation for the best-supported physiological role of this protein. The local gene symbol ""pabA"" is misleading in this pathway context; PP_0420 should be considered a trpG-like component for tryptophan module satisfiability."		genes/PSEPK/pabA/pabA-ai-review.yaml
sole_source		PSEPK	pabA	GO:0005829	cytosol	ACCEPT				The sequence is a soluble GATase-domain protein with no membrane or secretion features; cytosolic localization is appropriate.		genes/PSEPK/pabA/pabA-ai-review.yaml
sole_source		PSEPK	pabA	GO:0046654	tetrahydrofolate biosynthetic process	UNDECIDED				This protein may be homologous to PabA-family amidotransferases, but the supplied evidence does not establish a physiological tetrahydrofolate-biosynthetic role in KT2440. Leave undecided pending direct genetic or biochemical evidence for pABA/folate synthesis.		genes/PSEPK/pabA/pabA-ai-review.yaml
sole_source		PSEPK	panB	GO:0000287	magnesium ion binding	KEEP_AS_NON_CORE				The reviewed UniProt record specifies one magnesium ion per subunit and maps conserved magnesium-binding residues, consistent with the metal-dependent PanB family.		genes/PSEPK/panB/panB-ai-review.yaml
sole_source		PSEPK	panE	GO:0005737	cytoplasm	ACCEPT				Q88N64 has a soluble two-domain oxidoreductase architecture and no secretion or membrane feature, consistent with catalysis in the bacterial cytoplasm.		genes/PSEPK/panE/panE-ai-review.yaml
sole_source		PSEPK	panE	GO:0050661	NADP binding	KEEP_AS_NON_CORE				The PanE reaction uses NADPH/NADP+, and Q88N64 contains the expected Rossmann-like NAD(P)-binding architecture. The substrate-specific oxidoreductase activity is more informative as the core function.		genes/PSEPK/panE/panE-ai-review.yaml
sole_source		PSEPK	pcaQ	GO:0005829	cytosol	KEEP_AS_NON_CORE				Retain as a non-core location annotation; there is no evidence for membrane or organellar localization, and a LysR-family regulator acts on chromosomal DNA from the cytosol.		genes/PSEPK/pcaQ/pcaQ-ai-review.yaml
sole_source		PSEPK	pdxB	GO:0036001	'de novo' pyridoxal 5'-phosphate biosynthetic process	ACCEPT				The process term precisely captures the pathway context.		genes/PSEPK/pdxB/pdxB-ai-review.yaml
sole_source		PSEPK	pgi1	GO:0048029	monosaccharide binding	KEEP_AS_NON_CORE				Substrate binding is implicit in the catalytic activity already captured by GO:0004347; it is a correct but non-core supporting annotation.		genes/PSEPK/pgi1/pgi1-ai-review.yaml
sole_source		PSEPK	pgi2	GO:0048029	monosaccharide binding	KEEP_AS_NON_CORE				Retain as a supporting/non-core annotation rather than using it as the main functional summary.		genes/PSEPK/pgi2/pgi2-ai-review.yaml
sole_source		PSEPK	pgk	GO:0005524	ATP binding	ACCEPT						genes/PSEPK/pgk/pgk-ai-review.yaml
sole_source		PSEPK	pgk	GO:0006094	gluconeogenesis	ACCEPT						genes/PSEPK/pgk/pgk-ai-review.yaml
sole_source		PSEPK	pgk	GO:0043531	ADP binding	ACCEPT						genes/PSEPK/pgk/pgk-ai-review.yaml
sole_source		PSEPK	pgm	GO:0006166	purine ribonucleoside salvage	MARK_AS_OVER_ANNOTATED				Rejection confirmed on re-review, with the reason strengthened. GO:0006166 covers production of a purine nucleoside from its derivatives without de novo synthesis, a pathway entered through the ribose-1-phosphate / ribose-5-phosphate interconversion carried out by phosphopentomutase (DeoB), not by a		genes/PSEPK/pgm/pgm-ai-review.yaml
sole_source		PSEPK	phaZ	GO:0004806	triacylglycerol lipase activity	MODIFY				Replace the triacylglycerol-specific activity term with the dedicated PHA depolymerase term. PhaZ mobilizes intracellular mcl-PHA granules, not glycerolipids.		genes/PSEPK/phaZ/phaZ-ai-review.yaml
sole_source		PSEPK	phaZ	GO:0046503	glycerolipid catabolic process	MODIFY				GO:0042620 poly(3-hydroxyalkanoate) metabolic process is the closest existing biological-process term. A more specific catabolic child term would be preferable, but the current glycerolipid annotation should not be kept.		genes/PSEPK/phaZ/phaZ-ai-review.yaml
sole_source		PSEPK	phnX	GO:0005829	cytosol	KEEP_AS_NON_CORE				The TreeGrafter prediction is compatible with a soluble enzyme lacking membrane or secretion features, but Q88KT1 has no direct localization study.		genes/PSEPK/phnX/phnX-ai-review.yaml
sole_source		PSEPK	phnX	GO:0006281	DNA repair	REMOVE				DNA repair was co-propagated from the same ancestral TreeGrafter node as phosphoglycolate phosphatase activity, reflecting removal of 3'-phosphoglycolate from DNA breaks by another HAD-family role. The exact PhnX family, HAMAP rule, catalytic reaction, and genomic pairing with phnW instead support p		genes/PSEPK/phnX/phnX-ai-review.yaml
sole_source		PSEPK	pncB	GO:0005829	cytosol	ACCEPT				PncB is a soluble enzyme acting on cytosolic NAD+ precursors.		genes/PSEPK/pncB/pncB-ai-review.yaml
sole_source		PSEPK	pnp	GO:0000175	3'-5'-RNA exonuclease activity	KEEP_AS_NON_CORE				This valid directional parent captures 3'-to-5' exonucleolysis, while GO:0004654 states PNPase's defining phosphorolytic chemistry explicitly.		genes/PSEPK/pnp/pnp-ai-review.yaml
sole_source		PSEPK	ppc	GO:0005829	cytosol	ACCEPT				Consistent with the soluble enzyme class and TreeGrafter/PANTHER family inference; bacterial PEPC has no localization signals and acts in the cytoplasm.		genes/PSEPK/ppc/ppc-ai-review.yaml
sole_source		PSEPK	ppnP	GO:0005829	cytosol	KEEP_AS_NON_CORE				PpnP is reviewed as a soluble nucleoside phosphorylase; localization is inferred (TreeGrafter IEA) and falcon likewise infers cytoplasmic localization from salvage pathway architecture, so it should remain non-core.		genes/PSEPK/ppnP/ppnP-ai-review.yaml
sole_source		PSEPK	prpC	GO:0005975	carbohydrate metabolic process	REMOVE				"Re-review: the rejection stands. PrpC condenses propanoyl-CoA with oxaloacetate (UniProt CATALYTIC ACTIVITY) and UniProt assigns PATHWAY ""Organic acid metabolism; propanoate degradation"", so the carbon handled is an organic acid, not a carbohydrate. GO:0005975 is a wrong-branch propagation from the "		genes/PSEPK/prpC/prpC-ai-review.yaml
sole_source		PSEPK	prs	GO:0002189	ribose phosphate diphosphokinase complex	KEEP_AS_NON_CORE				The defining function is best captured by ribose phosphate diphosphokinase activity and PRPP biosynthesis; the homo-oligomeric assembly is supporting context. UniProt reports the subunit as a homohexamer.		genes/PSEPK/prs/prs-ai-review.yaml
sole_source		PSEPK	ptsN	GO:0030295	protein kinase activator activity	MODIFY				Dephosphorylated E. coli IIA(Ntr) activates KdpD, whereas KT2440 PtsN, mainly in its phosphorylated state, represses kdpFABC transcription through direct KdpD interaction. Protein kinase regulator activity captures the conserved mechanism without incorrectly fixing the direction as activation.		genes/PSEPK/ptsN/ptsN-ai-review.yaml
sole_source		PSEPK	ptxD	GO:0005829	cytosol	KEEP_AS_NON_CORE				Retain the plausible localization as ancillary; pathway order supports intracellular action but does not directly resolve cytosol versus broader cytoplasm.		genes/PSEPK/ptxD/ptxD-ai-review.yaml
sole_source		PSEPK	purB	GO:0005829	cytosol	KEEP_AS_NON_CORE				Cytosol is consistent with a soluble bacterial metabolic enzyme, but no direct localization evidence was found.		genes/PSEPK/purB/purB-ai-review.yaml
sole_source		PSEPK	purC	GO:0005829	cytosol	KEEP_AS_NON_CORE				Cytosol is consistent with a soluble bacterial metabolic enzyme, but no direct localization evidence was found.		genes/PSEPK/purC/purC-ai-review.yaml
sole_source		PSEPK	purH	GO:0005829	cytosol	KEEP_AS_NON_CORE				Cytosol is consistent with a soluble bacterial metabolic enzyme, but no direct localization evidence was found.		genes/PSEPK/purH/purH-ai-review.yaml
sole_source		PSEPK	purK	GO:0005829	cytosol	KEEP_AS_NON_CORE				Cytosol is consistent with a soluble bacterial metabolic enzyme, but no direct localization evidence was found.		genes/PSEPK/purK/purK-ai-review.yaml
sole_source		PSEPK	purM	GO:0004637	phosphoribosylamine-glycine ligase activity	REMOVE				Q88MA9 contains AIRS and AIRS_C domains (Pfam PF00586/PF02769) with PurM-specific IPR004733. It is the standalone FGAM cyclase, whereas phosphoribosylamine-glycine ligation requires the distinct GARS/PurD domain present in bifunctional ADE5,7 or trifunctional GART. PTN002237315 therefore conflates d		genes/PSEPK/purM/purM-ai-review.yaml
sole_source		PSEPK	purM	GO:0046084	adenine biosynthetic process	ACCEPT				The term is broader than a terminal free-base-release enzyme: current experimental GO:0046084 annotations include Candida ADE5:7 (A0A1D8PE67; PMID:17600079), an AIR-synthetase/GARS fusion, as well as yeast ADE8 and fission-yeast ade7. The Candida primary abstract reports an adenine-deficient deletio		genes/PSEPK/purM/purM-ai-review.yaml
sole_source		PSEPK	purN	GO:0005737	cytoplasm	KEEP_AS_NON_CORE				Cytoplasm is consistent with a soluble bacterial metabolic enzyme, but it is broad, electronically inferred, and not supported by direct localization evidence.		genes/PSEPK/purN/purN-ai-review.yaml
sole_source		PSEPK	purN	GO:0005829	cytosol	KEEP_AS_NON_CORE				Cytosol is consistent with a soluble bacterial metabolic enzyme, but no direct localization evidence was found.		genes/PSEPK/purN/purN-ai-review.yaml
sole_source		PSEPK	purT	GO:0005829	cytosol	KEEP_AS_NON_CORE				Cytosol is consistent with a soluble bacterial metabolic enzyme, but no direct localization evidence was found.		genes/PSEPK/purT/purT-ai-review.yaml
sole_source		PSEPK	puuA-I	GO:0006598	polyamine catabolic process	MODIFY				The substrate is specifically putrescine, so replace this generic polyamine parent with GO:0009447.		genes/PSEPK/puuA-I/puuA-I-ai-review.yaml
sole_source		PSEPK	puuB	GO:0005737	cytoplasm	KEEP_AS_NON_CORE				Retain the generic TreeGrafter location outside the core functional summary.		genes/PSEPK/puuB/puuB-ai-review.yaml
sole_source		PSEPK	pvdA	GO:0006879	intracellular iron ion homeostasis	MODIFY				GO:0006879 is too broad and indirect for a pathway enzyme. The more precise direct process term is GO:0002049 pyoverdine biosynthetic process.		genes/PSEPK/pvdA/pvdA-ai-review.yaml
sole_source		PSEPK	pvdD	GO:0005737	cytoplasm	ACCEPT				Pyoverdine precursor assembly occurs in the cytoplasm. Cytoplasm and cytosol are compatible; their overlap does not refute either localization.		genes/PSEPK/pvdD/pvdD-ai-review.yaml
sole_source		PSEPK	pvdD	GO:0005829	cytosol	ACCEPT				Cytosol is the correct localization. Falcon deep research confirms PvdD-mediated peptide assembly occurs in the cytoplasm before precursor export across the inner membrane and periplasmic maturation.		genes/PSEPK/pvdD/pvdD-ai-review.yaml
sole_source		PSEPK	pvdD	GO:0009366	enterobactin synthetase complex	REMOVE				The target PP_4219 genetic evidence and modular NRPS architecture establish a pyoverdine biosynthetic enzyme, not an enterobactin synthetase subunit. The shared nonribosomal assembly chemistry is insufficient for this specific complex assignment. The exact P. aeruginosa PvdL/PvdI/PvdJ/PvdD assembly 		genes/PSEPK/pvdD/pvdD-ai-review.yaml
sole_source		PSEPK	pvdE	GO:0034040	ATPase-coupled lipid transmembrane transporter activity	REMOVE				"Rejection confirmed on re-review, with an explicit reason added. GO:0034040 names a specific substrate class, transfer of a lipid across a membrane coupled to ATP hydrolysis. UniProt describes PvdE as the ""Pyoverdine ABC export system, fused ATPase and permease components"", and the peptide-directed "		genes/PSEPK/pvdE/pvdE-ai-review.yaml
sole_source		PSEPK	pycB	GO:0005737	cytoplasm	ACCEPT				PycB lacks membrane/secretion features and is expected to function in the bacterial cytoplasm with PycA in central-carbon anaplerosis.		genes/PSEPK/pycB/pycB-ai-review.yaml
sole_source		PSEPK	pycB	GO:0006094	gluconeogenesis	ACCEPT				Pyruvate carboxylase produces oxaloacetate from pyruvate, providing an anaplerotic input that supports gluconeogenic and central-carbon flux. The pathway report explicitly treats pycA/pycB as an anaplerotic oxaloacetate input rather than a cyclic TCA reaction.		genes/PSEPK/pycB/pycB-ai-review.yaml
sole_source		PSEPK	pyrB	GO:0005829	cytosol	KEEP_AS_NON_CORE				Plausible and useful localization, but secondary to the catalytic and pathway annotations.		genes/PSEPK/pyrB/pyrB-ai-review.yaml
sole_source		PSEPK	pyrC	GO:0005737	cytoplasm	MARK_AS_OVER_ANNOTATED				Retain cytosol as the narrower soluble-enzyme location.		genes/PSEPK/pyrC/pyrC-ai-review.yaml
sole_source		PSEPK	pyrC	GO:0005829	cytosol	KEEP_AS_NON_CORE				Plausible and more specific than cytoplasm, but secondary to the catalytic and pathway annotations.		genes/PSEPK/pyrC/pyrC-ai-review.yaml
sole_source		PSEPK	pyrC'	GO:0005737	cytoplasm	KEEP_AS_NON_CORE				Retain this plausible cellular-context annotation without treating it as core.		genes/PSEPK/pyrC'/pyrC'-ai-review.yaml
sole_source		PSEPK	pyrC'	GO:0006145	purine nucleobase catabolic process	REMOVE				This is an erroneous broad-family propagation from allantoinase-related proteins.		genes/PSEPK/pyrC'/pyrC'-ai-review.yaml
sole_source		PSEPK	pyrE	GO:0005737	cytoplasm	KEEP_AS_NON_CORE				Plausible and useful localization, but secondary to the catalytic and pathway annotations.		genes/PSEPK/pyrE/pyrE-ai-review.yaml
sole_source		PSEPK	pyrE	GO:0006207	'de novo' pyrimidine nucleobase biosynthetic process	MARK_AS_OVER_ANNOTATED				Retain the more specific de novo UMP process.		genes/PSEPK/pyrE/pyrE-ai-review.yaml
sole_source		PSEPK	pyrE	GO:0046132	pyrimidine ribonucleoside biosynthetic process	REMOVE				This TreeGrafter process transfer does not match the phosphorylated product of the reaction.		genes/PSEPK/pyrE/pyrE-ai-review.yaml
sole_source		PSEPK	pyrF	GO:0005829	cytosol	KEEP_AS_NON_CORE				Plausible and useful localization, but secondary to the catalytic and pathway annotations.		genes/PSEPK/pyrF/pyrF-ai-review.yaml
sole_source		PSEPK	pyrG	GO:0005829	cytosol	KEEP_AS_NON_CORE				The location is useful but not the defining function. Falcon deep research notes that bacterial CTPS is best supported as an intracellular, soluble/cytosolic enzyme, consistent with this annotation.		genes/PSEPK/pyrG/pyrG-ai-review.yaml
sole_source		PSEPK	pyrG	GO:0019856	pyrimidine nucleobase biosynthetic process	MARK_AS_OVER_ANNOTATED				Rejection confirmed on re-review, with the reason strengthened. GO:0019856 is defined as formation of pyrimidine nucleobases, i.e. the free 1,3-diazine bases, which are made upstream at the orotate/UMP stage. PyrG instead catalyses ATP-dependent amination of the already assembled nucleotide UTP to C		genes/PSEPK/pyrG/pyrG-ai-review.yaml
sole_source		PSEPK	pyrG	GO:0042802	identical protein binding	KEEP_AS_NON_CORE				The protein functions as an enzyme; self-association is the structural basis of its activity rather than an independent function. UniProt records a homotetramer, and falcon deep research describes how substrates (ATP/UTP) favor formation of the active tetramer, with the enzyme also able to assemble 		genes/PSEPK/pyrG/pyrG-ai-review.yaml
sole_source		PSEPK	rbsR	GO:0003700	DNA-binding transcription factor activity	MODIFY				The submitted repressor name and LacI-related family architecture support the repressor child term, while target and effector specificity remain unresolved.		genes/PSEPK/rbsR/rbsR-ai-review.yaml
sole_source		PSEPK	recB	GO:0005829	cytosol	KEEP_AS_NON_CORE				Reasonable localization for a DNA-repair enzyme but inferred (TreeGrafter); the functionally relevant compartment is the nucleoid-associated cytoplasm.		genes/PSEPK/recB/recB-ai-review.yaml
sole_source		PSEPK	recB	GO:0009338	exodeoxyribonuclease V complex	ACCEPT				RecB is an obligate subunit of the heterotrimeric RecBCD/ExoV complex; a core part_of annotation.		genes/PSEPK/recB/recB-ai-review.yaml
sole_source		PSEPK	relA	GO:0005886	plasma membrane	MARK_AS_OVER_ANNOTATED				This PANTHER/TreeGrafter IEA over-propagates a plasma membrane location to RelA. The protein has no transmembrane segments or membrane-targeting features, and the literature consensus places long RSH RelA enzymes in the cytosol associated with translating/stalled ribosomes (the mechanistically relev		genes/PSEPK/relA/relA-ai-review.yaml
sole_source		PSEPK	relA	GO:0008728	GTP diphosphokinase activity	ACCEPT				This matches the well-established and UniProt-supported primary activity of RelA (ppGpp synthase I) and the conserved synthetase domain of the RelA/SpoT family. Represents a core function of the gene.		genes/PSEPK/relA/relA-ai-review.yaml
sole_source		PSEPK	relA	GO:0008893	guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity	MARK_AS_OVER_ANNOTATED				RelA in gamma-proteobacteria (the E. coli/P. putida paradigm) functions primarily as a synthetase; the HD motif required for hydrolase chemistry is typically degenerate. The TreeGrafter inference cannot distinguish RelA from bifunctional SpoT/Rel within the RSH family. The hydrolase activity is not 		genes/PSEPK/relA/relA-ai-review.yaml
sole_source		PSEPK	relA	GO:0042594	response to starvation	ACCEPT				Consistent with the canonical role of RelA in the stringent response and supported in P. putida KT2440 by starvation/(p)ppGpp studies. A more precise term such as cellular response to starvation could be considered, but the current term is acceptable and informative.		genes/PSEPK/relA/relA-ai-review.yaml
sole_source		PSEPK	retS	GO:0071474	cellular hyperosmotic response	UNDECIDED				Re-review: changed from REMOVE to UNDECIDED. The rejection rested on the absence of KT2440-specific osmotic evidence rather than on positive contrary evidence, which is not sufficient grounds for removing a phylogenetic inference. Decisively, the falcon deep research states that the ligand sensed by		genes/PSEPK/retS/retS-ai-review.yaml
sole_source		PSEPK	rfbC	GO:0000271	polysaccharide biosynthetic process	MARK_AS_OVER_ANNOTATED				RfbC produces a soluble nucleotide-sugar precursor that may feed several glycans. Propagating the downstream generic assembly process to this epimerase is less informative than its direct dTDP-rhamnose process.		genes/PSEPK/rfbC/rfbC-ai-review.yaml
sole_source		PSEPK	rfbC	GO:0005829	cytosol	ACCEPT				TreeGrafter assigns cytosol, consistent with soluble RfbC.		genes/PSEPK/rfbC/rfbC-ai-review.yaml
sole_source		PSEPK	rfbD	GO:0005829	cytosol	ACCEPT				TreeGrafter assigns cytosol, consistent with soluble RfbD.		genes/PSEPK/rfbD/rfbD-ai-review.yaml
sole_source		PSEPK	rmlC	GO:0000271	polysaccharide biosynthetic process	MARK_AS_OVER_ANNOTATED				RmlC produces a soluble nucleotide-sugar precursor that may feed several glycans. Propagating the downstream generic assembly process to this epimerase is less informative than its direct dTDP-rhamnose process.		genes/PSEPK/rmlC/rmlC-ai-review.yaml
sole_source		PSEPK	rmlC	GO:0005829	cytosol	ACCEPT				TreeGrafter assigns cytosol, consistent with a soluble RmlC enzyme.		genes/PSEPK/rmlC/rmlC-ai-review.yaml
sole_source		PSEPK	rnc	GO:0010468	regulation of gene expression	KEEP_AS_NON_CORE				Post-transcriptional regulation of gene expression is a downstream consequence of RNase III cleavage of specific mRNAs/sRNAs; it is supported but generic and secondary to the core processing activities.		genes/PSEPK/rnc/rnc-ai-review.yaml
sole_source		PSEPK	rpiA	GO:0005829	cytosol	KEEP_AS_NON_CORE				Keep as location context while the catalytic activity remains the core function.		genes/PSEPK/rpiA/rpiA-ai-review.yaml
sole_source		PSEPK	rpiA	GO:0006014	D-ribose metabolic process	KEEP_AS_NON_CORE				Retain as compatible pathway context; use GO:0009052 and GO:0004751 for the core role.		genes/PSEPK/rpiA/rpiA-ai-review.yaml
sole_source		PSEPK	scpC	GO:0003986	acetyl-CoA hydrolase activity	MARK_AS_OVER_ANNOTATED				"Re-review: relaxed from REMOVE to MARK_AS_OVER_ANNOTATED. The CoA-transferase reading is better supported -- UniProt gives the SubName ""Propionyl-CoA:succinate CoA transferase"" (EC 2.8.3.-) and InterPro IPR017821 Succinate_CoA_transferase, and OpenScientist found a complete class-I CoA-transferase a"		genes/PSEPK/scpC/scpC-ai-review.yaml
sole_source		PSEPK	sdhA	GO:0009061	anaerobic respiration	MARK_AS_OVER_ANNOTATED				UniProt notes that two distinct FAD enzymes interconvert fumarate and succinate, with fumarate reductase (FrdA) used in anaerobic growth and succinate dehydrogenase used in aerobic growth. The forward SdhA is assigned to aerobic respiration; this TreeGrafter-propagated anaerobic respiration term ref		genes/PSEPK/sdhA/sdhA-ai-review.yaml
sole_source		PSEPK	sdhB	GO:0022904	respiratory electron transport chain	ACCEPT				SdhB is an electron-transfer subunit of respiratory Complex II. The complex bridges TCA-cycle succinate oxidation to the respiratory electron transport chain.		genes/PSEPK/sdhB/sdhB-ai-review.yaml
sole_source		PSEPK	sdhD	GO:0009055	electron transfer activity	ACCEPT				SdhD is a membrane anchor subunit with heme and ubiquinone-binding features, contributing to electron transfer from the catalytic head to the quinone pool.		genes/PSEPK/sdhD/sdhD-ai-review.yaml
sole_source		PSEPK	sdhD	GO:0017004	cytochrome complex assembly	MARK_AS_OVER_ANNOTATED				Re-review: relaxed from REMOVE to MARK_AS_OVER_ANNOTATED. GO:0017004 is defined as the aggregation, arrangement and bonding together of a cytochrome complex. UniProt describes SdhD as the membrane-anchoring subunit of succinate dehydrogenase that binds heme together with the second transmembrane sub		genes/PSEPK/sdhD/sdhD-ai-review.yaml
sole_source		PSEPK	secG	GO:0043952	protein transport by the Sec complex	ACCEPT				The conserved SecG family role directly supports this process.		genes/PSEPK/secG/secG-ai-review.yaml
sole_source		PSEPK	secG	GO:0065002	intracellular protein transmembrane transport	ACCEPT				The process is correct even though the subunit does not independently provide the transport activity.		genes/PSEPK/secG/secG-ai-review.yaml
sole_source		PSEPK	selD	GO:0005737	cytoplasm	ACCEPT				TreeGrafter assigns cytoplasm, and the reviewed sequence lacks signal peptide and transmembrane features.		genes/PSEPK/selD/selD-ai-review.yaml
sole_source		PSEPK	serB	GO:0000287	magnesium ion binding	KEEP_AS_NON_CORE				The Q88DB8 record assigns Mg2+ and places the protein in the Mg2+-dependent HAD-like SerB family.		genes/PSEPK/serB/serB-ai-review.yaml
sole_source		PSEPK	serB	GO:0005737	cytoplasm	KEEP_AS_NON_CORE				TreeGrafter provides indirect phylogenetic support for cytoplasmic localization, but no direct localization experiment is available for Q88DB8. Retain the annotation as secondary context rather than core function.		genes/PSEPK/serB/serB-ai-review.yaml
sole_source		PSEPK	speC	GO:0005737	cytoplasm	ACCEPT				The TreeGrafter annotation places the PANTHER ortholog in cytoplasm, and the exact sequence has no signal peptide or transmembrane topology in the fetched record. This remains a computational location assignment.		genes/PSEPK/speC/speC-ai-review.yaml
sole_source		PSEPK	ssb	GO:0009295	nucleoid	ACCEPT				SSB acts on chromosomal ssDNA and is expected at replication and DNA-maintenance foci in the nucleoid.		genes/PSEPK/ssb/ssb-ai-review.yaml
sole_source		PSEPK	ssuD	GO:0046306	alkanesulfonate catabolic process	ACCEPT				SsuD catalyzes desulfonation of alkanesulfonates to release sulfite, fitting the alkanesulfonate catabolic process; the deep research documents the ssu locus as central to organosulfur metabolism, enabling growth on alkanesulfonates as sulfur sources under sulfate starvation.		genes/PSEPK/ssuD/ssuD-ai-review.yaml
sole_source		PSEPK	sucA	GO:0005829	cytosol	ACCEPT				The protein lacks secretion or membrane-anchor features and acts in the soluble bacterial OGDH complex; TreeGrafter records the cytosol term for this clade.		genes/PSEPK/sucA/sucA-ai-review.yaml
sole_source		PSEPK	sucA	GO:0006099	tricarboxylic acid cycle	ACCEPT				SucA is the E1 component of OGDH, which performs the 2-oxoglutarate oxidation step of the TCA cycle with SucB and an Lpd-family E3.		genes/PSEPK/sucA/sucA-ai-review.yaml
sole_source		PSEPK	sucA	GO:0045252	oxoglutarate dehydrogenase complex	ACCEPT				SucA is the E1 component of the OGDH complex, and KT2440 genome context places sucA next to the sucB E2 gene and lpdG E3 gene.		genes/PSEPK/sucA/sucA-ai-review.yaml
sole_source		PSEPK	sucB	GO:0005829	cytosol	ACCEPT				SucB is a soluble central-carbon enzyme subunit acting in the bacterial cytosol as part of the 2-oxoglutarate dehydrogenase complex.		genes/PSEPK/sucB/sucB-ai-review.yaml
sole_source		PSEPK	sucC	GO:0005829	cytosol	ACCEPT				The bacterial SucCD complex is soluble and cytosolic, and the OpenScientist report found no mitochondrial presequence equivalent for the Q88FB2 beta subunit.		genes/PSEPK/sucC/sucC-ai-review.yaml
sole_source		PSEPK	sucC	GO:0006104	succinyl-CoA metabolic process	KEEP_AS_NON_CORE				Accurate but a more general process that is subsumed by the TCA-cycle SCS step; retain as non-core while representing the primary role with succinate-CoA ligase activity and TCA-cycle involvement.		genes/PSEPK/sucC/sucC-ai-review.yaml
sole_source		PSEPK	tatC-I	GO:0065002	intracellular protein transmembrane transport	ACCEPT				This valid parent process records transmembrane movement of intracellular folded-protein substrates; GO:0043953 supplies the Tat-specific context.		genes/PSEPK/tatC-I/tatC-I-ai-review.yaml
sole_source		PSEPK	tatC-II	GO:0065002	intracellular protein transmembrane transport	ACCEPT				This valid parent process records transmembrane movement of intracellular folded-protein substrates; GO:0043953 supplies the Tat-specific context.		genes/PSEPK/tatC-II/tatC-II-ai-review.yaml
sole_source		PSEPK	tauA	GO:0042918	alkanesulfonate transmembrane transport	MODIFY				TauA is specifically assigned to the taurine importer, so taurine transmembrane transport is the more informative process.		genes/PSEPK/tauA/tauA-ai-review.yaml
sole_source		PSEPK	tauC	GO:0010438	cellular response to sulfur starvation	UNDECIDED				E. coli tau genes are sulfate-starvation regulated, but this ortholog-level context does not demonstrate a KT2440 TauC sulfur-starvation response.		genes/PSEPK/tauC/tauC-ai-review.yaml
sole_source		PSEPK	tauD	GO:0005737	cytoplasm	ACCEPT				TauD is a soluble 2-oxoglutarate-dependent dioxygenase without membrane or export features.		genes/PSEPK/tauD/tauD-ai-review.yaml
sole_source		PSEPK	tgt	GO:0005737	cytoplasm	KEEP_AS_NON_CORE				Retain the valid broader location while using GO:0005829 in the core function.		genes/PSEPK/tgt/tgt-ai-review.yaml
sole_source		PSEPK	tgt	GO:0005829	cytosol	ACCEPT				TreeGrafter assigns cytosol, consistent with a soluble tRNA-modifying enzyme lacking targeting or membrane features.		genes/PSEPK/tgt/tgt-ai-review.yaml
sole_source		PSEPK	thiO	GO:0005737	cytoplasm	KEEP_AS_NON_CORE				Retain as a non-core cellular-component annotation for this soluble bacterial enzyme, but do not treat localization as a core function.		genes/PSEPK/thiO/thiO-ai-review.yaml
sole_source		PSEPK	tig	GO:0043022	ribosome binding	ACCEPT				Supported by the UniProt domain annotation (N-terminus binds the ribosome) and the subcellular location note that TF is bound to the ribosome near the exit tunnel. Ribosome binding is central to trigger factor's co-translational chaperone role.		genes/PSEPK/tig/tig-ai-review.yaml
sole_source		PSEPK	tig	GO:0043335	protein unfolding	KEEP_AS_NON_CORE				The current PAINT IBD assertion is experimentally seeded by E. coli trigger factor P0A850, and PMID:24812405 directly supports context-dependent unfoldase behavior. Retain the propagated BP for P. putida Tig, but as non-core because free-cytosolic unfoldase activity is weak and ribosome-enhanced unf		genes/PSEPK/tig/tig-ai-review.yaml
sole_source		PSEPK	tig	GO:0044183	protein folding chaperone	ACCEPT				Supported by the UniProt function and domain annotations stating TF acts as a chaperone and that the C-terminus has intrinsic chaperone activity on its own.		genes/PSEPK/tig/tig-ai-review.yaml
sole_source		PSEPK	tktA	GO:0005829	cytosol	KEEP_AS_NON_CORE				Keep as location context; the catalytic activity is the core annotation.		genes/PSEPK/tktA/tktA-ai-review.yaml
sole_source		PSEPK	tolC	GO:0015288	porin activity	MARK_AS_OVER_ANNOTATED				Retained as an over-annotation. GO:0015288 requires a channel whose transmembrane portion consists exclusively of beta-strands and which passes solutes smaller than 1000 Da by general diffusion. Q88EE6 belongs to the outer membrane factor (OMF, TC 1.B.17) family, architecturally distinct from the po		genes/PSEPK/tolC/tolC-ai-review.yaml
sole_source		PSEPK	tolC	GO:1990281	efflux pump complex	MODIFY				The type I protein secretion system complex term is more precise for LapE and better matches the literature on LapA export.		genes/PSEPK/tolC/tolC-ai-review.yaml
sole_source		PSEPK	tpiA	GO:0019563	glycerol catabolic process	KEEP_AS_NON_CORE				This TreeGrafter/PANTHER inference reflects TIM acting on the DHAP produced during glycerol breakdown rather than a glycerol-specific function. The activity is the same generic DHAP<->G3P isomerization already captured by the glycolysis/gluconeogenesis annotations; retain as a non-core specializatio		genes/PSEPK/tpiA/tpiA-ai-review.yaml
sole_source		PSEPK	tpiA	GO:0046166	glyceraldehyde-3-phosphate biosynthetic process	KEEP_AS_NON_CORE				A directional restatement (DHAP -> G3P) of the same reversible isomerization captured by the triose-phosphate isomerase activity and glycolysis/gluconeogenesis annotations. Biologically correct but redundant with the core terms; retain as non-core.		genes/PSEPK/tpiA/tpiA-ai-review.yaml
sole_source		PSEPK	trmB	GO:0043527	tRNA methyltransferase complex	MARK_AS_OVER_ANNOTATED				Retained as an over-annotation. The TreeGrafter source node (PANTHER:PTN002361431, family PTHR23417, which mixes bacterial KdtA and TrmB with eukaryotic Trm8/Trm82) carries the complex term from the eukaryotic Trm8-Trm82 heterodimeric tRNA m7G46 methyltransferase. Bacterial TrmB has no Trm82-like pa		genes/PSEPK/trmB/trmB-ai-review.yaml
sole_source		PSEPK	trpA	GO:0005829	cytosol	ACCEPT				Consistent with the soluble nature of the tryptophan synthase complex and the cytosolic localization of aromatic amino acid biosynthesis. Phylogeny-based (TreeGrafter) inference is reasonable for this conserved cytosolic enzyme.		genes/PSEPK/trpA/trpA-ai-review.yaml
sole_source		PSEPK	trpB	GO:0005737	cytoplasm	ACCEPT				TrpB has no signal peptide or transmembrane region and functions in cytoplasmic amino-acid biosynthesis as part of the soluble alpha2-beta2 tryptophan synthase complex. The TreeGrafter IEA assignment is consistent with the well-established localization of this enzyme family. The term is somewhat gen		genes/PSEPK/trpB/trpB-ai-review.yaml
sole_source		PSEPK	trpC	GO:0004640	phosphoribosylanthranilate isomerase activity	REMOVE				UniProt Q88QR6 (HAMAP MF_00134) annotates only the monofunctional IGPS activity (277 aa, single IGPS domain), with no PRAI/TrpF domain. The IEA TreeGrafter inference reflects the bifunctional TrpCF architecture of some lineages and is not applicable to this monofunctional Pseudomonas enzyme. This is		genes/PSEPK/trpC/trpC-ai-review.yaml
sole_source		PSEPK	trpD	GO:0005829	cytosol	ACCEPT				Appropriate cellular component for a cytoplasmic amino-acid biosynthetic enzyme; consistent with TreeGrafter inference across the family.		genes/PSEPK/trpD/trpD-ai-review.yaml
sole_source		PSEPK	ttgA	GO:0046677	response to antibiotic	KEEP_AS_NON_CORE				Experimental work in Pseudomonas links TtgABC to antibiotic efflux, but the broader core function is export of multiple toxic hydrophobic compounds. Keeping this term as non-core preserves a supported substrate class without mistaking it for the full functional scope.		genes/PSEPK/ttgA/ttgA-ai-review.yaml
sole_source		PSEPK	tusD	GO:0097163	sulfur carrier activity	ACCEPT				TreeGrafter and the TusD-specific InterPro assignment support the carrier role.		genes/PSEPK/tusD/tusD-ai-review.yaml
sole_source		PSEPK	tusE	GO:0002143	tRNA wobble position uridine thiolation	ACCEPT				TusE-specific family assignment and the tusBCDE locus support this pathway role.		genes/PSEPK/tusE/tusE-ai-review.yaml
sole_source		PSEPK	tusE	GO:0097163	sulfur carrier activity	ACCEPT				The TusE family assignment supports sulfur-carrier activity.		genes/PSEPK/tusE/tusE-ai-review.yaml
sole_source		PSEPK	tyrB	GO:0005829	cytosol	ACCEPT				Aromatic aminotransferases in this family are soluble cytoplasmic enzymes. No experimental KT2440 localization data exist, but the prediction is biologically appropriate and there is no evidence for periplasmic/membrane localization.		genes/PSEPK/tyrB/tyrB-ai-review.yaml
sole_source		PSEPK	tyrB	GO:0042802	identical protein binding	KEEP_AS_NON_CORE				Relaxed from MARK_AS_OVER_ANNOTATED. The claim is true rather than over-reaching: UniProt Q88LG1 records SUBUNIT: Homodimer, and class-I PLP aminotransferases build their active sites across the dimer interface, so identical protein binding is a correct statement about this protein. It is however an		genes/PSEPK/tyrB/tyrB-ai-review.yaml
sole_source		PSEPK	ubiD	GO:0005737	cytoplasm	KEEP_AS_NON_CORE				Relaxed from MARK_AS_OVER_ANNOTATED. UbiD is a peripheral inner-membrane enzyme that acts from the cytoplasmic face on the UbiA-generated prenylated aromatic intermediate, so GO:0005737 cytoplasm is correct for it (the definition covers the cell contents excluding the plasma membrane, and the record		genes/PSEPK/ubiD/ubiD-ai-review.yaml
sole_source		PSEPK	ubiD	GO:0005829	cytosol	KEEP_AS_NON_CORE				UniProt assigns peripheral association with the cytoplasmic side of the membrane. The cytosol call is phylogenetically transferred and has not been tested for PP_5213; notably, UbiD is not a member of the defined seven-protein E. coli Ubi metabolon.		genes/PSEPK/ubiD/ubiD-ai-review.yaml
sole_source		PSEPK	uppS	GO:0005829	cytosol	UNDECIDED				This is a TreeGrafter-inherited localization. The target UniProt record has no positive subcellular-location statement, so the exact compartment should not be accepted from absence of membrane features alone.		genes/PSEPK/uppS/uppS-ai-review.yaml
sole_source		PSEPK	uppS	GO:0016094	polyprenol biosynthetic process	ACCEPT				The direct UppS product is undecaprenyl diphosphate.		genes/PSEPK/uppS/uppS-ai-review.yaml
sole_source		PSEPK	uvrD	GO:0000725	recombinational repair	KEEP_AS_NON_CORE				Plausible conserved secondary pathway role.		genes/PSEPK/uvrD/uvrD-ai-review.yaml
sole_source		PSEPK	uvrD	GO:0005829	cytosol	ACCEPT				Coherent with UvrD action on chromosomal DNA.		genes/PSEPK/uvrD/uvrD-ai-review.yaml
sole_source		PSEPK	uvrD	GO:0033202	DNA helicase complex	KEEP_AS_NON_CORE				UvrD can oligomerize during unwinding, but this does not define its repair pathway.		genes/PSEPK/uvrD/uvrD-ai-review.yaml
sole_source		PSEPK	vacJ	GO:0120010	intermembrane phospholipid transfer	ACCEPT				Conserved MlaA/VacJ family function places Q88KX6 at the outer-membrane interface of intermembrane phospholipid transfer.		genes/PSEPK/vacJ/vacJ-ai-review.yaml
sole_source		PSEPK	ydiJ	GO:1903457	lactate catabolic process	MODIFY				Retain the existing process correction, now grounded in actual source-subfamily specificity rather than the PANTHER family name. PMID:36144368 shows negative lactate turnover in the characterized YdiJ ortholog; PMID:31064836 directly shows PP_4493-dependent D/L-lysine growth and D-2HG accumulation. 		genes/PSEPK/ydiJ/ydiJ-ai-review.yaml
sole_source		PSEPK	zwf	GO:0005829	cytosol	ACCEPT				This localization is compatible with both enzyme family expectations and the curated UniProt record, and there is no evidence for secretion or a membrane-confined role.		genes/PSEPK/zwf/zwf-ai-review.yaml
sole_source		PSEPK	zwfA	GO:0005829	cytosol	KEEP_AS_NON_CORE				Localization is compatible with ZwfA's central-carbon role, but the core reviewed function is its glucose-6-phosphate dehydrogenase chemistry and pathway placement.		genes/PSEPK/zwfA/zwfA-ai-review.yaml
sole_source		PSEPK	zwfB	GO:0005829	cytosol	KEEP_AS_NON_CORE				Keep as localization context; the G6PDH catalytic activity is the core function.		genes/PSEPK/zwfB/zwfB-ai-review.yaml
sole_source		PYROR	PoMZ_10221	GO:0006556	S-adenosylmethionine biosynthetic process	UNDECIDED				A MAT regulatory subunit can contribute to SAM synthesis alongside a separate catalytic enzyme. Therefore the reported presence of another SAM synthetase is not evidence that this process annotation is redundant or wrong. The focused OpenScientist report was critically incorporated. Its sequence-ide		genes/PYROR/PoMZ_10221/PoMZ_10221-ai-review.yaml
sole_source		PYROR	PoMZ_10221	GO:0048269	methionine adenosyltransferase complex	UNDECIDED				The human primary complex contains catalytic and regulatory subunits. A mammalian characterization does not establish universal absence of related fungal assemblies, and the recovered graft requires version-aware evaluation. The focused OpenScientist report was critically incorporated. Its sequence-		genes/PYROR/PoMZ_10221/PoMZ_10221-ai-review.yaml
sole_source		PYROR	PoMZ_10221	GO:0048270	methionine adenosyltransferase regulator activity	UNDECIDED				Sugar-nucleotide catalysis does not exclude a second interaction function. The human C-terminal motif comparison is relevant target-sequence evidence, but it is not a validated test for every regulatory interface in this family. The focused OpenScientist report was critically incorporated. Its seque		genes/PYROR/PoMZ_10221/PoMZ_10221-ai-review.yaml
sole_source		SACEN	A4F7P6	GO:0008610	lipid biosynthetic process	MODIFY				Wrong process. Replace with GO:1901115 (erythromycin biosynthetic process).		genes/SACEN/A4F7P6/A4F7P6-ai-review.yaml
sole_source		SACEN	ermE	GO:0005829	cytosol	ACCEPT				Correct cellular component.		genes/SACEN/ermE/ermE-ai-review.yaml
sole_source		SACEN	eryBVII	GO:0000271	polysaccharide biosynthetic process	MODIFY				Wrong process class; replace with GO:1901115 (erythromycin biosynthetic process).		genes/SACEN/eryBVII/eryBVII-ai-review.yaml
sole_source		SACEN	eryBVII	GO:0005829	cytosol	ACCEPT				Correct cellular component.		genes/SACEN/eryBVII/eryBVII-ai-review.yaml
sole_source		SACEN	eryBVII	GO:0019305	dTDP-rhamnose biosynthetic process	MODIFY				Wrong product/pathway (rhamnose vs the erythromycin deoxysugars). Replace with GO:1901115 (erythromycin biosynthetic process).		genes/SACEN/eryBVII/eryBVII-ai-review.yaml
sole_source		SACEN	eryCI	GO:0000271	polysaccharide biosynthetic process	MODIFY				Wrong process class. Replace with GO:1901115 (erythromycin biosynthetic process), the cluster-level process to which desosamine biosynthesis contributes.		genes/SACEN/eryCI/eryCI-ai-review.yaml
sole_source		SACEN	eryCIV	GO:0000271	polysaccharide biosynthetic process	MODIFY				Wrong process class; replace with GO:1901115 (erythromycin biosynthetic process), to which desosamine biosynthesis contributes.		genes/SACEN/eryCIV/eryCIV-ai-review.yaml
sole_source		SACEN	eryCIV	GO:0008483	transaminase activity	MODIFY				Re-reviewed after a blinded OpenScientist control run (file:SACEN/eryCIV/eryCIV-hypotheses/function-hypothesis-go-0008483/openscientist.md). The earlier UNDECIDED rested on a conflict between the dehydratase name and the transaminase term. That conflict is resolved in favour of transamination: EryCI		genes/SACEN/eryCIV/eryCIV-ai-review.yaml
sole_source		SACEN	eryCIV	GO:0030170	pyridoxal phosphate binding	ACCEPT				Correct cofactor for this PLP-dependent DegT/DnrJ/EryC1-family enzyme.		genes/SACEN/eryCIV/eryCIV-ai-review.yaml
sole_source		SALRS	PTSG_05882	GO:0000902	cell morphogenesis	MARK_AS_OVER_ANNOTATED				Cell morphogenesis is a process that unicellular organisms also have, so the term is not impossible. But the donor evidence is vertebrate classical-cadherin biology in tissues, and it reached F2UD23 only because TreeGrafter placed the protein on a node that PAINT restricts to Bilateria. Nothing link		genes/SALRS/PTSG_05882/PTSG_05882-ai-review.yaml
sole_source		SALRS	PTSG_05882	GO:0005912	adherens junction	REMOVE				The organism has no adherens junctions for the protein to be located in, and the protein lacks the beta-catenin-binding domain that recruits classical cadherins to them. The annotation results from grafting a choanoflagellate cadherin onto a Bilateria-only node.		genes/SALRS/PTSG_05882/PTSG_05882-ai-review.yaml
sole_source		SALRS	PTSG_05882	GO:0007043	cell-cell junction assembly	REMOVE				The donor process is assembly of cadherin-catenin adherens junctions, which choanoflagellates do not form. Nothing links F2UD23 to the assembly of any cell-cell junction.		genes/SALRS/PTSG_05882/PTSG_05882-ai-review.yaml
sole_source		SALRS	PTSG_05882	GO:0008013	beta-catenin binding	REMOVE				The protein lacks the domain through which cadherins bind beta-catenin, and no cadherin-beta-catenin complex is known outside animals. Even within animals, cadherins without that domain (e.g. Nematostella Dachsous) do not bind beta-catenin. The annotation is a pure family-level transfer contradicted		genes/SALRS/PTSG_05882/PTSG_05882-ai-review.yaml
sole_source		SALRS	PTSG_05882	GO:0016477	cell migration	MARK_AS_OVER_ANNOTATED				Unicellular choanoflagellates do move, so the process is not excluded. But the donor evidence is cadherin-dependent migration of animal cells within tissues, and no data tie this protein to cell movement.		genes/SALRS/PTSG_05882/PTSG_05882-ai-review.yaml
sole_source		SALRS	PTSG_05882	GO:0034332	adherens junction organization	REMOVE				The organism forms no adherens junctions, so the process cannot occur. The term reached this protein only through a graft onto a Bilateria-only node.		genes/SALRS/PTSG_05882/PTSG_05882-ai-review.yaml
sole_source		SALRS	PTSG_05882	GO:0045296	cadherin binding	MARK_AS_OVER_ANNOTATED				Cadherin-cadherin binding is plausible in principle for an EC-repeat protein, but it is untested. The donor evidence is trans binding between vertebrate cadherin ectodomains, whose binding interfaces are not conserved in this divergent protein.		genes/SALRS/PTSG_05882/PTSG_05882-ai-review.yaml
sole_source		SALRS	PTSG_06458	GO:0000902	cell morphogenesis	MARK_AS_OVER_ANNOTATED				Cell morphogenesis is a process that unicellular organisms also have, so the term is not impossible. But the donor evidence is vertebrate classical-cadherin biology in tissues, and it reached F2UFV3 only because TreeGrafter placed the protein on a node that PAINT restricts to Bilateria. Nothing link		genes/SALRS/PTSG_06458/PTSG_06458-ai-review.yaml
sole_source		SALRS	PTSG_06458	GO:0005912	adherens junction	REMOVE				The organism has no adherens junctions for the protein to be located in, and the protein lacks the beta-catenin-binding domain that recruits classical cadherins to them. The annotation results from grafting a choanoflagellate cadherin onto a Bilateria-only node.		genes/SALRS/PTSG_06458/PTSG_06458-ai-review.yaml
sole_source		SALRS	PTSG_06458	GO:0007043	cell-cell junction assembly	REMOVE				The donor process is assembly of cadherin-catenin adherens junctions, which choanoflagellates do not form. Nothing links F2UFV3 to the assembly of any cell-cell junction.		genes/SALRS/PTSG_06458/PTSG_06458-ai-review.yaml
sole_source		SALRS	PTSG_06458	GO:0008013	beta-catenin binding	REMOVE				The protein lacks the domain through which cadherins bind beta-catenin, and no cadherin-beta-catenin complex is known outside animals. Even within animals, cadherins without that domain (e.g. Nematostella Dachsous) do not bind beta-catenin. The annotation is a pure family-level transfer contradicted		genes/SALRS/PTSG_06458/PTSG_06458-ai-review.yaml
sole_source		SALRS	PTSG_06458	GO:0016477	cell migration	MARK_AS_OVER_ANNOTATED				Unicellular choanoflagellates do move, so the process is not excluded. But the donor evidence is cadherin-dependent migration of animal cells within tissues, and no data tie this protein to cell movement.		genes/SALRS/PTSG_06458/PTSG_06458-ai-review.yaml
sole_source		SALRS	PTSG_06458	GO:0034332	adherens junction organization	REMOVE				The organism forms no adherens junctions, so the process cannot occur. The term reached this protein only through a graft onto a Bilateria-only node.		genes/SALRS/PTSG_06458/PTSG_06458-ai-review.yaml
sole_source		SALRS	PTSG_06458	GO:0045296	cadherin binding	MARK_AS_OVER_ANNOTATED				Cadherin-cadherin binding is plausible in principle for an EC-repeat protein, but it is untested. The donor evidence is trans binding between vertebrate cadherin ectodomains, which has not been examined for any premetazoan cadherin.		genes/SALRS/PTSG_06458/PTSG_06458-ai-review.yaml
sole_source		SALRS	PTSG_11235	GO:0000902	cell morphogenesis	MARK_AS_OVER_ANNOTATED				Cell morphogenesis is a process that unicellular organisms also have, so the term is not impossible. But the donor evidence is vertebrate classical-cadherin biology in tissues, and it reached F2USU1 only because TreeGrafter placed the protein on a node that PAINT restricts to Bilateria. Nothing link		genes/SALRS/PTSG_11235/PTSG_11235-ai-review.yaml
sole_source		SALRS	PTSG_11235	GO:0005912	adherens junction	REMOVE				The organism has no adherens junctions for the protein to be located in, and the protein lacks the beta-catenin-binding domain that recruits classical cadherins to them. The annotation results from grafting a choanoflagellate cadherin onto a Bilateria-only node.		genes/SALRS/PTSG_11235/PTSG_11235-ai-review.yaml
sole_source		SALRS	PTSG_11235	GO:0007043	cell-cell junction assembly	REMOVE				The donor process is assembly of cadherin-catenin adherens junctions, which choanoflagellates do not form. Nothing links F2USU1 to the assembly of any cell-cell junction.		genes/SALRS/PTSG_11235/PTSG_11235-ai-review.yaml
sole_source		SALRS	PTSG_11235	GO:0008013	beta-catenin binding	REMOVE				The protein lacks the domain through which cadherins bind beta-catenin, and no cadherin-beta-catenin complex is known outside animals. Even within animals, cadherins without that domain (e.g. Nematostella Dachsous) do not bind beta-catenin. The annotation is a pure family-level transfer contradicted		genes/SALRS/PTSG_11235/PTSG_11235-ai-review.yaml
sole_source		SALRS	PTSG_11235	GO:0016477	cell migration	MARK_AS_OVER_ANNOTATED				Unicellular choanoflagellates do move, so the process is not excluded. But the donor evidence is cadherin-dependent migration of animal cells within tissues, and no data tie this protein to cell movement.		genes/SALRS/PTSG_11235/PTSG_11235-ai-review.yaml
sole_source		SALRS	PTSG_11235	GO:0034332	adherens junction organization	REMOVE				The organism forms no adherens junctions, so the process cannot occur. The term reached this protein only through a graft onto a Bilateria-only node.		genes/SALRS/PTSG_11235/PTSG_11235-ai-review.yaml
sole_source		SALRS	PTSG_11235	GO:0045296	cadherin binding	MARK_AS_OVER_ANNOTATED				Cadherin-cadherin binding is plausible in principle for an EC-repeat protein, but it is untested. The donor evidence is trans binding between vertebrate cadherin ectodomains, which has not been examined for any premetazoan cadherin.		genes/SALRS/PTSG_11235/PTSG_11235-ai-review.yaml
sole_source		SALRS	couscous	GO:0046354	mannan biosynthetic process	REMOVE				The term describes polysaccharide (hemicellulose/cell-wall mannan) biosynthesis, a fungal/plant-lineage function that the TreeGrafter node carries over from yeast Mnn2. There is no evidence that choanoflagellates synthesize a mannan polysaccharide, and Couscous substrates are unknown. The appropriat		genes/SALRS/couscous/couscous-ai-review.yaml
sole_source		SALRS	hippo	GO:0005737	cytoplasm	ACCEPT				Cytoplasm is the expected compartment for a soluble STE20 kinase without transmembrane or targeting signals, and it is true of every germinal-centre kinase group under the source node. The term is broad enough to be safe from the deep node placement. Accepted as a homology-based location that should		genes/SALRS/hippo/hippo-ai-review.yaml
sole_source		SALRS	warts	GO:0000082	G1/S transition of mitotic cell cycle	MARK_AS_OVER_ANNOTATED				G1/S transition is a eukaryote-wide process, so there is no taxon violation. But the donor evidence is a cell-cycle role of vertebrate LATS2 (mouse Lats2, human LATS2), which says little about a choanoflagellate. In S. rosetta, loss of warts slows rather than accelerates proliferation, and no cell-c		genes/SALRS/warts/warts-ai-review.yaml
sole_source		SALRS	warts	GO:0035329	hippo signaling	ACCEPT				Warts/LATS performs a step of the hippo signaling cascade (phosphorylating Yorkie), and the IBD node includes choanoflagellates. That placement is consistent with Capsaspora evidence that the Hippo-Warts-Yorkie cascade predates animals, so the family-level inference is sound and the term describes t		genes/SALRS/warts/warts-ai-review.yaml
sole_source		SALRS	warts	GO:0035556	intracellular signal transduction	KEEP_AS_NON_CORE				True for a signalling kinase but less informative than hippo signaling, which is also annotated. Kept as a non-core parent.		genes/SALRS/warts/warts-ai-review.yaml
sole_source		SALRS	warts	GO:0043065	positive regulation of apoptotic process	MARK_AS_OVER_ANNOTATED				The term is permitted for opisthokonts, so it is not a taxon violation, and a role in cell survival in a choanoflagellate is not impossible. But the donor biology is Yorkie-dependent control of an animal anti-apoptotic programme in growing tissue. There is no evidence that choanoflagellate Warts or 		genes/SALRS/warts/warts-ai-review.yaml
sole_source		SALRS	warts	GO:0046620	regulation of organ growth	REMOVE				"An organ is a multicellular anatomical structure of an animal or plant body, which choanoflagellates do not have, so the term cannot be true of this protein whatever its function. The source annotation is sound for mice. The fault is that an organ-level outcome term was placed at a node (""Metazoa-Ch"		genes/SALRS/warts/warts-ai-review.yaml
sole_source		SALRS	yorkie	GO:0005737	cytoplasm	KEEP_AS_NON_CORE				The propagation route is wrong: the term reaches a choanoflagellate Yorkie homolog from a node of insect and nematode MAGI-related proteins. The term itself is plausible on independent grounds, since Yorkie/YAP proteins shuttle between cytoplasm and nucleus and are held in the cytoplasm when phospho		genes/SALRS/yorkie/yorkie-ai-review.yaml
sole_source		SALRS	yorkie	GO:0007165	signal transduction	KEEP_AS_NON_CORE				The term is broad, and is plausible for a Yorkie homolog through its own family. A shared set of extracellular-matrix target genes for Warts and Yorkie fits a Warts-to-Yorkie pathway, but the phenotypes do not follow the animal pattern (warts loss enlarges rosettes, yet yorkie loss has no size effec		genes/SALRS/yorkie/yorkie-ai-review.yaml
sole_source		SALSP	mcr-4	GO:0009244	lipopolysaccharide core region biosynthetic process	MARK_AS_OVER_ANNOTATED				Retained as an over-annotation. GO:0009244 is defined as formation of the LPS core region, the roughly ten-saccharide inner/outer core oligosaccharide. MCR-family enzymes are phosphoethanolamine transferases that decorate the lipid A moiety (the accepted core function here is phosphatidylethanolamin		genes/SALSP/mcr-4/mcr-4-ai-review.yaml
sole_source		SHIFL	sctN	GO:0046933	proton-transporting ATP synthase activity, rotational mechanism	REMOVE				Contradicted by the biology of this protein. Spa47 is a soluble cytoplasmic ATP hydrolase with no transmembrane segment, no Fo-type proton channel and no reported synthetic activity; UniProt assigns it EC 7.4.2.8, the protein-translocating export reaction. Where the Shigella T3SS uses the proton mot		genes/SHIFL/sctN/sctN-ai-review.yaml
sole_source		SPHPI	Q53353	GO:0016121	carotene catabolic process	REMOVE				Contradicted by the gene's own IDA lignin catabolic process annotation; TreeGrafter over-propagation.		genes/SPHPI/Q53353/Q53353-ai-review.yaml
sole_source		SPHPI	lsdB	GO:0016121	carotene catabolic process	REMOVE				Contradicted by the gene's own IDA lignin catabolic process annotation; TreeGrafter over-propagation of a carotenoid-pathway term.		genes/SPHPI/lsdB/lsdB-ai-review.yaml
sole_source		STAAU	lytN	GO:0008932	lytic endotransglycosylase activity	REMOVE				The annotation arises from an over-propagated subfamily misassignment. PANTHER places LytN in PTHR33734:SF22 (a lytic transglycosylase subfamily), but LytN's experimentally characterized activities are hydrolytic amide/peptide cleavages, not the 1,6-anhydro-forming glycosidic cleavage that defines l		genes/STAAU/lytN/lytN-ai-review.yaml
sole_source		TAKRU	A0A674PKV4	GO:0005737	cytoplasm	KEEP_AS_NON_CORE						genes/TAKRU/A0A674PKV4/A0A674PKV4-ai-review.yaml
sole_source		TAKRU	A0A674PKV4	GO:0005886	plasma membrane	ACCEPT						genes/TAKRU/A0A674PKV4/A0A674PKV4-ai-review.yaml
sole_source		TAKRU	A0A674PKV4	GO:0005905	clathrin-coated pit	ACCEPT						genes/TAKRU/A0A674PKV4/A0A674PKV4-ai-review.yaml
sole_source		TAKRU	A0A674PKV4	GO:0030136	clathrin-coated vesicle	KEEP_AS_NON_CORE						genes/TAKRU/A0A674PKV4/A0A674PKV4-ai-review.yaml
sole_source		TAKRU	A0A674PKV4	GO:0048268	clathrin coat assembly	ACCEPT						genes/TAKRU/A0A674PKV4/A0A674PKV4-ai-review.yaml
sole_source		TAKRU	A0A674PKV4	GO:0048812	neuron projection morphogenesis	ACCEPT						genes/TAKRU/A0A674PKV4/A0A674PKV4-ai-review.yaml
sole_source		TAKRU	A0A674PKV4	GO:0072583	clathrin-dependent endocytosis	ACCEPT						genes/TAKRU/A0A674PKV4/A0A674PKV4-ai-review.yaml
sole_source		THLAR	TFP	GO:0005634	nucleus	MARK_AS_OVER_ANNOTATED				Relaxed from REMOVE. The rejection rested on absence of evidence rather than positive contrary evidence: the Falcon deep-research report states explicitly that no subcellular localization of TaTFP was found in the primary literature, and the gene notes record that direct localization is not experime		genes/THLAR/TFP/TFP-ai-review.yaml
sole_source		THLAR	TFP	GO:0005829	cytosol	ACCEPT						genes/THLAR/TFP/TFP-ai-review.yaml
sole_source		THLAR	TFP	GO:0030234	enzyme regulator activity	MODIFY						genes/THLAR/TFP/TFP-ai-review.yaml
sole_source		THLAR	TFP	GO:0080028	nitrile biosynthetic process	ACCEPT						genes/THLAR/TFP/TFP-ai-review.yaml
sole_source		TOBAC	PARA	GO:0005737	cytoplasm	KEEP_AS_NON_CORE				"The cytoplasm assignment is a reasonable family-level call: plant GSTs ""are predominantly expressed in the cytosol"" [PMID:11897031] and parA has no predicted targeting/transit peptide. However, there is a genuine experimental discrepancy: immunofluorescence and confocal imaging reported the parA pro"		genes/TOBAC/PARA/PARA-ai-review.yaml
sole_source		TRIV2	AmiC1	GO:0030288	outer membrane-bounded periplasmic space	ACCEPT						genes/TRIV2/AmiC1/AmiC1-ai-review.yaml
sole_source		TRIV2	AmiC2	GO:0030288	outer membrane-bounded periplasmic space	ACCEPT				Consistent with a secreted amidase acting on periplasmic septal PG; not wrong, though less specific than the septal localization observed for the AmiC2 ortholog.		genes/TRIV2/AmiC2/AmiC2-ai-review.yaml
sole_source		XENLA	uap1.S	GO:0006048	UDP-N-acetylglucosamine biosynthetic process	ACCEPT						genes/XENLA/uap1.S/uap1.S-ai-review.yaml
sole_source		YEREN	sctN	GO:0046933	proton-transporting ATP synthase activity, rotational mechanism	REMOVE				Contradicted by the biology of this protein: YscN consumes ATP to drive Yop export and transports no protons. The graft node sits outside the clade whose descendants carry the experimental evidence for the IBD, so this is a paralog over-propagation across a duplication node rather than an inherited 		genes/YEREN/sctN/sctN-ai-review.yaml