action	gene	file	taxon	propagated_term_id	propagated_term_label	graft_node	panther_family	panther_family_name	panther_subfamily	panther_subfamily_name	aspect	mode	mode_label	mode_source	mode_note	reviewer_reason
MARK_AS_OVER_ANNOTATED	A0A2K5UJ34	genes/MACFA/A0A2K5UJ34/A0A2K5UJ34-ai-review.yaml	Macaca fascicularis	GO:0032474	otolith morphogenesis	PTN001275231	PTHR31859	TETRATRICOPEPTIDE REPEAT PROTEIN 39 FAMILY MEMBER	PTHR31859:SF1	TETRATRICOPEPTIDE REPEAT PROTEIN 39C	biological_process	3	GENERIC_CONTEXT	curated	fish-specific structure (otolith) propagated to a mammal: taxon context	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.
MARK_AS_OVER_ANNOTATED	A0A8B6GS20	genes/MYTGA/A0A8B6GS20/A0A8B6GS20-ai-review.yaml	Mytilus galloprovincialis	GO:0010507	negative regulation of autophagy	PTN000086907	PTHR10807	MYOTUBULARIN-RELATED	PTHR10807:SF73	LD06050P	biological_process	2	PSEUDOENZYME	curated	MTMR9 pseudophosphatase (no catalytic Cys); regulatory role only	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.
MARK_AS_OVER_ANNOTATED	ALB	genes/CANLF/ALB/ALB-ai-review.yaml	Canis lupus familiaris	GO:0036094	small molecule binding	PTN000147397	PTHR11385	SERUM ALBUMIN-RELATED	PTHR11385:SF15	ALBUMIN	molecular_function	3	GENERIC_CONTEXT	heuristic	uninformative binding term	Uninformative broad parent of the specific binding functions.
MARK_AS_OVER_ANNOTATED	ALB	genes/FELCA/ALB/ALB-ai-review.yaml	Felis catus	GO:0036094	small molecule binding	PTN002604567	PTHR11385	SERUM ALBUMIN-RELATED	PTHR11385:SF15	ALBUMIN	molecular_function	3	GENERIC_CONTEXT	heuristic	uninformative binding term	Uninformative broad parent of the specific binding functions.
MARK_AS_OVER_ANNOTATED	Betv1	genes/BETPN/Betv1/Betv1-ai-review.yaml	Betula pendula	GO:0005634	nucleus	PTN007850272	PTHR31213	OS08G0374000 PROTEIN-RELATED	PTHR31213:SF55	STRESS-INDUCED PROTEIN SAM22	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	Over-propagated with the ABA-receptor annotations; inconsistent with the cytoplasmic localization of Bet v 1.
MARK_AS_OVER_ANNOTATED	DDO	genes/OCTVU/DDO/DDO-ai-review.yaml	Octopus vulgaris	GO:0005737	cytoplasm	PTN000898250	PTHR11530	D-AMINO ACID OXIDASE	PTHR11530:SF17	RE49860P	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	DDO has a C-terminal SKL microbody targeting signal (residues 334-336) and is annotated to peroxisomal matrix (GO:0005782) by ISS to human and bovine orthologs. Cytoplasm is too general and adds no information beyond the more specific peroxisomal matrix annotation.
MARK_AS_OVER_ANNOTATED	IRE1	genes/HYPJE/IRE1/IRE1-ai-review.yaml	Hypocrea jecorina (strain QM6a)	GO:0051082	unfolded protein binding	PTN001017826	PTHR13954	IRE1-RELATED	PTHR13954:SF6	NON-SPECIFIC SERINE_THREONINE PROTEIN KINASE	molecular_function	3	GENERIC_CONTEXT	curated	uninformative/obsolete binding term; sensor, not chaperone	GO:0051082 is now formally obsolete. While IRE1 detects unfolded proteins in the ER lumen, its binding serves a sensor/signaling function, not a chaperone function. IRE1 does not assist protein folding. The unfolded protein sensing function is already captured by GO:0036498 (IRE1-mediated unfolded p
MARK_AS_OVER_ANNOTATED	IRE1	genes/HYPJE/IRE1/IRE1-ai-review.yaml	Hypocrea jecorina (strain QM6a)	GO:0070059	intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress	PTN001017826	PTHR13954	IRE1-RELATED	PTHR13954:SF6	NON-SPECIFIC SERINE_THREONINE PROTEIN KINASE	biological_process	3	GENERIC_CONTEXT	curated	fungi lack classical apoptosis; mammalian-context process	Filamentous fungi do not have classical apoptosis. This annotation is inferred from mammalian IRE1 orthologs via TreeGrafter. Following the yeast IRE1 (P32361) precedent where the same annotation was marked as over-annotated for the same reason. The core function of T. reesei IRE1 is the UPR signali
MARK_AS_OVER_ANNOTATED	K9IMD0	genes/DESRO/K9IMD0/K9IMD0-ai-review.yaml	Desmodus rotundus	GO:0019731	antibacterial humoral response	PTN000159979	PTHR11485	TRANSFERRIN	PTHR11485:SF55	LACTOTRANSFERRIN	biological_process	4	MISPLACEMENT	curated	draculin: neofunctionalized lactoferrin homolog (anticoagulant), family process contradicted	No direct evidence for antibacterial humoral response in draculin studies; experimental data instead support anticoagulant activity in saliva [PMID:7740503; PMID:10556567; PMID:9795244].
MARK_AS_OVER_ANNOTATED	K9IWR0	genes/DESRO/K9IWR0/K9IWR0-ai-review.yaml	Desmodus rotundus	GO:0043123	positive regulation of canonical NF-kappaB signal transduction	PTN000158030	PTHR11471	TUMOR NECROSIS FACTOR FAMILY MEMBER	PTHR11471:SF31	LYMPHOTOXIN-ALPHA	biological_process	3	GENERIC_CONTEXT	curated	specific downstream signalling process inherited from mammalian lymphotoxin, unevidenced	Specific pathway regulation is not directly evidenced for this DESRO protein.
MARK_AS_OVER_ANNOTATED	K9IWR0	genes/DESRO/K9IWR0/K9IWR0-ai-review.yaml	Desmodus rotundus	GO:2001238	positive regulation of extrinsic apoptotic signaling pathway	PTN000158030	PTHR11471	TUMOR NECROSIS FACTOR FAMILY MEMBER	PTHR11471:SF31	LYMPHOTOXIN-ALPHA	biological_process	3	GENERIC_CONTEXT	curated	specific downstream signalling process inherited from mammalian lymphotoxin, unevidenced	Specific apoptotic pathway regulation is not directly evidenced for this protein.
MARK_AS_OVER_ANNOTATED	K9J287	genes/DESRO/K9J287/K9J287-ai-review.yaml	Desmodus rotundus	GO:0003677	DNA binding	PTN001684743	PTHR11371	DEOXYRIBONUCLEASE	PTHR11371:SF28	DEOXYRIBONUCLEASE-1-LIKE 1	molecular_function	1	GRANULARITY	heuristic	granularity keywords	Annotation is inferred from domain/TreeGrafter without direct experimental evidence.
MARK_AS_OVER_ANNOTATED	NCGR_LOCUS10166	genes/9POAL/NCGR_LOCUS10166/NCGR_LOCUS10166-ai-review.yaml	Miscanthus lutarioriparius	GO:0005737	cytoplasm		PTHR21256	HISTIDINOL DEHYDROGENASE HDH	PTHR21256:SF2	HISTIDINE BIOSYNTHESIS TRIFUNCTIONAL PROTEIN	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	The term is too general. For the HDH domain, the correct localization is chloroplast stroma (GO:0009570), which is already annotated. For the ARV1 domain, the correct localization is ER membrane (GO:0005789). Applied to a gene prediction artifact.
MARK_AS_OVER_ANNOTATED	NCGR_LOCUS10166	genes/9POAL/NCGR_LOCUS10166/NCGR_LOCUS10166-ai-review.yaml	Miscanthus lutarioriparius	GO:0005829	cytosol		PTHR21256	HISTIDINOL DEHYDROGENASE HDH	PTHR21256:SF2	HISTIDINE BIOSYNTHESIS TRIFUNCTIONAL PROTEIN	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	For the HDH domain, the mature protein is chloroplast stroma-localized, not cytosolic. For the ARV1 domain, the protein is ER membrane-localized. Cytosol is not the functional localization for either domain. Applied to a gene prediction artifact.
MARK_AS_OVER_ANNOTATED	NCGR_LOCUS10166	genes/9POAL/NCGR_LOCUS10166/NCGR_LOCUS10166-ai-review.yaml	Miscanthus lutarioriparius	GO:0009570	chloroplast stroma		PTHR21256	HISTIDINOL DEHYDROGENASE HDH	PTHR21256:SF2	HISTIDINE BIOSYNTHESIS TRIFUNCTIONAL PROTEIN	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	While this is the most accurate localization for the HDH domain, it is applied to a gene prediction artifact. The true HDH gene is NCGR_LOCUS4558 (A0A811MHP4). The chloroplast stroma localization is fundamentally incompatible with the ER membrane localization of the ARV1 domain on the same polypepti
MARK_AS_OVER_ANNOTATED	NCGR_LOCUS1270	genes/9POAL/NCGR_LOCUS1270/NCGR_LOCUS1270-ai-review.yaml	Miscanthus lutarioriparius	GO:0006000	fructose metabolic process	PTN004269459	PTHR11556	FRUCTOSE-1,6-BISPHOSPHATASE-RELATED	PTHR11556:SF1	FRUCTOSE-BISPHOSPHATASE	biological_process	1	GRANULARITY	heuristic	granularity keywords	Overly vague and misleading. The enzyme's biological role is in the Calvin cycle (GO:0019253), not in fructose metabolism per se. TreeGrafter annotation that fails to capture the specific biological context.
MARK_AS_OVER_ANNOTATED	NCGR_LOCUS1270	genes/9POAL/NCGR_LOCUS1270/NCGR_LOCUS1270-ai-review.yaml	Miscanthus lutarioriparius	GO:0006002	fructose 6-phosphate metabolic process	PTN004269459	PTHR11556	FRUCTOSE-1,6-BISPHOSPHATASE-RELATED	PTHR11556:SF1	FRUCTOSE-BISPHOSPHATASE	biological_process	1	GRANULARITY	heuristic	granularity keywords	Technically true but uninformative without Calvin cycle context. The reductive pentose-phosphate cycle (GO:0019253) annotation captures the specific biological process. This TreeGrafter annotation adds no useful information beyond what GO:0019253 already conveys.
MARK_AS_OVER_ANNOTATED	OCTS1	genes/OCTVU/OCTS1/OCTS1-ai-review.yaml	Octopus vulgaris	GO:0004364	glutathione transferase activity	PTN007515140	PTHR11571	GLUTATHIONE S-TRANSFERASE	PTHR11571:SF150	GLUTATHIONE S-TRANSFERASE	molecular_function	2	PSEUDOENZYME	heuristic	pseudo-enzyme keywords	GO:0004364 implies functional GST catalytic activity, but OCTS1 has lost this function through evolutionary co-option. The residual activity (~1/700 to 1/6000 of authentic GST) is biologically negligible. The protein's actual molecular function is as a structural constituent of the eye lens. Four ke
MARK_AS_OVER_ANNOTATED	OCTS1	genes/OCTVU/OCTS1/OCTS1-ai-review.yaml	Octopus vulgaris	GO:0006749	glutathione metabolic process	PTN007515140	PTHR11571	GLUTATHIONE S-TRANSFERASE	PTHR11571:SF150	GLUTATHIONE S-TRANSFERASE	biological_process	2	PSEUDOENZYME	heuristic	pseudo-enzyme keywords	"The biological process ""glutathione metabolic process"" implies that OCTS1 functions in the metabolism of glutathione. In reality, OCTS1 binds GSH as a structural cofactor to prevent its own aggregation and maintain lens transparency, not to metabolize glutathione. The catalytic turnover is negligibl"
MARK_AS_OVER_ANNOTATED	OLFML2A	genes/9PRIM/A0A8C9H4D2/A0A8C9H4D2-ai-review.yaml	Piliocolobus tephrosceles	GO:0007165	signal transduction	PTN000573914	PTHR23192	OLFACTOMEDIN-RELATED	PTHR23192:SF29	OLFACTOMEDIN-LIKE PROTEIN 2A	biological_process	3	GENERIC_CONTEXT	curated	generic signalling process for an ECM glycoprotein	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
MARK_AS_OVER_ANNOTATED	PP_3157	genes/PSEPK/PP_3157/PP_3157-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0042578	phosphoric ester hydrolase activity	PTN005150789	PTHR43200	PHOSPHATASE	PTHR43200:SF6	3'(2'),5'-BISPHOSPHATE NUCLEOTIDASE	molecular_function	1	GRANULARITY	heuristic	granularity keywords	The TreeGrafter term is a generic ancestor of the specific histidinol-phosphatase activity and does not identify the biological substrate.
MARK_AS_OVER_ANNOTATED	PP_4379	genes/PSEPK/PP_4379/PP_4379-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0044550	secondary metabolite biosynthetic process	PTN002147079	PTHR34069	3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 3	PTHR34069:SF2	BETA-KETOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE III	biological_process	3	GENERIC_CONTEXT	curated	process over-reach from KAS-III family membership	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
MARK_AS_OVER_ANNOTATED	PP_4545	genes/PSEPK/PP_4545/PP_4545-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0044550	secondary metabolite biosynthetic process	PTN002436757	PTHR34069	3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 3	PTHR34069:SF2	BETA-KETOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE III	biological_process	3	GENERIC_CONTEXT	curated	process over-reach from KAS-III family membership	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.
MARK_AS_OVER_ANNOTATED	alg8	genes/PSEPK/alg8/alg8-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0085029	extracellular matrix assembly	PTN002740694	PTHR22913	HYALURONAN SYNTHASE	PTHR22913:SF12	MANNURONAN SYNTHASE	biological_process	3	GENERIC_CONTEXT	curated	process over-reach; alginate biosynthesis is the defensible process	The term is conditionally compatible with the extracellular role of alginate, but PTN002740694 does not establish it for this target and the exact alginic acid biosynthetic process is the defensible core process.
MARK_AS_OVER_ANNOTATED	amaC	genes/PSEPK/amaC/amaC-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0042802	identical protein binding	PTN001725705	PTHR11879	ASPARTATE AMINOTRANSFERASE	PTHR11879:SF37	AROMATIC-AMINO-ACID AMINOTRANSFERASE	molecular_function	3	GENERIC_CONTEXT	heuristic	uninformative binding term	Self-association is a structural property and the generic binding term adds little beyond the enzymatic activity; protein-binding-style terms are discouraged for core curation.
MARK_AS_OVER_ANNOTATED	aprA	genes/DESVH/Q72DT2/Q72DT2-ai-review.yaml	Nitratidesulfovibrio vulgaris (Desulfovibrio vulgaris) Hildenborough	GO:0009055	electron transfer activity	PTN000908678	PTHR11632	SUCCINATE DEHYDROGENASE 2 FLAVOPROTEIN SUBUNIT	PTHR11632:SF51	SUCCINATE DEHYDROGENASE [UBIQUINONE] FLAVOPROTEIN SUBUNIT, MITOCHONDRIAL	molecular_function	4	MISPLACEMENT	curated	AprA cluster: APS reductase grafted onto SDH flavoprotein subfamily	While AprA participates in an electron-dependent reaction, the electron transfer activity per se is mediated by AprB (with its Fe-S clusters) and the QmoABC complex. AprA's role is catalytic reduction of APS using electrons delivered by AprB. This annotation conflates the catalytic function of AprA 
MARK_AS_OVER_ANNOTATED	argD	genes/PSEPK/argD/argD-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0042802	identical protein binding	PTN002279553	PTHR11986	AMINOTRANSFERASE CLASS III	PTHR11986:SF113	SUCCINYLORNITHINE TRANSAMINASE	molecular_function	3	GENERIC_CONTEXT	heuristic	uninformative binding term	The TreeGrafter term does not identify a distinct binding role beyond oligomerization of the enzyme.
MARK_AS_OVER_ANNOTATED	aroQ	genes/PSEPK/aroQ/aroQ-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0019631	quinate catabolic process	PTN000479790	PTHR21272	CATABOLIC 3-DEHYDROQUINASE	PTHR21272:SF3	CATABOLIC 3-DEHYDROQUINASE	biological_process	1	GRANULARITY	heuristic	family-level propagation stated	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 functions in quinate catabolism, and that role is normally carried by a distinct enz
MARK_AS_OVER_ANNOTATED	aroQ-III	genes/PSEPK/aroQ-III/aroQ-III-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0019631	quinate catabolic process	PTN000479790	PTHR21272	CATABOLIC 3-DEHYDROQUINASE	PTHR21272:SF3	CATABOLIC 3-DEHYDROQUINASE	biological_process	1	GRANULARITY	heuristic	family-level propagation stated	This TreeGrafter process propagation may be biologically plausible at the pathway-family level, but it is not paralog-specific. The core supported role of aroQ-III is the dehydroquinate dehydratase step feeding chorismate biosynthesis.
MARK_AS_OVER_ANNOTATED	aroQ1	genes/PSEPK/aroQ1/aroQ1-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0019631	quinate catabolic process	PTN002327525	PTHR21272	CATABOLIC 3-DEHYDROQUINASE	PTHR21272:SF3	CATABOLIC 3-DEHYDROQUINASE	biological_process	1	GRANULARITY	heuristic	family-level propagation stated	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.
MARK_AS_OVER_ANNOTATED	aroQ2	genes/PSEPK/aroQ2/aroQ2-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0019631	quinate catabolic process	PTN002327524	PTHR21272	CATABOLIC 3-DEHYDROQUINASE	PTHR21272:SF3	CATABOLIC 3-DEHYDROQUINASE	biological_process	1	GRANULARITY	heuristic	family-level propagation stated	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.
MARK_AS_OVER_ANNOTATED	aruC	genes/PSEPK/aruC/aruC-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0042802	identical protein binding	PTN002279542	PTHR11986	AMINOTRANSFERASE CLASS III	PTHR11986:SF79	ACETYLORNITHINE AMINOTRANSFERASE, MITOCHONDRIAL	molecular_function	3	GENERIC_CONTEXT	heuristic	uninformative binding term	The TreeGrafter term is less informative than the enzyme reaction and lacks target-specific oligomer evidence.
MARK_AS_OVER_ANNOTATED	bioD	genes/PSEPK/bioD/bioD-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0005829	cytosol	PTN002456225	PTHR43210	DETHIOBIOTIN SYNTHETASE	PTHR43210:SF5	DETHIOBIOTIN SYNTHETASE	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	The two terms do not describe distinct BioD pools in this bacterium, and the UniProt source explicitly uses cytoplasm.
MARK_AS_OVER_ANNOTATED	cpx	genes/DORPE/cpx/cpx-ai-review.yaml	Doryteuthis pealeii	GO:0031201	SNARE complex	PTN002703616	PTHR16705	COMPLEXIN	PTHR16705:SF4	COMPLEXIN	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	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. 
MARK_AS_OVER_ANNOTATED	dapA	genes/PSEPK/dapA__Q88NH2/dapA__Q88NH2-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0005829	cytosol	PTN002281418	PTHR12128	DIHYDRODIPICOLINATE SYNTHASE	PTHR12128:SF66	4-HYDROXY-2-OXOGLUTARATE ALDOLASE, MITOCHONDRIAL	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	No distinct DapA-I pool is established by the parent/child location pair.
MARK_AS_OVER_ANNOTATED	dapB	genes/PSEPK/dapB/dapB-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0005829	cytosol	PTN002324624	PTHR20836	DIHYDRODIPICOLINATE REDUCTASE	PTHR20836:SF0	4-HYDROXY-TETRAHYDRODIPICOLINATE REDUCTASE 1, CHLOROPLASTIC-RELATED	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	No distinct DapB pool is established by the parent/child location pair.
MARK_AS_OVER_ANNOTATED	dapF	genes/PSEPK/dapF__Q88CF3/dapF__Q88CF3-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0005829	cytosol	PTN002420849	PTHR31689	DIAMINOPIMELATE EPIMERASE, CHLOROPLASTIC	PTHR31689:SF0	DIAMINOPIMELATE EPIMERASE	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	No distinct DapF pool is established by the parent/child location pair.
MARK_AS_OVER_ANNOTATED	dapF	genes/PSEPK/dapF__Q88GD4/dapF__Q88GD4-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0005829	cytosol	PTN001271294	PTHR31689	DIAMINOPIMELATE EPIMERASE, CHLOROPLASTIC	PTHR31689:SF0	DIAMINOPIMELATE EPIMERASE	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	No distinct DapF pool is established by the parent/child location pair.
MARK_AS_OVER_ANNOTATED	davT	genes/PSEPK/davT/davT-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0042802	identical protein binding	PTN002633741	PTHR11986	AMINOTRANSFERASE CLASS III	PTHR11986:SF58	LEUCINE_METHIONINE RACEMASE	molecular_function	3	GENERIC_CONTEXT	heuristic	uninformative binding term	No mechanistic complex role is supplied, and the substrate-specific catalytic activity is the informative annotation.
MARK_AS_OVER_ANNOTATED	ddlA	genes/PSEPK/ddlA/ddlA-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0005829	cytosol	PTN000566195	PTHR23132	D-ALANINE--D-ALANINE LIGASE	PTHR23132:SF25	D-ALANINE--D-ALANINE LIGASE A	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	Retain GO:0005737 as the single informative cellular-component annotation.
MARK_AS_OVER_ANNOTATED	dinB	genes/PSEPK/dinB/dinB-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0005829	cytosol	PTN002253950	PTHR11076	DNA REPAIR POLYMERASE UMUC / TRANSFERASE FAMILY MEMBER	PTHR11076:SF33	DNA POLYMERASE KAPPA	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	Cytosol is consistent with the documented cytoplasmic location but is a more specific compartment term inferred electronically; it is redundant given the cytoplasm annotation and not independently supported for this protein.
MARK_AS_OVER_ANNOTATED	dxs	genes/PSEPK/dxs/dxs-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0016744	transketolase or transaldolase activity	PTN002457875	PTHR43322	1-D-DEOXYXYLULOSE 5-PHOSPHATE SYNTHASE-RELATED	PTHR43322:SF5	1-DEOXY-D-XYLULOSE-5-PHOSPHATE SYNTHASE, CHLOROPLASTIC	molecular_function	1	GRANULARITY	curated	family-level transketolase term over the specific DXS reaction	Dxs belongs to the transketolase family, but GO:0008661 identifies its exact physiological condensation reaction and should carry the core call.
MARK_AS_OVER_ANNOTATED	exbB	genes/PSEPK/exbB/exbB-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0017038	protein import	PTN004746214	PTHR30625	PROTEIN TOLQ	PTHR30625:SF16	BIOPOLYMER TRANSPORT PROTEIN EXBB	biological_process	3	GENERIC_CONTEXT	curated	process term does not describe PMF-coupled energization	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.
MARK_AS_OVER_ANNOTATED	fabB	genes/PSEPK/fabB/fabB-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0005829	cytosol	PTN002270989	PTHR11712	POLYKETIDE SYNTHASE-RELATED	PTHR11712:SF306	3-OXOACYL-[ACYL-CARRIER-PROTEIN] SYNTHASE 1	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	Cytosol adds no useful distinction for this bacterial soluble enzyme.
MARK_AS_OVER_ANNOTATED	fabV	genes/PSEPK/fabV/fabV-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0050343	trans-2-enoyl-CoA reductase (NADH) activity	PTN002206130	PTHR37480	ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH]	PTHR37480:SF1	ENOYL-[ACYL-CARRIER-PROTEIN] REDUCTASE [NADH]	molecular_function	1	GRANULARITY	curated	sibling substrate term (CoA vs ACP); subfamily correct	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.
MARK_AS_OVER_ANNOTATED	flgE	genes/PSEPK/flgE/flgE-ai-review.yaml	Pseudomonas putida KT2440	GO:0071978	bacterial-type flagellum-dependent swarming motility	PTN000764868	PTHR30435	FLAGELLAR PROTEIN	PTHR30435:SF1	FLAGELLAR HOOK PROTEIN FLGE	biological_process	3	GENERIC_CONTEXT	curated	specialised swarming process over-propagated to a structural hook protein	This term is likely over-annotated. FlgE is a core flagellar structural protein, so it may be required when a strain swarms, but swarming is a specialized surface-associated behavior with additional physiological determinants beyond simply encoding the hook subunit. There is no direct gene-specific 
MARK_AS_OVER_ANNOTATED	gcvH1	genes/PSEPK/gcvH1/gcvH1-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0005737	cytoplasm	PTN002271035	PTHR11715	GLYCINE CLEAVAGE SYSTEM H PROTEIN	PTHR11715:SF3	GLYCINE CLEAVAGE SYSTEM H PROTEIN-RELATED	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	Retain GO:0005829 as non-core location context instead of duplicating it with its parent.
MARK_AS_OVER_ANNOTATED	gcvH2	genes/PSEPK/gcvH2/gcvH2-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0005737	cytoplasm	PTN002271036	PTHR11715	GLYCINE CLEAVAGE SYSTEM H PROTEIN	PTHR11715:SF3	GLYCINE CLEAVAGE SYSTEM H PROTEIN-RELATED	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	Retain GO:0005829 as non-core location context instead of duplicating it with its parent.
MARK_AS_OVER_ANNOTATED	glgB	genes/PSEPK/glgB/glgB-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0005737	cytoplasm	PTN002462574	PTHR43651	1,4-ALPHA-GLUCAN-BRANCHING ENZYME	PTHR43651:SF3	1,4-ALPHA-GLUCAN-BRANCHING ENZYME	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	The accepted cytosol child term is the more precise of the two TreeGrafter locations; the parent adds no independent localization information.
MARK_AS_OVER_ANNOTATED	gshB	genes/PSEPK/gshB/gshB-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0016879	ligase activity, forming carbon-nitrogen bonds	PTN002330136	PTHR21621	RIBOSOMAL PROTEIN S6 MODIFICATION PROTEIN	PTHR21621:SF4	GLUTATHIONE SYNTHETASE	molecular_function	1	GRANULARITY	curated	broad ligase parent over glutathione synthase	GO:0004363 identifies the physiological substrates and should carry the core function.
MARK_AS_OVER_ANNOTATED	hisD	genes/PSEPK/hisD/hisD-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0005829	cytosol	PTN002327387	PTHR21256	HISTIDINOL DEHYDROGENASE HDH	PTHR21256:SF2	HISTIDINE BIOSYNTHESIS TRIFUNCTIONAL PROTEIN	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	The term is not biologically contradictory, but retaining both cytoplasm and its soluble cytosol subcompartment adds unsupported precision and duplicates the useful bacterial localization statement.
MARK_AS_OVER_ANNOTATED	hmgC	genes/PSEPK/hmgC/hmgC-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0004364	glutathione transferase activity	PTN002448156	PTHR42673	MALEYLACETOACETATE ISOMERASE	PTHR42673:SF21	GLUTATHIONE S-TRANSFERASE YFCF	molecular_function	1	GRANULARITY	heuristic	family-level propagation stated	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.
MARK_AS_OVER_ANNOTATED	hmgC	genes/PSEPK/hmgC/hmgC-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0006749	glutathione metabolic process	PTN002448156	PTHR42673	MALEYLACETOACETATE ISOMERASE	PTHR42673:SF21	GLUTATHIONE S-TRANSFERASE YFCF	biological_process	3	GENERIC_CONTEXT	heuristic	host lacks pathway/process	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.
MARK_AS_OVER_ANNOTATED	hutF	genes/PSEPK/hutF/hutF-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0019239	deaminase activity	PTN002462020	PTHR11271	GUANINE DEAMINASE	PTHR11271:SF48	AMIDOHYDROLASE-RELATED DOMAIN-CONTAINING PROTEIN	molecular_function	1	GRANULARITY	heuristic	granularity keywords	GO:0050416 is the informative child activity; the broad TreeGrafter deaminase annotation should not be treated as an independent core function.
MARK_AS_OVER_ANNOTATED	ilvA-I	genes/PSEPK/ilvA-I/ilvA-I-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0003941	L-serine ammonia-lyase activity	PTN002463974	PTHR48078	THREONINE DEHYDRATASE, MITOCHONDRIAL-RELATED	PTHR48078:SF11	THREONINE DEHYDRATASE, MITOCHONDRIAL	molecular_function	1	GRANULARITY	curated	sibling activity of the threonine/serine dehydratase family	Q88HB4 carries the biosynthetic-threonine-deaminase signature and an exact threonine reaction/pathway assignment. TreeGrafter transfer across the broader serine/threonine-dehydratase family does not establish a physiologically relevant serine reaction for this paralog.
MARK_AS_OVER_ANNOTATED	ilvA-I	genes/PSEPK/ilvA-I/ilvA-I-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0006565	L-serine catabolic process	PTN002463974	PTHR48078	THREONINE DEHYDRATASE, MITOCHONDRIAL-RELATED	PTHR48078:SF11	THREONINE DEHYDRATASE, MITOCHONDRIAL	biological_process	1	GRANULARITY	curated	sibling activity of the threonine/serine dehydratase family	This TreeGrafter call follows the broad enzyme family. The exact UniProt reaction and pathway record instead identify threonine use for 2-oxobutanoate supply in isoleucine biosynthesis.
MARK_AS_OVER_ANNOTATED	ilvA-I	genes/PSEPK/ilvA-I/ilvA-I-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0006567	L-threonine catabolic process	PTN002463974	PTHR48078	THREONINE DEHYDRATASE, MITOCHONDRIAL-RELATED	PTHR48078:SF11	THREONINE DEHYDRATASE, MITOCHONDRIAL	biological_process	1	GRANULARITY	curated	sibling catabolic process of the threonine/serine dehydratase family	GO:0006567 broadly covers reactions resulting in threonine breakdown, so the call is not chemically false. It is nevertheless misleading as a core physiological assignment because Q88HB4 channels the resulting 2-oxobutanoate into L-isoleucine biosynthesis rather than a dedicated threonine-degradatio
MARK_AS_OVER_ANNOTATED	ilvA-II	genes/PSEPK/ilvA-II/ilvA-II-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0003941	L-serine ammonia-lyase activity	PTN002463976	PTHR48078	THREONINE DEHYDRATASE, MITOCHONDRIAL-RELATED	PTHR48078:SF11	THREONINE DEHYDRATASE, MITOCHONDRIAL	molecular_function	1	GRANULARITY	curated	sibling activity of the threonine/serine dehydratase family	Q88CN1 carries the biosynthetic-threonine-deaminase signature and an exact threonine reaction/pathway assignment. TreeGrafter transfer across the broader serine/threonine-dehydratase family does not establish a physiologically relevant serine reaction for this paralog.
MARK_AS_OVER_ANNOTATED	ilvA-II	genes/PSEPK/ilvA-II/ilvA-II-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0006565	L-serine catabolic process	PTN002463976	PTHR48078	THREONINE DEHYDRATASE, MITOCHONDRIAL-RELATED	PTHR48078:SF11	THREONINE DEHYDRATASE, MITOCHONDRIAL	biological_process	1	GRANULARITY	curated	sibling activity of the threonine/serine dehydratase family	This TreeGrafter call follows the broad enzyme family. The exact UniProt reaction and pathway record instead identify threonine use for 2-oxobutanoate supply in isoleucine biosynthesis.
MARK_AS_OVER_ANNOTATED	ilvA-II	genes/PSEPK/ilvA-II/ilvA-II-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0006567	L-threonine catabolic process	PTN002463976	PTHR48078	THREONINE DEHYDRATASE, MITOCHONDRIAL-RELATED	PTHR48078:SF11	THREONINE DEHYDRATASE, MITOCHONDRIAL	biological_process	1	GRANULARITY	curated	sibling catabolic process of the threonine/serine dehydratase family	GO:0006567 broadly covers reactions resulting in threonine breakdown, so the call is not chemically false. It is nevertheless misleading as a core physiological assignment because Q88CN1 channels the resulting 2-oxobutanoate into L-isoleucine biosynthesis rather than a dedicated threonine-degradatio
MARK_AS_OVER_ANNOTATED	ilvH	genes/PSEPK/ilvH/ilvH-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0005829	cytosol	PTN002410438	PTHR30239	ACETOLACTATE SYNTHASE SMALL SUBUNIT	PTHR30239:SF0	ACETOLACTATE SYNTHASE SMALL SUBUNIT 1, CHLOROPLASTIC	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	No distinct IlvH pool is supported by the parent/child location pair.
MARK_AS_OVER_ANNOTATED	leuB	genes/PSEPK/leuB/leuB-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0005829	cytosol	PTN002452704	PTHR42979	3-ISOPROPYLMALATE DEHYDROGENASE	PTHR42979:SF1	3-ISOPROPYLMALATE DEHYDROGENASE	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	No distinct LeuB pool is supported by the parent/child location pair.
MARK_AS_OVER_ANNOTATED	mcr-1	genes/ECOLX/mcr-1/mcr-1-ai-review.yaml	Escherichia coli	GO:0009244	lipopolysaccharide core region biosynthetic process	PTN002019544	PTHR30443	INNER MEMBRANE PROTEIN	PTHR30443:SF0	PHOSPHOETHANOLAMINE TRANSFERASE EPTA	biological_process	1	GRANULARITY	curated	EptA node: lipid-A modification vs LPS-core process (sibling process)	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.
MARK_AS_OVER_ANNOTATED	mcr-3	genes/AERME/mcr-3/mcr-3-ai-review.yaml	Aeromonas media	GO:0009244	lipopolysaccharide core region biosynthetic process	PTN002019542	PTHR30443	INNER MEMBRANE PROTEIN	PTHR30443:SF0	PHOSPHOETHANOLAMINE TRANSFERASE EPTA	biological_process	1	GRANULARITY	curated	EptA node: lipid-A modification vs LPS-core process (sibling process)	MCR proteins modify lipid A to confer polymyxin resistance; they are not core LPS oligosaccharide biosynthetic enzymes.
MARK_AS_OVER_ANNOTATED	mcr-4	genes/SALSP/mcr-4/mcr-4-ai-review.yaml	Salmonella sp	GO:0009244	lipopolysaccharide core region biosynthetic process	PTN002019543	PTHR30443	INNER MEMBRANE PROTEIN	PTHR30443:SF0	PHOSPHOETHANOLAMINE TRANSFERASE EPTA	biological_process	1	GRANULARITY	curated	EptA node: lipid-A modification vs LPS-core process (sibling process)	MCR proteins modify lipid A to confer polymyxin resistance; they are not core LPS oligosaccharide biosynthetic enzymes.
MARK_AS_OVER_ANNOTATED	mcr2	genes/ECOLX/mcr2/mcr2-ai-review.yaml	Escherichia coli	GO:0009244	lipopolysaccharide core region biosynthetic process	PTN002019544	PTHR30443	INNER MEMBRANE PROTEIN	PTHR30443:SF0	PHOSPHOETHANOLAMINE TRANSFERASE EPTA	biological_process	1	GRANULARITY	curated	EptA node: lipid-A modification vs LPS-core process (sibling process)	MCR proteins modify lipid A to confer polymyxin resistance; they are not core LPS oligosaccharide biosynthetic enzymes.
MARK_AS_OVER_ANNOTATED	mobA	genes/PSEPK/mobA/mobA-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:1902758	bis(molybdopterin guanine dinucleotide)molybdenum biosynthetic process	PTN002318022	PTHR19136	MOLYBDENUM COFACTOR GUANYLYLTRANSFERASE	PTHR19136:SF81	MOLYBDENUM COFACTOR GUANYLYLTRANSFERASE	biological_process	3	GENERIC_CONTEXT	curated	downstream process over-reach (bis-MGD assembly)	Reviewed target UniProt supports Mo-MGD formation but does not establish downstream bis-MGD assembly by MobA.
MARK_AS_OVER_ANNOTATED	moeA	genes/PSEPK/moeA/moeA-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0005737	cytoplasm	PTN002229918	PTHR10192	MOLYBDOPTERIN BIOSYNTHESIS PROTEIN	PTHR10192:SF5	GEPHYRIN	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	Q88L14 acts in the soluble cytosol; retaining both cytoplasm and cytosol adds no distinct localization information.
MARK_AS_OVER_ANNOTATED	moeB	genes/PSEPK/moeB/moeB-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0005737	cytoplasm	PTN002250299	PTHR10953	UBIQUITIN-ACTIVATING ENZYME E1	PTHR10953:SF194	MOLYBDOPTERIN-SYNTHASE ADENYLYLTRANSFERASE	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	Q88PW3 acts on soluble MoaD in the cytosol; retaining both cytoplasm and cytosol adds no distinct localization information.
MARK_AS_OVER_ANNOTATED	mraY	genes/PSEPK/mraY/mraY-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0044038	cell wall macromolecule biosynthetic process	PTN002341405	PTHR22926	PHOSPHO-N-ACETYLMURAMOYL-PENTAPEPTIDE-TRANSFERASE	PTHR22926:SF5	PHOSPHO-N-ACETYLMURAMOYL-PENTAPEPTIDE-TRANSFERASE HOMOLOG	biological_process	1	GRANULARITY	curated	broad cell-wall parent over peptidoglycan biosynthesis	GO:0009252 is already present as the direct pathway term, making this broad cell-wall biosynthesis parent redundant.
MARK_AS_OVER_ANNOTATED	mraY	genes/PSEPK/mraY/mraY-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0071555	cell wall organization	PTN002341405	PTHR22926	PHOSPHO-N-ACETYLMURAMOYL-PENTAPEPTIDE-TRANSFERASE	PTHR22926:SF5	PHOSPHO-N-ACETYLMURAMOYL-PENTAPEPTIDE-TRANSFERASE HOMOLOG	biological_process	1	GRANULARITY	heuristic	granularity keywords	GO:0009252 is already present as the direct pathway term, making this broad cell-wall organization annotation redundant.
MARK_AS_OVER_ANNOTATED	mscL	genes/PSEPK/mscL/mscL-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0006811	monoatomic ion transport	PTN002410587	PTHR30266	MECHANOSENSITIVE CHANNEL MSCL	PTHR30266:SF2	LARGE-CONDUCTANCE MECHANOSENSITIVE CHANNEL	biological_process	1	GRANULARITY	curated	broad transport parent over mechanosensitive channel terms	MscL is a membrane channel; GO:0034220 monoatomic ion transmembrane transport and GO:0008381 mechanosensitive monoatomic ion channel activity better capture the function.
MARK_AS_OVER_ANNOTATED	murB	genes/PSEPK/murB/murB-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0005829	cytosol	PTN002326094	PTHR21071	UDP-N-ACETYLENOLPYRUVOYLGLUCOSAMINE REDUCTASE	PTHR21071:SF4	UDP-N-ACETYLENOLPYRUVOYLGLUCOSAMINE REDUCTASE	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	For this bacterial soluble enzyme the separate cytosol IEA adds no useful information beyond the directly assigned cytoplasm term and should not be carried into the core-function summary.
MARK_AS_OVER_ANNOTATED	murG	genes/PSEPK/murG/murG-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0016757	glycosyltransferase activity	PTN002325814	PTHR21015	UDP-N-ACETYLGLUCOSAMINE--N-ACETYLMURAMYL-(PENTAPEPTIDE) PYROPHOSPHORYL-UNDECAPRENOL N-ACETYLGLUCOSAMINE TRANSFERASE 1	PTHR21015:SF22	GLYCOSYLTRANSFERASE	molecular_function	1	GRANULARITY	heuristic	granularity keywords	The Rhea-derived term identifies both the lipid I acceptor and UDP-GlcNAc donor and should replace generic glycosyltransferase activity.
MARK_AS_OVER_ANNOTATED	murJ	genes/PSEPK/murJ/murJ-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0034204	lipid translocation	PTN002257100	PTHR47019	LIPID II FLIPPASE MURJ	PTHR47019:SF1	LIPID II FLIPPASE MURJ	biological_process	1	GRANULARITY	heuristic	granularity keywords	GO:0015836 identifies the transported lipid-linked peptidoglycan substrate and should replace generic lipid translocation.
MARK_AS_OVER_ANNOTATED	mutS	genes/PSEPK/mutS/mutS-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0003690	double-stranded DNA binding	PTN002260821	PTHR11361	DNA MISMATCH REPAIR PROTEIN MUTS FAMILY MEMBER	PTHR11361:SF34	DNA MISMATCH REPAIR PROTEIN MSH1, MITOCHONDRIAL	molecular_function	1	GRANULARITY	heuristic	granularity keywords	GO:0030983 is the informative substrate-specific term.
MARK_AS_OVER_ANNOTATED	mvaB	genes/PSEPK/mvaB/mvaB-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0046951	ketone body biosynthetic process	PTN002448903	PTHR42738	HYDROXYMETHYLGLUTARYL-COA LYASE	PTHR42738:SF7	HYDROXYMETHYLGLUTARYL-COA LYASE	biological_process	3	GENERIC_CONTEXT	curated	product-derived mammalian-context process on a bacterial enzyme	This product-derived process annotation overstates the physiological context; retain the experimentally supported leucine catabolic process instead.
MARK_AS_OVER_ANNOTATED	nuoE	genes/PSEPK/nuoE/nuoE-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0003954	NADH dehydrogenase activity	PTN002234036	PTHR10371	NADH DEHYDROGENASE UBIQUINONE FLAVOPROTEIN 2, MITOCHONDRIAL	PTHR10371:SF3	NADH DEHYDROGENASE [UBIQUINONE] FLAVOPROTEIN 2, MITOCHONDRIAL	molecular_function	3	GENERIC_CONTEXT	curated	whole-complex activity placed on a single subunit (NADH site is NuoF)	NADH oxidation occurs at NuoF; this subunit contributes to the assembled complex but does not independently oxidize NADH.
MARK_AS_OVER_ANNOTATED	nuoG	genes/PSEPK/nuoG/nuoG-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0003954	NADH dehydrogenase activity	PTN002267032	PTHR43105	RESPIRATORY NITRATE REDUCTASE	PTHR43105:SF10	NADH-QUINONE OXIDOREDUCTASE SUBUNIT G	molecular_function	3	GENERIC_CONTEXT	curated	whole-complex activity placed on a single subunit (NADH site is NuoF)	NADH oxidation occurs at NuoF; this subunit contributes to the assembled complex but does not independently oxidize NADH.
MARK_AS_OVER_ANNOTATED	nuoH	genes/PSEPK/nuoH/nuoH-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0003954	NADH dehydrogenase activity	PTN002262020	PTHR11432	NADH DEHYDROGENASE SUBUNIT 1	PTHR11432:SF3	NADH-UBIQUINONE OXIDOREDUCTASE CHAIN 1	molecular_function	3	GENERIC_CONTEXT	curated	whole-complex activity placed on a single subunit (NADH site is NuoF)	NADH oxidation occurs at NuoF; this subunit contributes to the assembled complex but does not independently oxidize NADH.
MARK_AS_OVER_ANNOTATED	nuoI	genes/PSEPK/nuoI/nuoI-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0003954	NADH dehydrogenase activity	PTN000091339	PTHR10849	NADH DEHYDROGENASE UBIQUINONE IRON-SULFUR PROTEIN 8, MITOCHONDRIAL	PTHR10849:SF20	NADH DEHYDROGENASE [UBIQUINONE] IRON-SULFUR PROTEIN 8, MITOCHONDRIAL	molecular_function	3	GENERIC_CONTEXT	curated	whole-complex activity placed on a single subunit (NADH site is NuoF)	NADH oxidation occurs at NuoF; this subunit contributes to the assembled complex but does not independently oxidize NADH.
MARK_AS_OVER_ANNOTATED	nuoL	genes/PSEPK/nuoL/nuoL-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0003954	NADH dehydrogenase activity	PTN002450313	PTHR42829	NADH-UBIQUINONE OXIDOREDUCTASE CHAIN 5	PTHR42829:SF2	NADH-UBIQUINONE OXIDOREDUCTASE CHAIN 5	molecular_function	3	GENERIC_CONTEXT	curated	whole-complex activity placed on a single subunit (NADH site is NuoF)	NADH oxidation occurs at NuoF; this subunit contributes to the assembled complex but does not independently oxidize NADH.
MARK_AS_OVER_ANNOTATED	nuoM	genes/PSEPK/nuoM/nuoM-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0003954	NADH dehydrogenase activity	PTN002460631	PTHR43507	NADH-UBIQUINONE OXIDOREDUCTASE CHAIN 4	PTHR43507:SF1	NADH-UBIQUINONE OXIDOREDUCTASE CHAIN 4	molecular_function	3	GENERIC_CONTEXT	curated	whole-complex activity placed on a single subunit (NADH site is NuoF)	NADH oxidation occurs at NuoF; this subunit contributes to the assembled complex but does not independently oxidize NADH.
MARK_AS_OVER_ANNOTATED	paaF	genes/PSEPK/paaF/paaF-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0006635	fatty acid beta-oxidation	PTN000235251	PTHR11941	ENOYL-COA HYDRATASE-RELATED	PTHR11941:SF54	ENOYL-COA HYDRATASE, MITOCHONDRIAL	biological_process	1	GRANULARITY	heuristic	family-level propagation stated	PaaF is encoded in the phenylacetate catabolic locus and is assigned to the lower phenylacetate pathway. The fatty-acid process annotation was transferred from a broad enoyl-CoA hydratase family.
MARK_AS_OVER_ANNOTATED	paaH	genes/PSEPK/paaH/paaH-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0006635	fatty acid beta-oxidation	PTN000592971	PTHR48075	3-HYDROXYACYL-COA DEHYDROGENASE FAMILY PROTEIN	PTHR48075:SF5	3-HYDROXYBUTYRYL-COA DEHYDROGENASE	biological_process	1	GRANULARITY	heuristic	family-level propagation stated	TreeGrafter transfers the canonical beta-oxidation role of this enzyme family, whereas PaaH is assigned to phenylacetate catabolism.
MARK_AS_OVER_ANNOTATED	paaJ	genes/PSEPK/paaJ/paaJ-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0006635	fatty acid beta-oxidation	PTN001291485	PTHR43853	3-KETOACYL-COA THIOLASE, PEROXISOMAL	PTHR43853:SF2	3-OXOADIPYL-COA_3-OXO-5,6-DEHYDROSUBERYL-COA THIOLASE	biological_process	1	GRANULARITY	heuristic	family-level propagation stated	TreeGrafter transfers the canonical role of thiolases in fatty-acid beta-oxidation, whereas the exact target is the PaaJ enzyme in the phenylacetate locus.
MARK_AS_OVER_ANNOTATED	pdxB	genes/PSEPK/pdxB/pdxB-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0005829	cytosol	PTN002452155	PTHR42938	FORMATE DEHYDROGENASE 1	PTHR42938:SF9	FORMATE DEHYDROGENASE 1	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	Retaining both terms duplicates the same useful localization statement for this soluble bacterial enzyme.
MARK_AS_OVER_ANNOTATED	pdxJ	genes/PSEPK/pdxJ/pdxJ-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0005829	cytosol	PTN002411800	PTHR30456	PYRIDOXINE 5'-PHOSPHATE SYNTHASE	PTHR30456:SF0	PYRIDOXINE 5'-PHOSPHATE SYNTHASE	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	Retaining both terms adds unsupported precision and duplicate context.
MARK_AS_OVER_ANNOTATED	purM	genes/PSEPK/purM/purM-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0046084	adenine biosynthetic process	PTN002237315	PTHR10520	TRIFUNCTIONAL PURINE BIOSYNTHETIC PROTEIN ADENOSINE-3-RELATED	PTHR10520:SF12	TRIFUNCTIONAL PURINE BIOSYNTHETIC PROTEIN ADENOSINE-3	biological_process	3	GENERIC_CONTEXT	curated	downstream process (adenine) beyond the enzyme's pathway step	PurM acts before IMP, whereas adenine synthesis branches downstream from IMP and is outside the boundary of this de novo IMP module.
MARK_AS_OVER_ANNOTATED	pyrG	genes/PSEPK/pyrG/pyrG-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0019856	pyrimidine nucleobase biosynthetic process	PTN000167579	PTHR11550	CTP SYNTHASE	PTHR11550:SF0	CTP SYNTHASE-RELATED	biological_process	1	GRANULARITY	curated	sibling/broad pyrimidine process over CTP synthesis	PyrG's direct pathway contribution is CTP synthesis, not general pyrimidine nucleobase biosynthesis.
MARK_AS_OVER_ANNOTATED	quiA	genes/PSEPK/quiA/quiA-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0008876	quinoprotein glucose dehydrogenase activity	PTN004940506	PTHR32303	QUINOPROTEIN ALCOHOL DEHYDROGENASE (CYTOCHROME C)	PTHR32303:SF4	QUINOPROTEIN GLUCOSE DEHYDROGENASE	molecular_function	4	MISPLACEMENT	curated	quinate vs glucose dehydrogenase; subfamily itself mis-labelled	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.
MARK_AS_OVER_ANNOTATED	relA	genes/PSEPK/relA/relA-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0005886	plasma membrane	PTN002327464	PTHR21262	GUANOSINE-3',5'-BIS DIPHOSPHATE 3'-PYROPHOSPHOHYDROLASE	PTHR21262:SF31	GTP PYROPHOSPHOKINASE	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	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
MARK_AS_OVER_ANNOTATED	relA	genes/PSEPK/relA/relA-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0008893	guanosine-3',5'-bis(diphosphate) 3'-diphosphatase activity	PTN002327464	PTHR21262	GUANOSINE-3',5'-BIS DIPHOSPHATE 3'-PYROPHOSPHOHYDROLASE	PTHR21262:SF31	GTP PYROPHOSPHOKINASE	molecular_function	1	GRANULARITY	curated	RelA/SpoT node hydrolase term on synthetase-only RelA (degenerate HD motif)	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 
MARK_AS_OVER_ANNOTATED	rfbC	genes/PSEPK/rfbC/rfbC-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0000271	polysaccharide biosynthetic process	PTN004530085	PTHR21047	DTDP-6-DEOXY-D-GLUCOSE-3,5 EPIMERASE	PTHR21047:SF2	THYMIDINE DIPHOSPHO-4-KETO-RHAMNOSE 3,5-EPIMERASE	biological_process	1	GRANULARITY	heuristic	granularity keywords	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.
MARK_AS_OVER_ANNOTATED	rlmE	genes/PSEPK/rlmE/rlmE-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0008173	RNA methyltransferase activity	PTN002249808	PTHR10920	RIBOSOMAL RNA METHYLTRANSFERASE	PTHR10920:SF18	RRNA METHYLTRANSFERASE 2, MITOCHONDRIAL	molecular_function	1	GRANULARITY	curated	broad RNA methyltransferase parent over rRNA Um2552 activity	GO:0008650 captures the exact 23S rRNA uridine 2'-O-ribose methyltransferase activity, including the specific substrate (U2552 in 23S rRNA). Falcon deep research confirms the enzyme installs the universally conserved Um2552 modification in 23S rRNA.
MARK_AS_OVER_ANNOTATED	rmlC	genes/PSEPK/rmlC/rmlC-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0000271	polysaccharide biosynthetic process	PTN004530085	PTHR21047	DTDP-6-DEOXY-D-GLUCOSE-3,5 EPIMERASE	PTHR21047:SF2	THYMIDINE DIPHOSPHO-4-KETO-RHAMNOSE 3,5-EPIMERASE	biological_process	1	GRANULARITY	heuristic	granularity keywords	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.
MARK_AS_OVER_ANNOTATED	sdhA	genes/PSEPK/sdhA/sdhA-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0009061	anaerobic respiration	PTN002267550	PTHR11632	SUCCINATE DEHYDROGENASE 2 FLAVOPROTEIN SUBUNIT	PTHR11632:SF51	SUCCINATE DEHYDROGENASE [UBIQUINONE] FLAVOPROTEIN SUBUNIT, MITOCHONDRIAL	biological_process	1	GRANULARITY	curated	PTHR11632 SDH/FRD heterogeneity: anaerobic-respiration sibling process on aerobic SdhA	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
MARK_AS_OVER_ANNOTATED	secD	genes/PSEPK/secD/secD-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0015031	protein transport	PTN002409401	PTHR30081	PROTEIN-EXPORT MEMBRANE PROTEIN SEC	PTHR30081:SF1	PROTEIN TRANSLOCASE SUBUNIT SECD	biological_process	1	GRANULARITY	heuristic	granularity keywords	The generic process term is redundant with the specific Sec-complex process.
MARK_AS_OVER_ANNOTATED	secF	genes/PSEPK/secF/secF-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0015031	protein transport	PTN002409392	PTHR30081	PROTEIN-EXPORT MEMBRANE PROTEIN SEC	PTHR30081:SF8	PROTEIN TRANSLOCASE SUBUNIT SECF	biological_process	1	GRANULARITY	heuristic	granularity keywords	The generic process term is redundant with the specific Sec-complex process.
MARK_AS_OVER_ANNOTATED	sfgA	genes/EMENI/sfgA/sfgA-ai-review.yaml	Emericella nidulans	GO:0045944	positive regulation of transcription by RNA polymerase II	PTN002288087	PTHR37534	TRANSCRIPTIONAL ACTIVATOR PROTEIN UGA3	PTHR37534:SF41	SFGA	biological_process	1	GRANULARITY	heuristic	granularity keywords	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 
MARK_AS_OVER_ANNOTATED	tatC-I	genes/PSEPK/tatC-I/tatC-I-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0009977	proton motive force dependent protein transmembrane transporter activity	PTN002411347	PTHR30371	SEC-INDEPENDENT PROTEIN TRANSLOCASE PROTEIN TATC	PTHR30371:SF0	SEC-INDEPENDENT PROTEIN TRANSLOCASE PROTEIN TATC, CHLOROPLASTIC-RELATED	molecular_function	3	GENERIC_CONTEXT	curated	whole-complex activity placed on a single subunit	TatC contributes to this whole-complex activity but does not independently enable it.
MARK_AS_OVER_ANNOTATED	tatC-II	genes/PSEPK/tatC-II/tatC-II-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0009977	proton motive force dependent protein transmembrane transporter activity	PTN002411347	PTHR30371	SEC-INDEPENDENT PROTEIN TRANSLOCASE PROTEIN TATC	PTHR30371:SF0	SEC-INDEPENDENT PROTEIN TRANSLOCASE PROTEIN TATC, CHLOROPLASTIC-RELATED	molecular_function	3	GENERIC_CONTEXT	curated	whole-complex activity placed on a single subunit	TatC contributes to this whole-complex activity but does not independently enable it.
MARK_AS_OVER_ANNOTATED	tolC	genes/PSEPK/tolC/tolC-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0015288	porin activity	PTN002011548	PTHR30026	OUTER MEMBRANE PROTEIN TOLC	PTHR30026:SF22	OUTER MEMBRANE EFFLUX PROTEIN	molecular_function	1	GRANULARITY	curated	generic sibling channel term for a secretion-specialised OM protein	The term captures the existence of a channel-like outer membrane conduit, but it is too generic and somewhat misleading for a secretion-specialized TolC/LapE protein whose best-supported role is in adhesin export.
MARK_AS_OVER_ANNOTATED	trmB	genes/PSEPK/trmB/trmB-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0043527	tRNA methyltransferase complex	PTN002361431	PTHR23417	3-DEOXY-D-MANNO-OCTULOSONIC-ACID TRANSFERASE/TRNA GUANINE-N 7 - -METHYLTRANSFERASE	PTHR23417:SF14	PENTACOTRIPEPTIDE-REPEAT REGION OF PRORP DOMAIN-CONTAINING PROTEIN	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	UniProt and GOA support TrmB as a SAM-dependent tRNA methyltransferase enzyme, but the current first-pass evidence does not establish membership in a specific tRNA methyltransferase complex for PSEPK TrmB.
MARK_AS_OVER_ANNOTATED	tsaA	genes/PSEPK/PP_1084/PP_1084-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0033554	cellular response to stress	PTN002242136	PTHR10681	THIOREDOXIN PEROXIDASE	PTHR10681:SF128	THIOREDOXIN-DEPENDENT PEROXIDE REDUCTASE, MITOCHONDRIAL	biological_process	3	GENERIC_CONTEXT	curated	generic stress-response process	Use peroxide detoxification and oxidative-stress annotations rather than this generic stress-response process.
MARK_AS_OVER_ANNOTATED	tyrB	genes/PSEPK/tyrB/tyrB-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0042802	identical protein binding	PTN002275473	PTHR11879	ASPARTATE AMINOTRANSFERASE	PTHR11879:SF37	AROMATIC-AMINO-ACID AMINOTRANSFERASE	molecular_function	3	GENERIC_CONTEXT	heuristic	uninformative binding term	"Homodimerization is a structural property rather than a distinct molecular function; the term adds little and is propagated electronically without direct evidence for this protein. Per curation guidance, generic ""protein binding""-type terms are discouraged."
MARK_AS_OVER_ANNOTATED	tyrS	genes/PSEPK/tyrS/tyrS-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0043039	tRNA aminoacylation	PTN002272564	PTHR11766	TYROSYL-TRNA SYNTHETASE	PTHR11766:SF1	TYROSINE--TRNA LIGASE	biological_process	1	GRANULARITY	curated	broad parent over tyrosyl-tRNA aminoacylation	This valid broad process is less informative than the separately present tyrosyl-tRNA aminoacylation annotation.
MARK_AS_OVER_ANNOTATED	ubiA	genes/PSEPK/ubiA/ubiA-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0016740	transferase activity	PTN004223178	PTHR11048	PRENYLTRANSFERASES	PTHR11048:SF28	4-HYDROXYBENZOATE POLYPRENYLTRANSFERASE, MITOCHONDRIAL	molecular_function	1	GRANULARITY	heuristic	granularity keywords	GO:0008412 captures the exact reaction class.
MARK_AS_OVER_ANNOTATED	ubiC	genes/PSEPK/ubiC/ubiC-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0005829	cytosol	PTN002446048	PTHR38683	CHORISMATE PYRUVATE-LYASE	PTHR38683:SF1	CHORISMATE PYRUVATE-LYASE	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	Retain the supported parent cytoplasm term rather than treating its cytosol child as independently established.
MARK_AS_OVER_ANNOTATED	ubiD	genes/PSEPK/ubiD/ubiD-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0005737	cytoplasm	PTN002409573	PTHR30108	3-OCTAPRENYL-4-HYDROXYBENZOATE CARBOXY-LYASE-RELATED	PTHR30108:SF17	FERULIC ACID DECARBOXYLASE 1	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	The record also carries cytosol and plasma-membrane annotations; the broad cytoplasm parent adds no useful localization information.
MARK_AS_OVER_ANNOTATED	ubiG	genes/PSEPK/ubiG/ubiG-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0008168	methyltransferase activity	PTN002460086	PTHR43464	METHYLTRANSFERASE	PTHR43464:SF19	UBIQUINONE BIOSYNTHESIS O-METHYLTRANSFERASE, MITOCHONDRIAL	molecular_function	1	GRANULARITY	heuristic	granularity keywords	GO:0061542 and GO:0102208 capture the two evolved UbiG activities.
MARK_AS_OVER_ANNOTATED	ubiK	genes/PSEPK/ubiK/ubiK-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0005829	cytosol	PTN002445503	PTHR38040	UBIQUINONE BIOSYNTHESIS ACCESSORY FACTOR UBIK	PTHR38040:SF1	UBIQUINONE BIOSYNTHESIS ACCESSORY FACTOR UBIK	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	Retaining both near-equivalent locations adds no biological resolution for this bacterial protein; GO:0005737 is directly supported by UniProt.
MARK_AS_OVER_ANNOTATED	zwf	genes/PSEPK/zwf/zwf-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0009051	pentose-phosphate shunt, oxidative branch	PTN002765778	PTHR23429	GLUCOSE-6-PHOSPHATE 1-DEHYDROGENASE G6PD	PTHR23429:SF0	GLUCOSE-6-PHOSPHATE 1-DEHYDROGENASE	biological_process	1	GRANULARITY	heuristic	family-level propagation stated	The annotation likely reflects family-level pathway propagation rather than paralog-specific physiological evidence.
MODIFY	A0A8B6GS20	genes/MYTGA/A0A8B6GS20/A0A8B6GS20-ai-review.yaml	Mytilus galloprovincialis	GO:0046856	phosphatidylinositol dephosphorylation	PTN000086907	PTHR10807	MYOTUBULARIN-RELATED	PTHR10807:SF73	LD06050P	biological_process	2	PSEUDOENZYME	heuristic	pseudo-enzyme keywords	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.
MODIFY	A4F7P6	genes/SACEN/A4F7P6/A4F7P6-ai-review.yaml	Saccharopolyspora erythraea (strain ATCC 11635 / DSM 40517 / JCM 4748 / NBRC 13426 / NCIMB 8594 / NRRL 2338)	GO:0008610	lipid biosynthetic process	PTN000160696	PTHR11487	THIOESTERASE	PTHR11487:SF0	S-ACYL FATTY ACID SYNTHASE THIOESTERASE, MEDIUM CHAIN	biological_process	1	GRANULARITY	curated	FAS-family process term on a PKS thioesterase (erythromycin)	Wrong process. Replace with GO:1901115 (erythromycin biosynthetic process).
MODIFY	AP180	genes/DORPE/AP180/AP180-ai-review.yaml	Doryteuthis pealeii	GO:0008021	synaptic vesicle	PTN000536703	PTHR22951	CLATHRIN ASSEMBLY PROTEIN	PTHR22951:SF5	PHOSPHATIDYLINOSITOL-BINDING CLATHRIN ASSEMBLY PROTEIN LAP	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	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.
MODIFY	AmiC1	genes/NOSS1/AmiC1/AmiC1-ai-review.yaml	Nostoc sp. (strain PCC 7120 / SAG 25.82 / UTEX 2576)	GO:0030288	outer membrane-bounded periplasmic space	PTN002018865					cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	Modify. Anabaena is Gram-negative and the mature amidase acts in the periplasmic/ cell-wall compartment, so a periplasmic call is not wrong. However, the experimentally documented and functionally relevant location is the division septum and the polar neck of differentiating heterocysts (GFP fusions
MODIFY	CTR1	genes/OCTVU/CTR1/CTR1-ai-review.yaml	Octopus vulgaris	GO:0042277	peptide binding	PTN001202415	PTHR24241	NEUROPEPTIDE RECEPTOR-RELATED G-PROTEIN COUPLED RECEPTOR	PTHR24241:SF161	G-PROTEIN COUPLED RECEPTORS FAMILY 1 PROFILE DOMAIN-CONTAINING PROTEIN	molecular_function	1	GRANULARITY	heuristic	granularity keywords	"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"
MODIFY	CTR2	genes/OCTVU/CTR2/CTR2-ai-review.yaml	Octopus vulgaris	GO:0042277	peptide binding	PTN001202415	PTHR24241	NEUROPEPTIDE RECEPTOR-RELATED G-PROTEIN COUPLED RECEPTOR	PTHR24241:SF161	G-PROTEIN COUPLED RECEPTORS FAMILY 1 PROFILE DOMAIN-CONTAINING PROTEIN	molecular_function	1	GRANULARITY	heuristic	granularity keywords	"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"
MODIFY	K9IFT7	genes/DESRO/K9IFT7/K9IFT7-ai-review.yaml	Desmodus rotundus	GO:0002227	innate immune response in mucosa	PTN000483423	PTHR21388	BETA-DEFENSIN-RELATED	PTHR21388:SF9	BETA-DEFENSIN 1	biological_process	3	GENERIC_CONTEXT	curated	over-specific mammalian-context immune process on a bat defensin	Use the more general defense response to bacterium term supported by bactericidal activity.
MODIFY	K9IFT7	genes/DESRO/K9IFT7/K9IFT7-ai-review.yaml	Desmodus rotundus	GO:0050829	defense response to Gram-negative bacterium	PTN000483423	PTHR21388	BETA-DEFENSIN-RELATED	PTHR21388:SF9	BETA-DEFENSIN 1	biological_process	3	GENERIC_CONTEXT	curated	over-specific mammalian-context immune process on a bat defensin	Use a broader defense response to bacterium term.
MODIFY	K9IFT7	genes/DESRO/K9IFT7/K9IFT7-ai-review.yaml	Desmodus rotundus	GO:0050830	defense response to Gram-positive bacterium	PTN000483423	PTHR21388	BETA-DEFENSIN-RELATED	PTHR21388:SF9	BETA-DEFENSIN 1	biological_process	3	GENERIC_CONTEXT	curated	over-specific mammalian-context immune process on a bat defensin	Use a broader defense response to bacterium term.
MODIFY	OPR	genes/OCTVU/OPR/OPR-ai-review.yaml	Octopus vulgaris	GO:0032870	cellular response to hormone stimulus	PTN001202415	PTHR24241	NEUROPEPTIDE RECEPTOR-RELATED G-PROTEIN COUPLED RECEPTOR	PTHR24241:SF161	G-PROTEIN COUPLED RECEPTORS FAMILY 1 PROFILE DOMAIN-CONTAINING PROTEIN	biological_process	1	GRANULARITY	heuristic	granularity keywords	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
MODIFY	OPR	genes/OCTVU/OPR/OPR-ai-review.yaml	Octopus vulgaris	GO:0042277	peptide binding	PTN001202415	PTHR24241	NEUROPEPTIDE RECEPTOR-RELATED G-PROTEIN COUPLED RECEPTOR	PTHR24241:SF161	G-PROTEIN COUPLED RECEPTORS FAMILY 1 PROFILE DOMAIN-CONTAINING PROTEIN	molecular_function	1	GRANULARITY	heuristic	granularity keywords	"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 "
MODIFY	PP_2213	genes/PSEPK/PP_2213/PP_2213-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0004321	fatty-acyl-CoA synthase activity	PTN000644270	PTHR43605	ACYL-COENZYME A SYNTHETASE	PTHR43605:SF10	ACYL-COA SYNTHETASE MEDIUM CHAIN FAMILY MEMBER 3	molecular_function	1	GRANULARITY	curated	broad acyl-CoA synthetase family term	Replace or supplement this broad term with GO:0015645 (fatty acid ligase activity) based on the UniProt family and reaction evidence.
MODIFY	PP_3117	genes/PSEPK/PP_3117/PP_3117-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0006281	DNA repair	PTN009155960	PTHR35369	BLR3025 PROTEIN-RELATED	PTHR35369:SF3	TRANSLESION DNA SYNTHESIS-ASSOCIATED PROTEIN IMUA	biological_process	3	GENERIC_CONTEXT	curated	generic DNA-repair process on a damage-tolerance accessory protein	ImuA is an accessory component of the mutagenic DnaE2 damage-tolerance pathway rather than a canonical repair enzyme.
MODIFY	PP_5298	genes/PSEPK/PP_5298/PP_5298-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0006598	polyamine catabolic process	PTN000938594	PTHR43235	GLUTAMINE AMIDOTRANSFERASE PB2B2.05-RELATED	PTHR43235:SF1	GLUTAMINE AMIDOTRANSFERASE PB2B2.05-RELATED	biological_process	1	GRANULARITY	heuristic	granularity keywords	The substrate is specifically a putrescine-derived intermediate, so replace this generic polyamine parent with GO:0009447.
MODIFY	Saro_0802	genes/NOVAD/Saro_0802/Saro_0802-ai-review.yaml	Novosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CCUG 56034 / CIP 105152 / NBRC 16084 / F199)	GO:0016121	carotene catabolic process	PTN000830280	PTHR10543	BETA-CAROTENE DIOXYGENASE	PTHR10543:SF89	CAROTENOID 9,10(9',10')-CLEAVAGE DIOXYGENASE 1	biological_process	4	MISPLACEMENT	curated	stilbene vs carotenoid cleavage; subfamily itself mis-labelled	Replace with GO:0046272 (stilbene catabolic process), matching the demonstrated stilbene-cleavage activity. Same TreeGrafter over-propagation as the carotenoid MF term.
MODIFY	Saro_2809	genes/NOVAD/Saro_2809/Saro_2809-ai-review.yaml	Novosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CCUG 56034 / CIP 105152 / NBRC 16084 / F199)	GO:0016121	carotene catabolic process	PTN000830280	PTHR10543	BETA-CAROTENE DIOXYGENASE	PTHR10543:SF89	CAROTENOID 9,10(9',10')-CLEAVAGE DIOXYGENASE 1	biological_process	4	MISPLACEMENT	curated	stilbene vs carotenoid cleavage; subfamily itself mis-labelled	Replace with GO:0046272 (stilbene catabolic process). Same TreeGrafter over-propagation as the carotenoid MF term.
MODIFY	TFP	genes/THLAR/TFP/TFP-ai-review.yaml	Thlaspi arvense	GO:0030234	enzyme regulator activity	PTN008234626	PTHR47435	KELCH REPEAT PROTEIN (AFU_ORTHOLOGUE AFUA_5G12780)	PTHR47435:SF7	EPITHIOSPECIFIER PROTEIN	molecular_function	1	GRANULARITY	curated	outdated node term (regulator) for a specifier protein now known as a C-S lyase	"Outdated molecular-function framing. Specifier proteins were historically viewed as accessory factors that ""regulate"" myrosinase product outcome, but TaTFP is now established as a catalyst in its own right - an Fe(2+)-dependent carbon-sulfur lyase (sulfolyase, EC 4.8.1.8) that eliminates sulfate fro"
MODIFY	aceK	genes/PSEPK/aceK/aceK-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0004721	phosphoprotein phosphatase activity	PTN002446796	PTHR39559	-	PTHR39559:SF1	ISOCITRATE DEHYDROGENASE KINASE_PHOSPHATASE	molecular_function	1	GRANULARITY	heuristic	granularity keywords	The phosphatase activity is real and ATP-dependent, but the substrate is specifically phospho-isocitrate dehydrogenase, so the precise IDH phosphatase term better represents the function than a generic phosphoprotein phosphatase term.
MODIFY	ahpC	genes/PSEPK/ahpC/ahpC-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0005829	cytosol	PTN000074135	PTHR10681	THIOREDOXIN PEROXIDASE	PTHR10681:SF121	ALKYL HYDROPEROXIDE REDUCTASE C	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	Cytoplasm is the clearer and less redundant cellular component term for this bacterial enzyme.
MODIFY	ahpC	genes/PSEPK/ahpC/ahpC-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0008379	thioredoxin peroxidase activity	PTN000074135	PTHR10681	THIOREDOXIN PEROXIDASE	PTHR10681:SF121	ALKYL HYDROPEROXIDE REDUCTASE C	molecular_function	1	GRANULARITY	heuristic	granularity keywords	A donor-independent peroxiredoxin term is safer for the AhpC subunit itself than a thioredoxin-specific term.
MODIFY	ahpC	genes/PSEPK/ahpC/ahpC-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0042744	hydrogen peroxide catabolic process	PTN000074135	PTHR10681	THIOREDOXIN PEROXIDASE	PTHR10681:SF121	ALKYL HYDROPEROXIDE REDUCTASE C	biological_process	1	GRANULARITY	curated	sibling/too-narrow process; broader oxidant detoxification fits AhpC	A broader oxidant-detoxification term better reflects the known chemistry of AhpC.
MODIFY	aprA	genes/DESVH/Q72DT2/Q72DT2-ai-review.yaml	Nitratidesulfovibrio vulgaris (Desulfovibrio vulgaris) Hildenborough	GO:0005886	plasma membrane	PTN000908678	PTHR11632	SUCCINATE DEHYDROGENASE 2 FLAVOPROTEIN SUBUNIT	PTHR11632:SF51	SUCCINATE DEHYDROGENASE [UBIQUINONE] FLAVOPROTEIN SUBUNIT, MITOCHONDRIAL	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	AprA is a soluble cytoplasmic protein, not a plasma membrane protein. The TreeGrafter annotation likely propagated from succinate dehydrogenase family members which are membrane-associated. AprA functions in the cytoplasm where it receives electrons from the membrane-associated Qmo complex.
MODIFY	aprA	genes/DESVH/Q72DT2/Q72DT2-ai-review.yaml	Nitratidesulfovibrio vulgaris (Desulfovibrio vulgaris) Hildenborough	GO:0009061	anaerobic respiration	PTN000908678	PTHR11632	SUCCINATE DEHYDROGENASE 2 FLAVOPROTEIN SUBUNIT	PTHR11632:SF51	SUCCINATE DEHYDROGENASE [UBIQUINONE] FLAVOPROTEIN SUBUNIT, MITOCHONDRIAL	biological_process	1	GRANULARITY	heuristic	granularity keywords	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.
MODIFY	bcsA	genes/PSEPK/bcsA/bcsA-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0016758	hexosyltransferase activity	PTN001634554	PTHR43867	CELLULOSE SYNTHASE CATALYTIC SUBUNIT A [UDP-FORMING]	PTHR43867:SF2	CELLULOSE SYNTHASE CATALYTIC SUBUNIT A [UDP-FORMING]	molecular_function	1	GRANULARITY	heuristic	granularity keywords	UniProt and GOA assign the specific UDP-forming cellulose synthase activity, which is more informative than the generic hexosyltransferase parent.
MODIFY	benD	genes/PSEPK/benD/benD-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0016616	oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor	PTN002460465	PTHR42760	SHORT-CHAIN DEHYDROGENASES/REDUCTASES FAMILY MEMBER	PTHR42760:SF123	OXIDOREDUCTASE	molecular_function	1	GRANULARITY	heuristic	granularity keywords	BenD is not merely a generic CH-OH oxidoreductase. Its substrate and reaction are specifically the benzoate cis-diol to catechol conversion step.
MODIFY	celX	genes/ACET2/P15329/P15329-ai-review.yaml	Acetivibrio thermocellus	GO:0004622	phosphatidylcholine lysophospholipase A1 activity	PTN002411393	PTHR30383	THIOESTERASE 1/PROTEASE 1/LYSOPHOSPHOLIPASE L1	PTHR30383:SF5	SGNH HYDROLASE-TYPE ESTERASE DOMAIN-CONTAINING PROTEIN	molecular_function	1	GRANULARITY	curated	sibling esterase substrate term from the SGNH node; family correct	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
MODIFY	clpX	genes/PSEPK/clpX/clpX-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0009376	HslUV protease complex	PTN002258935	PTHR48102	ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPX-LIKE, MITOCHONDRIAL-RELATED	PTHR48102:SF7	ATP-DEPENDENT CLP PROTEASE ATP-BINDING SUBUNIT CLPX-LIKE, MITOCHONDRIAL	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	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.
MODIFY	cpx	genes/DORPE/cpx/cpx-ai-review.yaml	Doryteuthis pealeii	GO:0016079	synaptic vesicle exocytosis	PTN002703616	PTHR16705	COMPLEXIN	PTHR16705:SF4	COMPLEXIN	biological_process	1	GRANULARITY	curated	core-component process where a regulation term fits; sibling relation	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
MODIFY	ech	genes/PSEPK/ech/ech-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0008300	isoprenoid catabolic process	PTN002873559	PTHR42964	ENOYL-COA HYDRATASE	PTHR42964:SF1	POLYKETIDE BIOSYNTHESIS ENOYL-COA HYDRATASE PKSH-RELATED	biological_process	4	MISPLACEMENT	heuristic	mis-placement keywords	Ech acts on aromatic hydroxycinnamoyl-CoA thioesters in ferulate catabolism, not on isoprenoids.
MODIFY	eryAI	genes/SACEN/eryAI/eryAI-ai-review.yaml	Saccharopolyspora erythraea (strain ATCC 11635 / DSM 40517 / JCM 4748 / NBRC 13426 / NCIMB 8594 / NRRL 2338)	GO:0004312	fatty acid synthase activity	PTN000918870	PTHR43775	FATTY ACID SYNTHASE	PTHR43775:SF51	INACTIVE PHENOLPHTHIOCEROL SYNTHESIS POLYKETIDE SYNTHASE TYPE I PKS1-RELATED	molecular_function	1	GRANULARITY	curated	PTHR43775 family-level FAS term on a PKS subfamily	Wrong product class. Replace with GO:0016218 (polyketide synthase activity).
MODIFY	eryAII	genes/SACEN/eryAII/eryAII-ai-review.yaml	Saccharopolyspora erythraea (strain ATCC 11635 / DSM 40517 / JCM 4748 / NBRC 13426 / NCIMB 8594 / NRRL 2338)	GO:0004312	fatty acid synthase activity	PTN000918870	PTHR43775	FATTY ACID SYNTHASE	PTHR43775:SF51	INACTIVE PHENOLPHTHIOCEROL SYNTHESIS POLYKETIDE SYNTHASE TYPE I PKS1-RELATED	molecular_function	1	GRANULARITY	curated	PTHR43775 family-level FAS term on a PKS subfamily	Wrong product class. Replace with GO:0016218 (polyketide synthase activity).
MODIFY	eryAIII	genes/SACEN/eryAIII/eryAIII-ai-review.yaml	Saccharopolyspora erythraea (strain ATCC 11635 / DSM 40517 / JCM 4748 / NBRC 13426 / NCIMB 8594 / NRRL 2338)	GO:0004312	fatty acid synthase activity	PTN000918870	PTHR43775	FATTY ACID SYNTHASE	PTHR43775:SF51	INACTIVE PHENOLPHTHIOCEROL SYNTHESIS POLYKETIDE SYNTHASE TYPE I PKS1-RELATED	molecular_function	1	GRANULARITY	curated	PTHR43775 family-level FAS term on a PKS subfamily	Wrong product class. Replace with GO:0016218 (polyketide synthase activity).
MODIFY	eryBVII	genes/SACEN/eryBVII/eryBVII-ai-review.yaml	Saccharopolyspora erythraea (strain ATCC 11635 / DSM 40517 / JCM 4748 / NBRC 13426 / NCIMB 8594 / NRRL 2338)	GO:0000271	polysaccharide biosynthetic process	PTN002325964	PTHR21047	DTDP-6-DEOXY-D-GLUCOSE-3,5 EPIMERASE	PTHR21047:SF2	THYMIDINE DIPHOSPHO-4-KETO-RHAMNOSE 3,5-EPIMERASE	biological_process	1	GRANULARITY	curated	sugar-nucleotide family process over erythromycin deoxysugar biosynthesis	Wrong process class; replace with GO:1901115 (erythromycin biosynthetic process).
MODIFY	eryBVII	genes/SACEN/eryBVII/eryBVII-ai-review.yaml	Saccharopolyspora erythraea (strain ATCC 11635 / DSM 40517 / JCM 4748 / NBRC 13426 / NCIMB 8594 / NRRL 2338)	GO:0019305	dTDP-rhamnose biosynthetic process	PTN002325964	PTHR21047	DTDP-6-DEOXY-D-GLUCOSE-3,5 EPIMERASE	PTHR21047:SF2	THYMIDINE DIPHOSPHO-4-KETO-RHAMNOSE 3,5-EPIMERASE	biological_process	1	GRANULARITY	curated	sibling deoxysugar pathway (rhamnose) over erythromycin deoxysugar	Wrong product/pathway (rhamnose vs the erythromycin deoxysugars). Replace with GO:1901115 (erythromycin biosynthetic process).
MODIFY	eryCI	genes/SACEN/eryCI/eryCI-ai-review.yaml	Saccharopolyspora erythraea (strain ATCC 11635 / DSM 40517 / JCM 4748 / NBRC 13426 / NCIMB 8594 / NRRL 2338)	GO:0000271	polysaccharide biosynthetic process	PTN002015832	PTHR30244	TRANSAMINASE	PTHR30244:SF36	3-OXO-GLUCOSE-6-PHOSPHATE:GLUTAMATE AMINOTRANSFERASE	biological_process	1	GRANULARITY	curated	sugar-nucleotide family process over erythromycin deoxysugar biosynthesis	Wrong process class. Replace with GO:1901115 (erythromycin biosynthetic process), the cluster-level process to which desosamine biosynthesis contributes.
MODIFY	eryCIV	genes/SACEN/eryCIV/eryCIV-ai-review.yaml	Saccharopolyspora erythraea (strain ATCC 11635 / DSM 40517 / JCM 4748 / NBRC 13426 / NCIMB 8594 / NRRL 2338)	GO:0000271	polysaccharide biosynthetic process	PTN000767067	PTHR30244	TRANSAMINASE	PTHR30244:SF9	PROTEIN RV3402C	biological_process	1	GRANULARITY	curated	sugar-nucleotide family process over erythromycin deoxysugar biosynthesis	Wrong process class; replace with GO:1901115 (erythromycin biosynthetic process), to which desosamine biosynthesis contributes.
MODIFY	fcs	genes/PSEPK/fcs/fcs-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0006631	fatty acid metabolic process	PTN008449823	PTHR43201	ACYL-COA SYNTHETASE	PTHR43201:SF32	2-SUCCINYLBENZOATE--COA LIGASE, CHLOROPLASTIC_PEROXISOMAL	biological_process	4	MISPLACEMENT	heuristic	mis-placement keywords	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
MODIFY	fcs	genes/PSEPK/fcs/fcs-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0031956	medium-chain fatty acid-CoA ligase activity	PTN008449823	PTHR43201	ACYL-COA SYNTHETASE	PTHR43201:SF32	2-SUCCINYLBENZOATE--COA LIGASE, CHLOROPLASTIC_PEROXISOMAL	molecular_function	4	MISPLACEMENT	curated	feruloyl-CoA synthetase grafted onto a different ANL-superfamily subfamily	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
MODIFY	ftsY	genes/PSEPK/ftsY/ftsY-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0006605	protein targeting	PTN002455079	PTHR43134	SIGNAL RECOGNITION PARTICLE RECEPTOR SUBUNIT ALPHA	PTHR43134:SF1	SIGNAL RECOGNITION PARTICLE RECEPTOR SUBUNIT ALPHA	biological_process	1	GRANULARITY	heuristic	granularity keywords	This parent term is correct but too broad. Replace it with GO:0006614, which captures the SRP-dependent cotranslational mechanism documented for FtsY.
MODIFY	fur	genes/PSEPK/fur/fur-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0008270	zinc ion binding	PTN002431809	PTHR33202	ZINC UPTAKE REGULATION PROTEIN	PTHR33202:SF2	FERRIC UPTAKE REGULATION PROTEIN	molecular_function	1	GRANULARITY	curated	sibling metal-cofactor term (Zn vs Fe) from the node	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
MODIFY	hemBB	genes/PSEPK/hemBB/hemBB-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0008270	zinc ion binding	PTN000894573	PTHR11458	DELTA-AMINOLEVULINIC ACID DEHYDRATASE	PTHR11458:SF0	DELTA-AMINOLEVULINIC ACID DEHYDRATASE	molecular_function	1	GRANULARITY	curated	sibling metal-cofactor term (Zn vs Mg) from the node	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.
MODIFY	mcr-1	genes/ECOLX/mcr-1/mcr-1-ai-review.yaml	Escherichia coli	GO:0016776	phosphotransferase activity, phosphate group as acceptor	PTN002019544	PTHR30443	INNER MEMBRANE PROTEIN	PTHR30443:SF0	PHOSPHOETHANOLAMINE TRANSFERASE EPTA	molecular_function	1	GRANULARITY	curated	EptA node carries a sibling phosphotransferase term instead of pEtN transferase	Replace the over-general parent with the specific characterised activity (GO:0043838).
MODIFY	mcr-3	genes/AERME/mcr-3/mcr-3-ai-review.yaml	Aeromonas media	GO:0016776	phosphotransferase activity, phosphate group as acceptor	PTN002019542	PTHR30443	INNER MEMBRANE PROTEIN	PTHR30443:SF0	PHOSPHOETHANOLAMINE TRANSFERASE EPTA	molecular_function	1	GRANULARITY	curated	EptA node carries a sibling phosphotransferase term instead of pEtN transferase	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.
MODIFY	mcr-4	genes/SALSP/mcr-4/mcr-4-ai-review.yaml	Salmonella sp	GO:0016776	phosphotransferase activity, phosphate group as acceptor	PTN002019543	PTHR30443	INNER MEMBRANE PROTEIN	PTHR30443:SF0	PHOSPHOETHANOLAMINE TRANSFERASE EPTA	molecular_function	1	GRANULARITY	curated	EptA node carries a sibling phosphotransferase term instead of pEtN transferase	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.
MODIFY	mcr2	genes/ECOLX/mcr2/mcr2-ai-review.yaml	Escherichia coli	GO:0016776	phosphotransferase activity, phosphate group as acceptor	PTN002019544	PTHR30443	INNER MEMBRANE PROTEIN	PTHR30443:SF0	PHOSPHOETHANOLAMINE TRANSFERASE EPTA	molecular_function	1	GRANULARITY	curated	EptA node carries a sibling phosphotransferase term instead of pEtN transferase	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.
MODIFY	mdr	genes/STABO/mdr/mdr-ai-review.yaml	Starmerella bombicola	GO:0015421	ABC-type oligopeptide transporter activity	PTN008681462	PTHR43394	ATP-DEPENDENT PERMEASE MDL1, MITOCHONDRIAL	PTHR43394:SF11	ATP-BINDING CASSETTE TRANSPORTER	molecular_function	4	MISPLACEMENT	curated	ABC transporter substrate class wrong (sophorolipid vs oligopeptide)	The transporter is described as an ABC MDR-family protein linked to sophorolipid export, not oligopeptide transport. [PMID:34998388, PMID:23964782]
MODIFY	metB	genes/PSEPK/metB/metB-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0016846	carbon-sulfur lyase activity	PTN008330292	PTHR11808	TRANS-SULFURATION ENZYME FAMILY MEMBER	PTHR11808:SF80	CYSTATHIONINE GAMMA-LYASE	molecular_function	1	GRANULARITY	curated	broad C-S lyase parent over cystathionine gamma-synthase	MetB-family cystathionine gamma-synthase is the specific trans-sulfuration first-step activity represented in the module.
MODIFY	metH	genes/PSEPK/metH/metH-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0050667	homocysteine metabolic process	PTN002326308	PTHR45833	METHIONINE SYNTHASE	PTHR45833:SF1	METHIONINE SYNTHASE	biological_process	1	GRANULARITY	heuristic	granularity keywords	MetH consumes homocysteine to make methionine in the de novo methionine biosynthesis pathway; L-methionine biosynthetic process is the better process term.
MODIFY	mluA	genes/METEA/mluA/mluA-ai-review.yaml	Methylorubrum extorquens AM1	GO:0015344	siderophore uptake transmembrane transporter activity	PTN004950207	PTHR32552	FERRICHROME IRON RECEPTOR-RELATED	PTHR32552:SF82	FCUA PROTEIN	molecular_function	1	GRANULARITY	curated	over-specific substrate (siderophore) from the node on a TonB-dependent receptor	Wrong specificity but correct general activity. The TreeGrafter-propagated iron-siderophore uptake term over-specifies the substrate. The protein performs TonB-energized active uptake transport, but of a lanthanide-metallophore rather than an iron-siderophore; generalize to transmembrane transporter
MODIFY	moeB	genes/PSEPK/moeB/moeB-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0016779	nucleotidyltransferase activity	PTN002250299	PTHR10953	UBIQUITIN-ACTIVATING ENZYME E1	PTHR10953:SF194	MOLYBDOPTERIN-SYNTHASE ADENYLYLTRANSFERASE	molecular_function	1	GRANULARITY	heuristic	granularity keywords	The Rhea reaction specifies ATP-dependent adenylylation of the MoaD C terminus.
MODIFY	opgG	genes/PSEPK/opgG/opgG-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0051274	beta-glucan biosynthetic process	PTN002412129	PTHR30504	GLUCANS BIOSYNTHESIS PROTEIN	PTHR30504:SF4	GLUCANS BIOSYNTHESIS PROTEIN G	biological_process	1	GRANULARITY	curated	broad beta-glucan parent over OPG biosynthesis	OpgG is assigned to osmoregulated periplasmic glucan biosynthesis; GO:1900727 captures that pathway more specifically than beta-glucan biosynthetic process.
MODIFY	pcaK	genes/PSEPK/pcaK/pcaK-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0046942	carboxylic acid transport	PTN002781836	PTHR23508	CARBOXYLIC ACID TRANSPORTER PROTEIN HOMOLOG	PTHR23508:SF10	CARBOXYLIC ACID TRANSPORTER PROTEIN HOMOLOG	biological_process	1	GRANULARITY	curated	broad carboxylic acid transport parent	GO:0015718 monocarboxylic acid transport is a better process-level match to the demonstrated substrate class than GO:0046942. This keeps the process annotation aligned with the narrower molecular function replacement GO:0008028.
MODIFY	pcaK	genes/PSEPK/pcaK/pcaK-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0046943	carboxylic acid transmembrane transporter activity	PTN002781836	PTHR23508	CARBOXYLIC ACID TRANSPORTER PROTEIN HOMOLOG	PTHR23508:SF10	CARBOXYLIC ACID TRANSPORTER PROTEIN HOMOLOG	molecular_function	1	GRANULARITY	curated	broad carboxylic acid transporter parent	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.
MODIFY	phaZ	genes/PSEPK/phaZ/phaZ-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0004806	triacylglycerol lipase activity	PTN002251178	PTHR43433	HYDROLASE, ALPHA/BETA FOLD FAMILY PROTEIN	PTHR43433:SF5	AB HYDROLASE-1 DOMAIN-CONTAINING PROTEIN	molecular_function	1	GRANULARITY	heuristic	granularity keywords	Replace the triacylglycerol-specific activity term with the dedicated PHA depolymerase term. PhaZ mobilizes intracellular mcl-PHA granules, not glycerolipids.
MODIFY	phaZ	genes/PSEPK/phaZ/phaZ-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0046503	glycerolipid catabolic process	PTN002251178	PTHR43433	HYDROLASE, ALPHA/BETA FOLD FAMILY PROTEIN	PTHR43433:SF5	AB HYDROLASE-1 DOMAIN-CONTAINING PROTEIN	biological_process	1	GRANULARITY	curated	AB-hydrolase family lipid process on a PHA depolymerase; subfamily generic	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.
MODIFY	ptsN	genes/PSEPK/ptsN/ptsN-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0030295	protein kinase activator activity	PTN002412134	PTHR47738	PTS SYSTEM FRUCTOSE-LIKE EIIA COMPONENT-RELATED	PTHR47738:SF1	NITROGEN REGULATORY PROTEIN	molecular_function	1	GRANULARITY	curated	sibling regulator term (activator vs regulator)	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.
MODIFY	ptxS	genes/PSEPK/ptxS/ptxS-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0003700	DNA-binding transcription factor activity	PTN002409864	PTHR30146	LACI-RELATED TRANSCRIPTIONAL REPRESSOR	PTHR30146:SF145	RIBOSE OPERON REPRESSOR	molecular_function	1	GRANULARITY	curated	broad transcription factor parent over repressor child	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.
MODIFY	purM	genes/PSEPK/purM/purM-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0006164	purine nucleotide biosynthetic process	PTN002237315	PTHR10520	TRIFUNCTIONAL PURINE BIOSYNTHETIC PROTEIN ADENOSINE-3-RELATED	PTHR10520:SF12	TRIFUNCTIONAL PURINE BIOSYNTHETIC PROTEIN ADENOSINE-3	biological_process	1	GRANULARITY	curated	broad purine-nucleotide parent over de novo IMP biosynthesis	Replace the broad purine-nucleotide process with de novo IMP biosynthesis.
MODIFY	putP	genes/PSEPK/putP/putP-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0015193	L-proline transmembrane transporter activity	PTN005155986	PTHR48086	SODIUM/PROLINE SYMPORTER-RELATED	PTHR48086:SF3	SODIUM_PROLINE SYMPORTER	molecular_function	1	GRANULARITY	curated	broad transporter term over Na+:proline symporter	The exact record establishes the transported substrate and sodium coupling, captured together by GO:0005298.
MODIFY	puuA-I	genes/PSEPK/puuA-I/puuA-I-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0006598	polyamine catabolic process	PTN000465124	PTHR43785	GAMMA-GLUTAMYLPUTRESCINE SYNTHETASE	PTHR43785:SF12	TYPE-1 GLUTAMINE SYNTHETASE 2	biological_process	1	GRANULARITY	heuristic	granularity keywords	The substrate is specifically putrescine, so replace this generic polyamine parent with GO:0009447.
MODIFY	pvdA	genes/PSEPK/pvdA/pvdA-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0006879	intracellular iron ion homeostasis	PTN002346172	PTHR42802	MONOOXYGENASE	PTHR42802:SF1	L-ORNITHINE N(5)-MONOOXYGENASE	biological_process	1	GRANULARITY	heuristic	granularity keywords	GO:0006879 is too broad and indirect for a pathway enzyme. The more precise direct process term is GO:0002049 pyoverdine biosynthetic process.
MODIFY	pvdD	genes/PSEPK/pvdD/pvdD-ai-review.yaml	Pseudomonas putida KT2440	GO:0005737	cytoplasm	PTN005148629	PTHR45527	NONRIBOSOMAL PEPTIDE SYNTHETASE	PTHR45527:SF1	FATTY ACID SYNTHASE	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	Cytoplasm is correct but under-specific. Falcon deep research confirms pyoverdine peptide assembly begins in the cytoplasm and that the PvdD-class NRPSs explore the cytoplasm, supporting the more specific cytosol localization term.
MODIFY	pvdD	genes/PSEPK/pvdD/pvdD-ai-review.yaml	Pseudomonas putida KT2440	GO:0009239	enterobactin biosynthetic process	PTN005148629	PTHR45527	NONRIBOSOMAL PEPTIDE SYNTHETASE	PTHR45527:SF1	FATTY ACID SYNTHASE	biological_process	4	MISPLACEMENT	curated	EntF-specific enterobactin process on a pyoverdine NRPS module	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.
MODIFY	pvdD	genes/PSEPK/pvdD/pvdD-ai-review.yaml	Pseudomonas putida KT2440	GO:0047527	2,3-dihydroxybenzoate-serine ligase activity	PTN005148629	PTHR45527	NONRIBOSOMAL PEPTIDE SYNTHETASE	PTHR45527:SF1	FATTY ACID SYNTHASE	molecular_function	4	MISPLACEMENT	curated	EntF-specific DHB-serine ligase term on a pyoverdine NRPS module	The DHB-serine ligase activity is an enterobactin (EntF) over-transfer error. Falcon deep research indicates PvdD catalyzes addition of amino-acid residues (e.g. L-Lys, L-hfOrn, and L-Thr) as a pyoverdine NRPS, so the correct molecular function is amino acid ligation activity by a nonribosomal pepti
MODIFY	rfbC	genes/PSEPK/rfbC/rfbC-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0016854	racemase and epimerase activity	PTN004530085	PTHR21047	DTDP-6-DEOXY-D-GLUCOSE-3,5 EPIMERASE	PTHR21047:SF2	THYMIDINE DIPHOSPHO-4-KETO-RHAMNOSE 3,5-EPIMERASE	molecular_function	1	GRANULARITY	heuristic	granularity keywords	Replace with the substrate-specific dTDP-rhamnose epimerase term.
MODIFY	rmlC	genes/PSEPK/rmlC/rmlC-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0016854	racemase and epimerase activity	PTN004530085	PTHR21047	DTDP-6-DEOXY-D-GLUCOSE-3,5 EPIMERASE	PTHR21047:SF2	THYMIDINE DIPHOSPHO-4-KETO-RHAMNOSE 3,5-EPIMERASE	molecular_function	1	GRANULARITY	heuristic	granularity keywords	Replace with the substrate-specific RmlC activity.
MODIFY	selB	genes/PSEPK/selB/selB-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0006414	translational elongation	PTN000562234	PTHR43721	ELONGATION FACTOR TU-RELATED	PTHR43721:SF9	GTP-BINDING PROTEIN 1	biological_process	1	GRANULARITY	heuristic	granularity keywords	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.
MODIFY	tauA	genes/PSEPK/tauA/tauA-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0042918	alkanesulfonate transmembrane transport	PTN001246836	PTHR30024	ALIPHATIC SULFONATES-BINDING PROTEIN-RELATED	PTHR30024:SF47	TAURINE-BINDING PERIPLASMIC PROTEIN	biological_process	1	GRANULARITY	curated	broad alkanesulfonate transport over taurine transport	TauA is specifically assigned to the taurine importer, so taurine transmembrane transport is the more informative process.
MODIFY	tauD	genes/PSEPK/tauD/tauD-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0006790	sulfur compound metabolic process	PTN002411909	PTHR30468	ALPHA-KETOGLUTARATE-DEPENDENT SULFONATE DIOXYGENASE	PTHR30468:SF1	ALPHA-KETOGLUTARATE-DEPENDENT SULFONATE DIOXYGENASE	biological_process	1	GRANULARITY	curated	broad sulfur-metabolism parent	Replace the broad sulfur-metabolism term with the substrate-specific catabolic process.
MODIFY	tolC	genes/PSEPK/tolC/tolC-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:1990281	efflux pump complex	PTN002011548	PTHR30026	OUTER MEMBRANE PROTEIN TOLC	PTHR30026:SF22	OUTER MEMBRANE EFFLUX PROTEIN	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	The type I protein secretion system complex term is more precise for LapE and better matches the literature on LapA export.
MODIFY	ydiJ	genes/PSEPK/ydiJ/ydiJ-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0004458	D-lactate dehydrogenase (cytochrome) activity	PTN001714929	PTHR11748	D-LACTATE DEHYDROGENASE	PTHR11748:SF119	D-2-HYDROXYGLUTARATE DEHYDROGENASE	molecular_function	1	GRANULARITY	curated	lactate sibling MF from the node; subfamily (D-2-HG dehydrogenase) is correct	"The protein is a D-2-hydroxyglutarate dehydrogenase (EC 1.1.99.39), not a D-lactate dehydrogenase. The lactate-specific activity is not supported; replace with the specific demonstrated activity. This D-lactate-dehydrogenase transfer derives from the broad PANTHER family-level name (PTHR11748 ""D-LAC"
MODIFY	ydiJ	genes/PSEPK/ydiJ/ydiJ-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0008720	D-lactate dehydrogenase (NAD+) activity	PTN001714929	PTHR11748	D-LACTATE DEHYDROGENASE	PTHR11748:SF119	D-2-HYDROXYGLUTARATE DEHYDROGENASE	molecular_function	1	GRANULARITY	curated	lactate sibling MF from the node; subfamily (D-2-HG dehydrogenase) is correct	"YdiJ is FAD-dependent and oxidizes D-2-hydroxyglutarate with an unspecified acceptor (EC 1.1.99.39), not an NAD+-dependent D-lactate dehydrogenase. Replace with the specific demonstrated activity. This D-lactate-dehydrogenase transfer derives from the broad PANTHER family-level name (PTHR11748 ""D-LA"
MODIFY	ydiJ	genes/PSEPK/ydiJ/ydiJ-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:1903457	lactate catabolic process	PTN001714929	PTHR11748	D-LACTATE DEHYDROGENASE	PTHR11748:SF119	D-2-HYDROXYGLUTARATE DEHYDROGENASE	biological_process	1	GRANULARITY	curated	lactate sibling process from the node; subfamily (D-2-HG dehydrogenase) is correct	Deletion of ydiJ blocks growth on D-lysine and causes D-2-hydroxyglutarate accumulation, placing it in lysine catabolism (and 2-oxoglutarate metabolism via its product), not lactate catabolism.
REMOVE	ADAR2	genes/DOROP/ADAR2/ADAR2-ai-review.yaml	Doryteuthis opalescens	GO:0008251	tRNA-specific adenosine deaminase activity	PTN000098697	PTHR10910	EUKARYOTE SPECIFIC DSRNA BINDING PROTEIN	PTHR10910:SF62	AT07585P-RELATED	molecular_function	4	MISPLACEMENT	curated	ADAR grafted onto tRNA-specific ADAT branch	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 
REMOVE	I7J3R9	genes/9CAUD/g022/g022-ai-review.yaml	Tequatrovirus	GO:0006302	double-strand break repair	PTN000015309	PTHR10133	DNA POLYMERASE I	PTHR10133:SF27	DNA POLYMERASE NU	biological_process	0	UNCLASSIFIED	none		This annotation should be removed rather than marked as over-annotated. There is no evidence that this phage polymerase functions in double-strand break repair. The TreeGrafter prediction appears to be based on superficial homology to bacterial Pol I without considering the specialized viral context
REMOVE	IRE1	genes/HYPJE/IRE1/IRE1-ai-review.yaml	Hypocrea jecorina (strain QM6a)	GO:1990604	IRE1-TRAF2-ASK1 complex	PTN001017826	PTHR13954	IRE1-RELATED	PTHR13954:SF6	NON-SPECIFIC SERINE_THREONINE PROTEIN KINASE	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	The IRE1-TRAF2-ASK1 complex is a metazoan-specific signaling complex. TRAF2 and ASK1 have no orthologs in T. reesei or other filamentous fungi. This TreeGrafter annotation is incorrectly propagated from metazoan orthologs and is biologically impossible in this organism.
REMOVE	K9IJK6	genes/DESRO/K9IJK6/K9IJK6-ai-review.yaml	Desmodus rotundus	GO:0014909	smooth muscle cell migration	PTN000667065	PTHR24264	TRYPSIN-RELATED	PTHR24264:SF42	TISSUE-TYPE PLASMINOGEN ACTIVATOR	biological_process	3	GENERIC_CONTEXT	curated	mammalian-context cell-migration process on a bat salivary plasminogen activator	No experimental support for smooth muscle cell migration; UniProt notes a secreted plasminogen activator with caution about conserved residues.
REMOVE	K9IJK6	genes/DESRO/K9IJK6/K9IJK6-ai-review.yaml	Desmodus rotundus	GO:0048008	platelet-derived growth factor receptor signaling pathway	PTN000667065	PTHR24264	TRYPSIN-RELATED	PTHR24264:SF42	TISSUE-TYPE PLASMINOGEN ACTIVATOR	biological_process	3	GENERIC_CONTEXT	heuristic	host lacks pathway/process	No experimental support or UniProt evidence for PDGF receptor pathway involvement in DESRO K9IJK6.
REMOVE	K9IMD0	genes/DESRO/K9IMD0/K9IMD0-ai-review.yaml	Desmodus rotundus	GO:0005769	early endosome	PTN000159979	PTHR11485	TRANSFERRIN	PTHR11485:SF55	LACTOTRANSFERRIN	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	No experimental evidence for endosomal localization in draculin studies, which describe the protein as a saliva/extracellular anticoagulant [PMID:7740503; PMID:10556567].
REMOVE	K9IMD0	genes/DESRO/K9IMD0/K9IMD0-ai-review.yaml	Desmodus rotundus	GO:0005886	plasma membrane	PTN000159979	PTHR11485	TRANSFERRIN	PTHR11485:SF55	LACTOTRANSFERRIN	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	The literature characterizes draculin as a saliva protein, with no evidence for plasma membrane localization [PMID:7740503; PMID:10556567].
REMOVE	K9IMD0	genes/DESRO/K9IMD0/K9IMD0-ai-review.yaml	Desmodus rotundus	GO:0055037	recycling endosome	PTN000159979	PTHR11485	TRANSFERRIN	PTHR11485:SF55	LACTOTRANSFERRIN	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	No evidence for endosomal recycling localization; saliva secretion supports extracellular localization [PMID:7740503; PMID:10556567].
REMOVE	K9J287	genes/DESRO/K9J287/K9J287-ai-review.yaml	Desmodus rotundus	GO:0005634	nucleus	PTN001684743	PTHR11371	DEOXYRIBONUCLEASE	PTHR11371:SF28	DEOXYRIBONUCLEASE-1-LIKE 1	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	UniProt subcellular location indicates endoplasmic reticulum, not nucleus.
REMOVE	NCGR_LOCUS1270	genes/9POAL/NCGR_LOCUS1270/NCGR_LOCUS1270-ai-review.yaml	Miscanthus lutarioriparius	GO:0005737	cytoplasm	PTN004269459	PTHR11556	FRUCTOSE-1,6-BISPHOSPHATASE-RELATED	PTHR11556:SF1	FRUCTOSE-BISPHOSPHATASE	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	"Incorrect localization. This protein has a chloroplast transit peptide and is classified as chloroplastic by UniProt (ARBA), HAMAP (MF_01855), and FunFam (3.30.540.10:FF:000014 ""Fructose-1,6-bisphosphatase, chloroplastic""). The cytoplasm annotation is a TreeGrafter error from the PANTHER family that"
REMOVE	NCGR_LOCUS1270	genes/9POAL/NCGR_LOCUS1270/NCGR_LOCUS1270-ai-review.yaml	Miscanthus lutarioriparius	GO:0005829	cytosol	PTN004269459	PTHR11556	FRUCTOSE-1,6-BISPHOSPHATASE-RELATED	PTHR11556:SF1	FRUCTOSE-BISPHOSPHATASE	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	Incorrect localization. Same TreeGrafter isoform confusion as the cytoplasm annotation. In maize (a closely related C4 grass), the chloroplastic FBPase is primarily in bundle sheath cells, while cytosolic FBPase is in mesophyll cytoplasm for sucrose synthesis. The PANTHER family PTHR11556 encompasse
REMOVE	NCGR_LOCUS1270	genes/9POAL/NCGR_LOCUS1270/NCGR_LOCUS1270-ai-review.yaml	Miscanthus lutarioriparius	GO:0005986	sucrose biosynthetic process	PTN004269459	PTHR11556	FRUCTOSE-1,6-BISPHOSPHATASE-RELATED	PTHR11556:SF1	FRUCTOSE-BISPHOSPHATASE	biological_process	0	UNCLASSIFIED	none		Incorrect annotation. Sucrose biosynthesis is catalyzed by the cytosolic FBPase isoform, not the chloroplastic one. This TreeGrafter annotation (PANTHER:PTN004269459) likely resulted from failure to distinguish between chloroplastic and cytosolic FBPase paralogs within the PTHR11556 family. Loss of 
REMOVE	NCGR_LOCUS1270	genes/9POAL/NCGR_LOCUS1270/NCGR_LOCUS1270-ai-review.yaml	Miscanthus lutarioriparius	GO:0006094	gluconeogenesis	PTN004269459	PTHR11556	FRUCTOSE-1,6-BISPHOSPHATASE-RELATED	PTHR11556:SF1	FRUCTOSE-BISPHOSPHATASE	biological_process	0	UNCLASSIFIED	none		Incorrect annotation. Gluconeogenesis involves the cytosolic FBPase, not the chloroplastic isoform. The regulation of cpFBPase (thioredoxin-mediated redox regulation) differs fundamentally from the allosteric regulation (by fructose-2,6-bisphosphate and AMP) of the cytosolic/gluconeogenic FBPase. Th
REMOVE	NCGR_LOCUS27674	genes/9POAL/NCGR_LOCUS27674/NCGR_LOCUS27674-ai-review.yaml	Miscanthus lutarioriparius	GO:0005504	fatty acid binding	PTN009208978	PTHR47284	FATTY-ACID-BINDING PROTEIN 2	PTHR47284:SF3	FATTY-ACID-BINDING PROTEIN 2	molecular_function	3	GENERIC_CONTEXT	curated	chimeric gene-model artifact, not a biological failure of the graft	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]. 
REMOVE	NaODC_candidate_DCOR	genes/NICAT/NaODC_candidate_DCOR/NaODC_candidate_DCOR-ai-review.yaml	Nicotiana attenuata	GO:0005737	cytoplasm	PTN004264316	PTHR11482	ARGININE/DIAMINOPIMELATE/ORNITHINE DECARBOXYLASE	PTHR11482:SF6	ORNITHINE DECARBOXYLASE 1-RELATED	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	UniProt supports chloroplast/plastid localization instead of cytoplasm for this accession.
REMOVE	NaODC_candidate_ODC	genes/NICAT/NaODC_candidate_ODC/NaODC_candidate_ODC-ai-review.yaml	Nicotiana attenuata	GO:0005737	cytoplasm	PTN004264314	PTHR11482	ARGININE/DIAMINOPIMELATE/ORNITHINE DECARBOXYLASE	PTHR11482:SF63	ORNITHINE DECARBOXYLASE	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	UniProt supports chloroplast/plastid localization instead, so the TreeGrafter cytoplasm inference is not the preferred assignment.
REMOVE	NaPMT3	genes/NICAT/NaPMT3/NaPMT3-ai-review.yaml	Nicotiana attenuata	GO:0004766	spermidine synthase activity	PTN004269893	PTHR11558	SPERMIDINE/SPERMINE SYNTHASE	PTHR11558:SF53	PUTRESCINE N-METHYLTRANSFERASE 1	molecular_function	1	GRANULARITY	curated	PTHR11558 family-level spermidine synthase term; subfamily already says PMT	PMT proteins evolved from spermidine synthase but now catalyze putrescine N-methylation in alkaloid biosynthesis.
REMOVE	NaPMT3	genes/NICAT/NaPMT3/NaPMT3-ai-review.yaml	Nicotiana attenuata	GO:0008295	spermidine biosynthetic process	PTN004269893	PTHR11558	SPERMIDINE/SPERMINE SYNTHASE	PTHR11558:SF53	PUTRESCINE N-METHYLTRANSFERASE 1	biological_process	1	GRANULARITY	curated	PTHR11558 family-level spermidine process; subfamily already says PMT	PMT3 channels putrescine into alkaloid biosynthesis rather than spermidine biosynthesis.
REMOVE	NaUGT1_candidate_UGT85A2_0	genes/NICAT/NaUGT1_candidate_UGT85A2_0/NaUGT1_candidate_UGT85A2_0-ai-review.yaml	Nicotiana attenuata	GO:0080043	quercetin 3-O-glucosyltransferase activity	PTN007550104	PTHR11926	GLUCOSYL/GLUCURONOSYL TRANSFERASES	PTHR11926:SF1392	GLYCOSYLTRANSFERASE	molecular_function	1	GRANULARITY	curated	family-level flavonoid UGT substrate term; subfamily generic; substrate unproven	Current evidence supports a specialized nicotine-pathway glucosyltransferase role rather than quercetin glucosylation.
REMOVE	NaUGT1_candidate_UGT85A2_0	genes/NICAT/NaUGT1_candidate_UGT85A2_0/NaUGT1_candidate_UGT85A2_0-ai-review.yaml	Nicotiana attenuata	GO:0080044	quercetin 7-O-glucosyltransferase activity	PTN007550104	PTHR11926	GLUCOSYL/GLUCURONOSYL TRANSFERASES	PTHR11926:SF1392	GLYCOSYLTRANSFERASE	molecular_function	1	GRANULARITY	curated	family-level flavonoid UGT substrate term; subfamily generic; substrate unproven	The reviewed pathway evidence favors nicotinic acid glucosylation, not flavonoid 7-O-glucosylation.
REMOVE	PMT1	genes/NICAT/NaPMT1.1/NaPMT1.1-ai-review.yaml	Nicotiana attenuata	GO:0004766	spermidine synthase activity	PTN004269893	PTHR11558	SPERMIDINE/SPERMINE SYNTHASE	PTHR11558:SF53	PUTRESCINE N-METHYLTRANSFERASE 1	molecular_function	1	GRANULARITY	curated	PTHR11558 family-level spermidine synthase term; subfamily already says PMT	PMT proteins evolved from spermidine synthase but catalyze S-adenosylmethionine-dependent methylation of putrescine, not spermidine synthesis.
REMOVE	PMT1	genes/NICAT/NaPMT1.1/NaPMT1.1-ai-review.yaml	Nicotiana attenuata	GO:0008295	spermidine biosynthetic process	PTN004269893	PTHR11558	SPERMIDINE/SPERMINE SYNTHASE	PTHR11558:SF53	PUTRESCINE N-METHYLTRANSFERASE 1	biological_process	1	GRANULARITY	curated	PTHR11558 family-level spermidine process; subfamily already says PMT	PMT1 generates N-methylputrescine as a dedicated nicotine-pathway intermediate; the spermidine-process assignment is an ancestral family overcall.
REMOVE	PMT2	genes/NICAT/NaPMT1.2/NaPMT1.2-ai-review.yaml	Nicotiana attenuata	GO:0004766	spermidine synthase activity	PTN004269898	PTHR11558	SPERMIDINE/SPERMINE SYNTHASE	PTHR11558:SF53	PUTRESCINE N-METHYLTRANSFERASE 1	molecular_function	1	GRANULARITY	curated	PTHR11558 family-level spermidine synthase term; subfamily already says PMT	PMT2 belongs to a lineage derived from spermidine synthase but now performs specialized methyltransferase chemistry in nicotine biosynthesis.
REMOVE	PMT2	genes/NICAT/NaPMT1.2/NaPMT1.2-ai-review.yaml	Nicotiana attenuata	GO:0008295	spermidine biosynthetic process	PTN004269898	PTHR11558	SPERMIDINE/SPERMINE SYNTHASE	PTHR11558:SF53	PUTRESCINE N-METHYLTRANSFERASE 1	biological_process	1	GRANULARITY	curated	PTHR11558 family-level spermidine process; subfamily already says PMT	The same family-level overtransfer that caused the spermidine synthase activity annotation also incorrectly projects PMT2 into the spermidine process.
REMOVE	PP_0094	genes/PSEPK/PP_0094/PP_0094-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0004713	protein tyrosine kinase activity	PTN002459616	PTHR43434	PHOSPHOGLYCOLATE PHOSPHATASE	PTHR43434:SF20	5'-NUCLEOTIDASE	molecular_function	0	UNCLASSIFIED	none		PP_0094 has HAD phosphohydrolase motifs and a PGP-like cap domain; OpenScientist specifically interprets the cap as supporting small-metabolite phosphatase activity rather than protein phosphorylation.
REMOVE	PP_1257	genes/PSEPK/PP_1257/PP_1257-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0008840	4-hydroxy-tetrahydrodipicolinate synthase activity	PTN002637266	PTHR12128	DIHYDRODIPICOLINATE SYNTHASE	PTHR12128:SF72	DIHYDRODIPICOLINATE SYNTHASE	molecular_function	4	MISPLACEMENT	heuristic	mis-placement keywords	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.
REMOVE	PP_1703	genes/PSEPK/PP_1703/PP_1703-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0016020	membrane	PTN000177398	PTHR43105	RESPIRATORY NITRATE REDUCTASE	PTHR43105:SF9	NADPH-FE(3+) OXIDOREDUCTASE SUBUNIT ALPHA	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	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
REMOVE	PP_1969	genes/PSEPK/PP_1969/PP_1969-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0061799	cyclic pyranopterin monophosphate synthase activity	PTN008586333	PTHR22960	MOLYBDOPTERIN COFACTOR SYNTHESIS PROTEIN A	PTHR22960:SF0	MOLYBDENUM COFACTOR BIOSYNTHESIS PROTEIN 1	molecular_function	1	GRANULARITY	curated	wrong node term: MoaC step attached to the MoaA node	Even canonical bacterial MoaA forms the cyclic GTP intermediate; MoaC converts that intermediate to cPMP.
REMOVE	PP_2482	genes/PSEPK/PP_2482/PP_2482-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0061799	cyclic pyranopterin monophosphate synthase activity	PTN008586334	PTHR22960	MOLYBDOPTERIN COFACTOR SYNTHESIS PROTEIN A	PTHR22960:SF0	MOLYBDENUM COFACTOR BIOSYNTHESIS PROTEIN 1	molecular_function	1	GRANULARITY	curated	wrong node term: MoaC step attached to the MoaA node	Even canonical bacterial MoaA forms the cyclic GTP intermediate; MoaC converts that intermediate to cPMP.
REMOVE	PP_2528	genes/PSEPK/PP_2528/PP_2528-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0004124	cysteine synthase activity	PTN002887252	PTHR43797	HOMOCYSTEINE/CYSTEINE SYNTHASE	PTHR43797:SF2	HOMOCYSTEINE_CYSTEINE SYNTHASE	molecular_function	1	GRANULARITY	curated	sibling sulfhydrylase term (cysteine vs homocysteine) from the node	The local protein name, EC assignment, and methionine-pathway context point to O-acetylhomoserine sulfhydrylase activity rather than O-acetylserine sulfhydrylase/cysteine synthase activity.
REMOVE	PP_3599	genes/PSEPK/PP_3599/PP_3599-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0008840	4-hydroxy-tetrahydrodipicolinate synthase activity	PTN001740851	PTHR12128	DIHYDRODIPICOLINATE SYNTHASE	PTHR12128:SF19	5-DEHYDRO-4-DEOXYGLUCARATE DEHYDRATASE 2-RELATED	molecular_function	1	GRANULARITY	curated	DapA-family MF on the KDGDH subfamily (subfamily correct)	Although KDGDH has a DapA-like TIM-barrel fold, Q88GW8 is a reviewed protein assigned to the substrate-specific IPR017655/NF002958/TIGR03249 families and Rhea 24608. The broad PAINT node propagated the activity of a paralogous DapA branch.
REMOVE	Pks1	genes/METBS/Pks1/Pks1-ai-review.yaml	Metarhizium brunneum ARSEF 3297	GO:0004312	fatty acid synthase activity	PTN008685048	PTHR43775	FATTY ACID SYNTHASE	PTHR43775:SF45	CONIDIAL PIGMENT POLYKETIDE SYNTHASE ALB1	molecular_function	1	GRANULARITY	curated	FAS family-level term on a PKS subfamily (ALB1)	Incorrect annotation. PKS1 is a polyketide synthase, not a fatty acid synthase. While both use similar chemistry, they produce different products (aromatic polyketides vs fatty acids).
REMOVE	Q53353	genes/SPHPI/Q53353/Q53353-ai-review.yaml	Sphingomonas paucimobilis	GO:0010436	carotenoid dioxygenase activity	PTN000830280	PTHR10543	BETA-CAROTENE DIOXYGENASE	PTHR10543:SF89	CAROTENOID 9,10(9',10')-CLEAVAGE DIOXYGENASE 1	molecular_function	4	MISPLACEMENT	curated	lignostilbene vs carotenoid cleavage; subfamily itself mis-labelled	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.
REMOVE	Q53353	genes/SPHPI/Q53353/Q53353-ai-review.yaml	Sphingomonas paucimobilis	GO:0016121	carotene catabolic process	PTN000830280	PTHR10543	BETA-CAROTENE DIOXYGENASE	PTHR10543:SF89	CAROTENOID 9,10(9',10')-CLEAVAGE DIOXYGENASE 1	biological_process	4	MISPLACEMENT	curated	lignostilbene vs carotenoid cleavage; subfamily itself mis-labelled	Contradicted by the gene's own IDA lignin catabolic process annotation; TreeGrafter over-propagation.
REMOVE	Saro_0802	genes/NOVAD/Saro_0802/Saro_0802-ai-review.yaml	Novosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CCUG 56034 / CIP 105152 / NBRC 16084 / F199)	GO:0010436	carotenoid dioxygenase activity	PTN000830280	PTHR10543	BETA-CAROTENE DIOXYGENASE	PTHR10543:SF89	CAROTENOID 9,10(9',10')-CLEAVAGE DIOXYGENASE 1	molecular_function	4	MISPLACEMENT	heuristic	mis-placement keywords	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
REMOVE	Saro_2809	genes/NOVAD/Saro_2809/Saro_2809-ai-review.yaml	Novosphingobium aromaticivorans (strain ATCC 700278 / DSM 12444 / CCUG 56034 / CIP 105152 / NBRC 16084 / F199)	GO:0010436	carotenoid dioxygenase activity	PTN000830280	PTHR10543	BETA-CAROTENE DIOXYGENASE	PTHR10543:SF89	CAROTENOID 9,10(9',10')-CLEAVAGE DIOXYGENASE 1	molecular_function	4	MISPLACEMENT	curated	stilbene vs carotenoid cleavage; subfamily itself mis-labelled	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.
REMOVE	TFP	genes/THLAR/TFP/TFP-ai-review.yaml	Thlaspi arvense	GO:0005634	nucleus	PTN008234626	PTHR47435	KELCH REPEAT PROTEIN (AFU_ORTHOLOGUE AFUA_5G12780)	PTHR47435:SF7	EPITHIOSPECIFIER PROTEIN	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	Over-propagated phylogenetic (TreeGrafter) localization. TaTFP is a cytosolic glucosinolate-breakdown specifier protein; there is no evidence for nuclear localization, and a nuclear compartment is implausible for an enzyme that processes myrosinase-generated aglucones in the cytoplasm after tissue d
REMOVE	accD	genes/PSEPK/accD/accD-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0009329	acetate CoA-transferase complex	PTN002452836	PTHR42995	ACETYL-COENZYME A CARBOXYLASE CARBOXYL TRANSFERASE SUBUNIT BETA, CHLOROPLASTIC	PTHR42995:SF5	ACETYL-COENZYME A CARBOXYLASE CARBOXYL TRANSFERASE SUBUNIT BETA, CHLOROPLASTIC	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	AccD is a subunit of acetyl-CoA carboxylase, not the acetate CoA-transferase complex. The TreeGrafter assignment conflicts with the reviewed UniProt complex description.
REMOVE	acoA	genes/PSEPK/acoA/acoA-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0004739	pyruvate dehydrogenase (acetyl-transferring) activity	PTN002264059	PTHR11516	PYRUVATE DEHYDROGENASE E1 COMPONENT, ALPHA SUBUNIT BACTERIAL AND ORGANELLAR	PTHR11516:SF60	PYRUVATE DEHYDROGENASE E1 COMPONENT SUBUNIT ALPHA	molecular_function	0	UNCLASSIFIED	none		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
REMOVE	acoA	genes/PSEPK/acoA/acoA-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0006086	pyruvate decarboxylation to acetyl-CoA	PTN002264059	PTHR11516	PYRUVATE DEHYDROGENASE E1 COMPONENT, ALPHA SUBUNIT BACTERIAL AND ORGANELLAR	PTHR11516:SF60	PYRUVATE DEHYDROGENASE E1 COMPONENT SUBUNIT ALPHA	biological_process	1	GRANULARITY	heuristic	granularity keywords	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.
REMOVE	alg8	genes/PSEPK/alg8/alg8-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0030213	hyaluronan biosynthetic process	PTN002740694	PTHR22913	HYALURONAN SYNTHASE	PTHR22913:SF12	MANNURONAN SYNTHASE	biological_process	1	GRANULARITY	curated	sibling polysaccharide (hyaluronan) process from the family node; subfamily says mannuronan	Alg8 polymerizes mannuronate in bacterial alginate biosynthesis, not vertebrate-type hyaluronan.
REMOVE	alg8	genes/PSEPK/alg8/alg8-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0050501	hyaluronan synthase activity	PTN002740694	PTHR22913	HYALURONAN SYNTHASE	PTHR22913:SF12	MANNURONAN SYNTHASE	molecular_function	1	GRANULARITY	curated	sibling polysaccharide (hyaluronan) MF from the family node; subfamily says mannuronan	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
REMOVE	alr	genes/PSEPK/alr/alr-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0005829	cytosol	PTN002021362	PTHR30511	ALANINE RACEMASE	PTHR30511:SF0	ALANINE RACEMASE, CATABOLIC-RELATED	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	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.
REMOVE	alr	genes/PSEPK/alr/alr-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0030632	D-alanine biosynthetic process	PTN002021362	PTHR30511	ALANINE RACEMASE	PTHR30511:SF0	ALANINE RACEMASE, CATABOLIC-RELATED	biological_process	1	GRANULARITY	curated	family-level biosynthetic process on the catabolic racemase subfamily	Remove this over-transferred process annotation.
REMOVE	aprA	genes/DESVH/Q72DT2/Q72DT2-ai-review.yaml	Nitratidesulfovibrio vulgaris (Desulfovibrio vulgaris) Hildenborough	GO:0000104	succinate dehydrogenase activity	PTN000908678	PTHR11632	SUCCINATE DEHYDROGENASE 2 FLAVOPROTEIN SUBUNIT	PTHR11632:SF51	SUCCINATE DEHYDROGENASE [UBIQUINONE] FLAVOPROTEIN SUBUNIT, MITOCHONDRIAL	molecular_function	4	MISPLACEMENT	curated	AprA cluster: APS reductase grafted onto SDH flavoprotein subfamily	AprA does not catalyze succinate dehydrogenation. The structural similarity with succinate dehydrogenase flavoproteins (shared FAD-binding domain) does not imply functional equivalence. AprA specifically reduces APS to sulfite and AMP as part of dissimilatory sulfate reduction. This is a clear case 
REMOVE	argG	genes/PSEPK/argG/argG-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0000050	urea cycle	PTN002266045	PTHR11587	ARGININOSUCCINATE SYNTHASE	PTHR11587:SF2	ARGININOSUCCINATE SYNTHASE	biological_process	3	GENERIC_CONTEXT	curated	urea cycle absent from KT2440 (host context)	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
REMOVE	benB	genes/PSEPK/benB/benB-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0019380	3-phenylpropionate catabolic process	PTN002447682	PTHR41534	BLR3401 PROTEIN	PTHR41534:SF1	BLR3401 PROTEIN	biological_process	0	UNCLASSIFIED	none		BenB belongs to the benABCD benzoate catabolic branch, while the available KT2440 pathway literature maps ben genes to benzoate catabolism rather than 3-phenylpropionate catabolism.
REMOVE	benD	genes/PSEPK/benD/benD-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0030497	fatty acid elongation	PTN002460465	PTHR42760	SHORT-CHAIN DEHYDROGENASES/REDUCTASES FAMILY MEMBER	PTHR42760:SF123	OXIDOREDUCTASE	biological_process	1	GRANULARITY	curated	broad SDR-lineage family process on a benzoate-degradation reductase	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.
REMOVE	celC	genes/ACET2/celC/celC-ai-review.yaml	Acetivibrio thermocellus (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372)	GO:0008422	beta-glucosidase activity	PTN001262731	PTHR31297	GLUCAN ENDO-1,6-BETA-GLUCOSIDASE B	PTHR31297:SF41	ENDOGLUCANASE, PUTATIVE (AFU_ORTHOLOGUE AFUA_5G01830)-RELATED	molecular_function	1	GRANULARITY	curated	sibling glycosidase term (beta-glucosidase vs endoglucanase); subfamily correct	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
REMOVE	celC	genes/ACET2/celC/celC-ai-review.yaml	Acetivibrio thermocellus (strain ATCC 27405 / DSM 1237 / JCM 9322 / NBRC 103400 / NCIMB 10682 / NRRL B-4536 / VPI 7372)	GO:0009986	cell surface	PTN001262731	PTHR31297	GLUCAN ENDO-1,6-BETA-GLUCOSIDASE B	PTHR31297:SF41	ENDOGLUCANASE, PUTATIVE (AFU_ORTHOLOGUE AFUA_5G01830)-RELATED	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	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
REMOVE	cfr	genes/STAWA/cfr/cfr-ai-review.yaml	Staphylococcus warneri	GO:0030488	tRNA methylation	PTN002022544	PTHR30544	23S RRNA METHYLTRANSFERASE	PTHR30544:SF5	RADICAL SAM CORE DOMAIN-CONTAINING PROTEIN	biological_process	1	GRANULARITY	curated	radical-SAM family process (tRNA) on an rRNA methyltransferase	Cfr's supported substrate is 23S rRNA A2503, not tRNA. The tRNA methylation annotation likely comes from broader radical-SAM methylthiotransferase family context.
REMOVE	clpV	genes/PSEPK/clpV/clpV-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0034605	cellular response to heat	PTN005170413	PTHR11638	ATP-DEPENDENT CLP PROTEASE	PTHR11638:SF184	ATPASE WITH CHAPERONE ACTIVITY	biological_process	1	GRANULARITY	curated	Clp/Hsp100 family heat-shock process on the T6SS ClpV subfamily	The ClpV-specific domain and K1 locus establish T6SS sheath recycling rather than a heat-shock role.
REMOVE	cpi-2	genes/BRUMA/cpi-2/cpi-2-ai-review.yaml	Brugia malayi	GO:0005737	cytoplasm	PTN008193545	PTHR46186	CYSTATIN	PTHR46186:SF2	CYSTATIN	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	TreeGrafter phylogenetic propagation to cytoplasm. CPI-2 is a secreted protein with an N-terminal signal peptide (residues 1-25) and acts extracellularly and within host endosomal/lysosomal compartments; its established biology is extracellular, not cytoplasmic. This is a generic, poorly supported l
REMOVE	dapE	genes/PSEPK/dapE/dapE-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0006526	L-arginine biosynthetic process	PTN002887524	PTHR43808	ACETYLORNITHINE DEACETYLASE	PTHR43808:SF31	N-ACETYL-L-CITRULLINE DEACETYLASE	biological_process	4	MISPLACEMENT	curated	DapE grafted onto an N-acetylcitrulline deacetylase subfamily	Q88MP5 has the DapE-specific reaction, pathway assignment, and NCBIfam:TIGR01246 signature.
REMOVE	dapE	genes/PSEPK/dapE/dapE-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0008777	acetylornithine deacetylase activity	PTN002887524	PTHR43808	ACETYLORNITHINE DEACETYLASE	PTHR43808:SF31	N-ACETYL-L-CITRULLINE DEACETYLASE	molecular_function	4	MISPLACEMENT	curated	DapE grafted onto an N-acetylcitrulline deacetylase subfamily	Q88MP5 is assigned to the proteobacterial DapE subfamily and EC 3.5.1.18; no evidence supports acetylornithine as its physiological substrate.
REMOVE	davA	genes/PSEPK/davA/davA-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0050126	N-carbamoylputrescine amidase activity	PTN001132736	PTHR43674	NITRILASE C965.09-RELATED	PTHR43674:SF2	BETA-UREIDOPROPIONASE	molecular_function	0	UNCLASSIFIED	none		DavA acts on 5-aminopentanamide in lysine catabolism; the putrescine-biosynthesis activity was propagated from a broader nitrilase-family node and conflicts with the exact pathway role.
REMOVE	davD	genes/PSEPK/davD/davD-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0004777	succinate-semialdehyde dehydrogenase (NAD+) activity	PTN002458567	PTHR43353	SUCCINATE-SEMIALDEHYDE DEHYDROGENASE, MITOCHONDRIAL	PTHR43353:SF5	SUCCINATE-SEMIALDEHYDE DEHYDROGENASE, MITOCHONDRIAL	molecular_function	4	MISPLACEMENT	curated	glutarate- vs succinate-semialdehyde substrate; SSADH subfamily	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.
REMOVE	fbp	genes/PSEPK/fbp/fbp-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0005986	sucrose biosynthetic process	PTN002265199	PTHR11556	FRUCTOSE-1,6-BISPHOSPHATASE-RELATED	PTHR11556:SF35	SEDOHEPTULOSE-1,7-BISPHOSPHATASE, CHLOROPLASTIC	biological_process	3	GENERIC_CONTEXT	heuristic	host lacks pathway/process	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
REMOVE	fibrolase	genes/AGKCO/fibrolase/fibrolase-ai-review.yaml	Agkistrodon contortrix contortrix	GO:0005886	plasma membrane	PTN002628616	PTHR11905	ADAM A DISINTEGRIN AND METALLOPROTEASE DOMAIN	PTHR11905:SF32	DISINTEGRIN AND METALLOPROTEINASE DOMAIN-CONTAINING PROTEIN 28	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	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
REMOVE	flgE	genes/PSEPK/flgE/flgE-ai-review.yaml	Pseudomonas putida KT2440	GO:0005829	cytosol	PTN000764868	PTHR30435	FLAGELLAR PROTEIN	PTHR30435:SF1	FLAGELLAR HOOK PROTEIN FLGE	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	This annotation should be removed. FlgE is explicitly identified as the flagellar hook protein and described as the flexible connector between filament and basal-body drive apparatus, which is inconsistent with a soluble cytosolic localization. The cytosol term appears to be a TreeGrafter overcall f
REMOVE	fogD	genes/ASPRC/fogD/fogD-ai-review.yaml	Aspergillus ruber (strain CBS 135680)	GO:0000140	acylglycerone-phosphate reductase (NADP+) activity	PTN001211783	PTHR44169	NADPH-DEPENDENT 1-ACYLDIHYDROXYACETONE PHOSPHATE REDUCTASE	PTHR44169:SF3	SHORT-CHAIN DEHYDROGENASE SRDE	molecular_function	1	GRANULARITY	curated	PTHR44169 family-level lipid-enzyme term on the SrdE subfamily (secondary-metabolite SDR)	Incorrect function propagated from Ayr1p/DHAP reductase family members in PANTHER PTHR44169. fogD is a secondary metabolite biosynthetic enzyme, not a lipid metabolism enzyme. No experimental or bioinformatic evidence supports this activity for fogD.
REMOVE	fogD	genes/ASPRC/fogD/fogD-ai-review.yaml	Aspergillus ruber (strain CBS 135680)	GO:0004806	triacylglycerol lipase activity	PTN001211783	PTHR44169	NADPH-DEPENDENT 1-ACYLDIHYDROXYACETONE PHOSPHATE REDUCTASE	PTHR44169:SF3	SHORT-CHAIN DEHYDROGENASE SRDE	molecular_function	1	GRANULARITY	curated	PTHR44169 family-level lipid-enzyme term on the SrdE subfamily (secondary-metabolite SDR)	Completely wrong reaction type. fogD is an oxidoreductase (EC 1.1.1.-), not a hydrolase/lipase. No SDR enzyme catalyzes triacylglycerol lipase activity. This represents a clear error in phylogenetic annotation transfer.
REMOVE	fogD	genes/ASPRC/fogD/fogD-ai-review.yaml	Aspergillus ruber (strain CBS 135680)	GO:0005783	endoplasmic reticulum	PTN001211783	PTHR44169	NADPH-DEPENDENT 1-ACYLDIHYDROXYACETONE PHOSPHATE REDUCTASE	PTHR44169:SF3	SHORT-CHAIN DEHYDROGENASE SRDE	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	No experimental or bioinformatic evidence supports ER localization. fogD lacks signal peptides and transmembrane domains. The annotation is incorrectly propagated from lipid metabolism enzymes in the same PANTHER family.
REMOVE	fogD	genes/ASPRC/fogD/fogD-ai-review.yaml	Aspergillus ruber (strain CBS 135680)	GO:0005811	lipid droplet	PTN001211783	PTHR44169	NADPH-DEPENDENT 1-ACYLDIHYDROXYACETONE PHOSPHATE REDUCTASE	PTHR44169:SF3	SHORT-CHAIN DEHYDROGENASE SRDE	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	No evidence for lipid droplet localization. fogD is a secondary metabolite biosynthetic enzyme, not a lipid metabolism enzyme. Incorrectly propagated from Ayr1p-like DHAP reductases.
REMOVE	fogD	genes/ASPRC/fogD/fogD-ai-review.yaml	Aspergillus ruber (strain CBS 135680)	GO:0006654	phosphatidic acid biosynthetic process	PTN001211783	PTHR44169	NADPH-DEPENDENT 1-ACYLDIHYDROXYACETONE PHOSPHATE REDUCTASE	PTHR44169:SF3	SHORT-CHAIN DEHYDROGENASE SRDE	biological_process	1	GRANULARITY	curated	PTHR44169 family-level lipid process on the SrdE subfamily	fogD has no role in phospholipid or phosphatidic acid biosynthesis. It is a secondary metabolite biosynthetic enzyme involved in flavoglaucin production. Incorrectly propagated from lipid metabolism enzymes.
REMOVE	fogD	genes/ASPRC/fogD/fogD-ai-review.yaml	Aspergillus ruber (strain CBS 135680)	GO:0019433	triglyceride catabolic process	PTN001211783	PTHR44169	NADPH-DEPENDENT 1-ACYLDIHYDROXYACETONE PHOSPHATE REDUCTASE	PTHR44169:SF3	SHORT-CHAIN DEHYDROGENASE SRDE	biological_process	1	GRANULARITY	curated	PTHR44169 family-level lipid process on the SrdE subfamily	fogD has no role in triglyceride catabolism. It is a biosynthetic enzyme (not catabolic) and an oxidoreductase (not a lipase). Incorrectly propagated from PANTHER family PTHR44169.
REMOVE	galB	genes/PSEPK/galB/galB-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0016811	hydrolase activity, acting on carbon-nitrogen (but not peptide) bonds, in linear amides	PTN001770600	PTHR12993	N-ACETYLGLUCOSAMINYL-PHOSPHATIDYLINOSITOL DE-N-ACETYLASE-RELATED	PTHR12993:SF29	BLR3841 PROTEIN	molecular_function	4	MISPLACEMENT	curated	hydratase grafted onto an amide-hydrolase branch	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.
REMOVE	galE	genes/PSEPK/galE/galE-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0033499	beta-D-galactose catabolic process via UDP-galactose, Leloir pathway	PTN008684687	PTHR43725	UDP-GLUCOSE 4-EPIMERASE	PTHR43725:SF53	UDP-ARABINOSE 4-EPIMERASE 1	biological_process	3	GENERIC_CONTEXT	curated	Leloir pathway not satisfiable in this proteome (host context)	This TreeGrafter process propagation over-interprets a broadly used nucleotide-sugar epimerase as evidence for a complete pathway that is not satisfiable in this proteome.
REMOVE	gcl	genes/PSEPK/gcl/gcl-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0005948	acetolactate synthase complex	PTN002317630	PTHR18968	THIAMINE PYROPHOSPHATE ENZYMES	PTHR18968:SF14	GLYOXYLATE CARBOLIGASE	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	Gcl is annotated and described as glyoxylate carboligase, not as an acetolactate synthase complex subunit.
REMOVE	gcl	genes/PSEPK/gcl/gcl-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0009099	L-valine biosynthetic process	PTN002317630	PTHR18968	THIAMINE PYROPHOSPHATE ENZYMES	PTHR18968:SF14	GLYOXYLATE CARBOLIGASE	biological_process	1	GRANULARITY	curated	ALS family-level valine process on the glyoxylate carboligase subfamily	The gene product is glyoxylate carboligase in glyoxylate catabolism, not acetolactate synthase or a valine-biosynthetic enzyme.
REMOVE	glnA	genes/PSEPK/glnA/glnA-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0016020	membrane	PTN002459220	PTHR43407	GLUTAMINE SYNTHETASE	PTHR43407:SF2	GLUTAMINE SYNTHETASE	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	TreeGrafter-propagated localization that conflicts with the experimentally established and UniProt-annotated cytoplasmic localization of glutamine synthetase. GS is a soluble cytoplasmic enzyme with no membrane association; this is a spurious electronic annotation.
REMOVE	groES	genes/PSEPK/groES/groES-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0046872	metal ion binding	PTN002243569	PTHR10772	10 KDA HEAT SHOCK PROTEIN	PTHR10772:SF58	CO-CHAPERONIN GROES	molecular_function	0	UNCLASSIFIED	none		This is a TreeGrafter/PANTHER tree-based over-annotation without support in the experimental or structural literature for GroES family proteins. Metal ion binding is not a known molecular function of the co-chaperonin.
REMOVE	hisA	genes/PSEPK/hisA/hisA-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0000162	L-tryptophan biosynthetic process	PTN002454225	PTHR43090	1-(5-PHOSPHORIBOSYL)-5-[(5-PHOSPHORIBOSYLAMINO)METHYLIDENEAMINO] IMIDAZOLE-4-CARBOXAMIDE ISOMERASE	PTHR43090:SF2	1-(5-PHOSPHORIBOSYL)-5-[(5-PHOSPHORIBOSYLAMINO)METHYLIDENEAMINO] IMIDAZOLE-4-CARBOXAMIDE ISOMERASE	biological_process	1	GRANULARITY	curated	bifunctional PriA node term (TrpF) on monofunctional HisA	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
REMOVE	infC	genes/PSEPK/infC/infC-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0016020	membrane	PTN002249955	PTHR10938	TRANSLATION INITIATION FACTOR IF-3	PTHR10938:SF0	TRANSLATION INITIATION FACTOR IF-3, MITOCHONDRIAL	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	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.
REMOVE	kdsC	genes/PSEPK/kdsC/kdsC-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0008781	N-acylneuraminate cytidylyltransferase activity	PTN000486303	PTHR21485	HAD SUPERFAMILY MEMBERS CMAS AND KDSC	PTHR21485:SF3	N-ACYLNEURAMINATE CYTIDYLYLTRANSFERASE	molecular_function	4	MISPLACEMENT	heuristic	mis-placement keywords	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.
REMOVE	liuC	genes/PSEPK/liuC/liuC-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0008300	isoprenoid catabolic process	PTN002452383	PTHR42964	ENOYL-COA HYDRATASE	PTHR42964:SF1	POLYKETIDE BIOSYNTHESIS ENOYL-COA HYDRATASE PKSH-RELATED	biological_process	3	GENERIC_CONTEXT	curated	acyclic-terpene utilisation absent in KT2440 (host context)	P. putida KT2440 lacks the acyclic-terpene utilization context and was experimentally unable to grow on acyclic terpenes, while retaining leucine and isovalerate utilization.
REMOVE	lolD	genes/PSEPK/lolD/lolD-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0022857	transmembrane transporter activity	PTN002383677	PTHR24220	IMPORT ATP-BINDING PROTEIN	PTHR24220:SF689	LIPOPROTEIN-RELEASING SYSTEM ATP-BINDING PROTEIN LOLD	molecular_function	3	GENERIC_CONTEXT	curated	whole-complex transport activity placed on the peripheral ATPase subunit	LolD is a peripheral ATPase rather than a transmembrane transporter; transport activity belongs to the assembled LolCDE complex.
REMOVE	lolD	genes/PSEPK/lolD/lolD-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0055085	transmembrane transport	PTN002383677	PTHR24220	IMPORT ATP-BINDING PROTEIN	PTHR24220:SF689	LIPOPROTEIN-RELEASING SYSTEM ATP-BINDING PROTEIN LOLD	biological_process	3	GENERIC_CONTEXT	curated	generic transport process that mis-describes lipoprotein extrusion	GO:0055085 requires movement across a membrane, whereas LolCDE mechanically extrudes lipid-anchored cargo from the membrane surface into the periplasm.
REMOVE	lpdV	genes/PSEPK/lpdV/lpdV-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0006103	2-oxoglutarate metabolic process	PTN002340777	PTHR22912	DISULFIDE OXIDOREDUCTASE	PTHR22912:SF160	DIHYDROLIPOYL DEHYDROGENASE	biological_process	4	MISPLACEMENT	heuristic	mis-placement keywords	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.
REMOVE	lsdB	genes/SPHPI/lsdB/lsdB-ai-review.yaml	Sphingomonas paucimobilis	GO:0010436	carotenoid dioxygenase activity	PTN000830280	PTHR10543	BETA-CAROTENE DIOXYGENASE	PTHR10543:SF89	CAROTENOID 9,10(9',10')-CLEAVAGE DIOXYGENASE 1	molecular_function	4	MISPLACEMENT	curated	lignostilbene vs carotenoid cleavage; subfamily itself mis-labelled	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).
REMOVE	lsdB	genes/SPHPI/lsdB/lsdB-ai-review.yaml	Sphingomonas paucimobilis	GO:0016121	carotene catabolic process	PTN000830280	PTHR10543	BETA-CAROTENE DIOXYGENASE	PTHR10543:SF89	CAROTENOID 9,10(9',10')-CLEAVAGE DIOXYGENASE 1	biological_process	4	MISPLACEMENT	curated	lignostilbene vs carotenoid cleavage; subfamily itself mis-labelled	Contradicted by the gene's own IDA lignin catabolic process annotation; TreeGrafter over-propagation of a carotenoid-pathway term.
REMOVE	lytN	genes/STAAU/lytN/lytN-ai-review.yaml	Staphylococcus aureus	GO:0008932	lytic endotransglycosylase activity	PTN001856296	PTHR33734	LYSM DOMAIN-CONTAINING GPI-ANCHORED PROTEIN 2	PTHR33734:SF22	MEMBRANE-BOUND LYTIC MUREIN TRANSGLYCOSYLASE D	molecular_function	4	MISPLACEMENT	curated	hydrolase placed in a lytic transglycosylase subfamily	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
REMOVE	mazG	genes/PSEPK/mazG/mazG-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0046047	TTP catabolic process	PTN002412313	PTHR30522	NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE	PTHR30522:SF0	NUCLEOSIDE TRIPHOSPHATE PYROPHOSPHOHYDROLASE	biological_process	1	GRANULARITY	curated	sibling substrate term (ribo-TTP) from the node	GO:0046047 is defined for ribosylthymine triphosphate, whereas the canonical deoxythymidine substrate is represented separately by GO:0046076 and is already present on Q88MB7. The family evidence supports the eight standard ribo- and deoxyribonucleoside triphosphates, not the unusual ribothymidine n
REMOVE	mdcD	genes/METEA/mdcD/mdcD-ai-review.yaml	Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1)	GO:0003989	acetyl-CoA carboxylase activity	PTN002873918	PTHR42995	ACETYL-COENZYME A CARBOXYLASE CARBOXYL TRANSFERASE SUBUNIT BETA, CHLOROPLASTIC	PTHR42995:SF1	MALONATE DECARBOXYLASE BETA SUBUNIT	molecular_function	1	GRANULARITY	curated	acetyl-CoA carboxylase family MF on the malonate decarboxylase subfamily	"Incorrect function assignment due to sequence homology with acetyl-CoA carboxylase beta subunit. MdcD is a decarboxylase (carboxy-lyase), not a carboxylase (ligase). The PANTHER family PTHR42995 includes both ACC and MDC beta subunits, but the specific subfamily SF1 is correctly ""MALONATE DECARBOXYL"
REMOVE	mdcD	genes/METEA/mdcD/mdcD-ai-review.yaml	Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1)	GO:0006633	fatty acid biosynthetic process	PTN002873918	PTHR42995	ACETYL-COENZYME A CARBOXYLASE CARBOXYL TRANSFERASE SUBUNIT BETA, CHLOROPLASTIC	PTHR42995:SF1	MALONATE DECARBOXYLASE BETA SUBUNIT	biological_process	1	GRANULARITY	curated	acetyl-CoA carboxylase family process on the malonate decarboxylase subfamily	MdcD participates in malonate catabolism, not fatty acid biosynthesis. The protein is part of the malonate decarboxylase complex which degrades malonate to acetate, the opposite metabolic direction from fatty acid synthesis which builds fatty acids from acetyl-CoA via malonyl-CoA intermediates.
REMOVE	mdcD	genes/METEA/mdcD/mdcD-ai-review.yaml	Methylorubrum extorquens (strain ATCC 14718 / DSM 1338 / JCM 2805 / NCIMB 9133 / AM1)	GO:2001295	malonyl-CoA biosynthetic process	PTN002873918	PTHR42995	ACETYL-COENZYME A CARBOXYLASE CARBOXYL TRANSFERASE SUBUNIT BETA, CHLOROPLASTIC	PTHR42995:SF1	MALONATE DECARBOXYLASE BETA SUBUNIT	biological_process	1	GRANULARITY	curated	acetyl-CoA carboxylase family process on the malonate decarboxylase subfamily	MdcD catalyzes decarboxylation, not carboxylation. The malonate decarboxylase complex breaks down malonate to acetate + CO2, which is the opposite of malonyl-CoA biosynthesis (which adds CO2 to acetyl-CoA to form malonyl-CoA).
REMOVE	mdh	genes/METEA/mdh/mdh-ai-review.yaml	Methylorubrum extorquens AM1	GO:0004459	L-lactate dehydrogenase (NAD+) activity	PTN002875914	PTHR43128	L-2-HYDROXYCARBOXYLATE DEHYDROGENASE (NAD(P)(+))	PTHR43128:SF16	L-LACTATE DEHYDROGENASE	molecular_function	4	MISPLACEMENT	heuristic	mis-placement keywords	"This annotation is incorrect. This protein is malate dehydrogenase (EC 1.1.1.37), not lactate dehydrogenase (EC 1.1.1.27). The enzyme catalyzes the oxidation of malate to oxaloacetate, not lactate to pyruvate. This appears to be a misannotation by TreeGrafter. [file:METEA/mdh/mdh-uniprot.txt, ""Malat"
REMOVE	mdh	genes/METEA/mdh/mdh-ai-review.yaml	Methylorubrum extorquens AM1	GO:0006089	lactate metabolic process	PTN002875914	PTHR43128	L-2-HYDROXYCARBOXYLATE DEHYDROGENASE (NAD(P)(+))	PTHR43128:SF16	L-LACTATE DEHYDROGENASE	biological_process	4	MISPLACEMENT	heuristic	mis-placement keywords	"This annotation is incorrect. This enzyme metabolizes malate, not lactate. This appears to be a misannotation by TreeGrafter, likely due to the structural similarity between the LDH/MDH superfamily members. [file:METEA/mdh/mdh-uniprot.txt, ""Malate dehydrogenase""; ""(S)-malate + NAD(+) = oxaloacetate "
REMOVE	mdh	genes/PSEPK/mdh/mdh-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0004459	L-lactate dehydrogenase (NAD+) activity	PTN002454946	PTHR43128	L-2-HYDROXYCARBOXYLATE DEHYDROGENASE (NAD(P)(+))	PTHR43128:SF16	L-LACTATE DEHYDROGENASE	molecular_function	4	MISPLACEMENT	heuristic	mis-placement keywords	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
REMOVE	mdh	genes/PSEPK/mdh/mdh-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0006089	lactate metabolic process	PTN002454946	PTHR43128	L-2-HYDROXYCARBOXYLATE DEHYDROGENASE (NAD(P)(+))	PTHR43128:SF16	L-LACTATE DEHYDROGENASE	biological_process	4	MISPLACEMENT	heuristic	mis-placement keywords	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
REMOVE	mdr	genes/STABO/mdr/mdr-ai-review.yaml	Starmerella bombicola	GO:0005743	mitochondrial inner membrane	PTN008681462	PTHR43394	ATP-DEPENDENT PERMEASE MDL1, MITOCHONDRIAL	PTHR43394:SF11	ATP-BINDING CASSETTE TRANSPORTER	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	SbSLMdr.1 is reported as the transporter responsible for sophorolipid export and transporter knockout reduces secretion to ~10% of wild type; this is inconsistent with a mitochondrial inner membrane annotation. [PMID:34998388, PMID:23516968]
REMOVE	mdr	genes/STABO/mdr/mdr-ai-review.yaml	Starmerella bombicola	GO:0090374	oligopeptide export from mitochondrion	PTN008681462	PTHR43394	ATP-DEPENDENT PERMEASE MDL1, MITOCHONDRIAL	PTHR43394:SF11	ATP-BINDING CASSETTE TRANSPORTER	biological_process	3	GENERIC_CONTEXT	curated	mitochondrial-context process on a fungal secondary-metabolite exporter	The transporter is linked to sophorolipid export; the mitochondrial oligopeptide export process is unsupported. [PMID:34998388, PMID:23516968]
REMOVE	merA	genes/PSEAI/merA/merA-ai-review.yaml	Pseudomonas aeruginosa	GO:0003955	NAD(P)H dehydrogenase (quinone) activity	PTN005140324	PTHR43014	MERCURIC REDUCTASE	PTHR43014:SF2	MERCURIC REDUCTASE	molecular_function	1	GRANULARITY	curated	family-level flavoprotein disulfide reductase term on mercuric reductase	MerA specifically reduces mercury ions, not quinones. The enzyme's substrate specificity is for Hg(II), not quinone molecules.
REMOVE	moaA	genes/PSEPK/moaA/moaA-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0061799	cyclic pyranopterin monophosphate synthase activity	PTN002344120	PTHR22960	MOLYBDOPTERIN COFACTOR SYNTHESIS PROTEIN A	PTHR22960:SF0	MOLYBDENUM COFACTOR BIOSYNTHESIS PROTEIN 1	molecular_function	1	GRANULARITY	curated	wrong node term: MoaC step attached to the MoaA node	MoaA makes the cyclic GTP intermediate; the distinct MoaC enzyme converts that intermediate to cPMP.
REMOVE	moeB	genes/PSEPK/moeB/moeB-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0004792	thiosulfate-cyanide sulfurtransferase activity	PTN002250299	PTHR10953	UBIQUITIN-ACTIVATING ENZYME E1	PTHR10953:SF194	MOLYBDOPTERIN-SYNTHASE ADENYLYLTRANSFERASE	molecular_function	1	GRANULARITY	curated	rhodanese/ThiF family term on the MoeB subfamily	MoeB activates MoaD by ATP-dependent adenylylation; it does not use thiosulfate or cyanide in the assigned reaction.
REMOVE	moeB	genes/PSEPK/moeB/moeB-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0008146	sulfotransferase activity	PTN002250299	PTHR10953	UBIQUITIN-ACTIVATING ENZYME E1	PTHR10953:SF194	MOLYBDOPTERIN-SYNTHASE ADENYLYLTRANSFERASE	molecular_function	1	GRANULARITY	heuristic	granularity keywords	MoeB adenylates MoaD; sulfur loading is a separate reaction supplied by a sulfur-donor system.
REMOVE	mqo1	genes/PSEPK/mqo1/mqo1-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0047545	(S)-2-hydroxyglutarate dehydrogenase activity	PTN001015070	PTHR43104	L-2-HYDROXYGLUTARATE DEHYDROGENASE, MITOCHONDRIAL	PTHR43104:SF2	L-2-HYDROXYGLUTARATE DEHYDROGENASE, MITOCHONDRIAL	molecular_function	4	MISPLACEMENT	curated	malate:quinone oxidoreductase grafted onto an L-2-HG dehydrogenase subfamily	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
REMOVE	mqo2	genes/PSEPK/mqo2/mqo2-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0047545	(S)-2-hydroxyglutarate dehydrogenase activity	PTN001015070	PTHR43104	L-2-HYDROXYGLUTARATE DEHYDROGENASE, MITOCHONDRIAL	PTHR43104:SF2	L-2-HYDROXYGLUTARATE DEHYDROGENASE, MITOCHONDRIAL	molecular_function	4	MISPLACEMENT	curated	malate:quinone oxidoreductase grafted onto an L-2-HG dehydrogenase subfamily	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.
REMOVE	mqo3	genes/PSEPK/mqo3/mqo3-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0047545	(S)-2-hydroxyglutarate dehydrogenase activity	PTN001015070	PTHR43104	L-2-HYDROXYGLUTARATE DEHYDROGENASE, MITOCHONDRIAL	PTHR43104:SF2	L-2-HYDROXYGLUTARATE DEHYDROGENASE, MITOCHONDRIAL	molecular_function	4	MISPLACEMENT	curated	malate:quinone oxidoreductase grafted onto an L-2-HG dehydrogenase subfamily	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.
REMOVE	mupP	genes/PSEPK/mupP/mupP-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0006281	DNA repair	PTN002459629	PTHR43434	PHOSPHOGLYCOLATE PHOSPHATASE	PTHR43434:SF23	PHOSPHOGLYCOLATE PHOSPHATASE	biological_process	4	MISPLACEMENT	curated	MurNAc-6P phosphatase grafted onto a phosphoglycolate phosphatase subfamily	MupP is characterized as a MurNAc-6P phosphatase in peptidoglycan recycling, not a DNA repair protein.
REMOVE	mupP	genes/PSEPK/mupP/mupP-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0008967	phosphoglycolate phosphatase activity	PTN002459629	PTHR43434	PHOSPHOGLYCOLATE PHOSPHATASE	PTHR43434:SF23	PHOSPHOGLYCOLATE PHOSPHATASE	molecular_function	4	MISPLACEMENT	curated	MurNAc-6P phosphatase grafted onto a phosphoglycolate phosphatase subfamily	The characterized substrate is MurNAc-6P, with narrow substrate specificity.
REMOVE	nicD	genes/PSEPK/nicD/nicD-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0016020	membrane	PTN001661081	PTHR43798	MONOACYLGLYCEROL LIPASE	PTHR43798:SF33	HYDROLASE, PUTATIVE (AFU_ORTHOLOGUE AFUA_2G14860)-RELATED	cellular_component	3	GENERIC_CONTEXT	heuristic	CC term	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
REMOVE	nicR	genes/PSEPK/nicR/nicR-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0006950	response to stress	PTN008652328	PTHR33164	TRANSCRIPTIONAL REGULATOR, MARR FAMILY	PTHR33164:SF95	TRANSCRIPTIONAL REGULATOR	biological_process	3	GENERIC_CONTEXT	curated	generic stress-response process	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
REMOVE	nspC	genes/PSEPK/nspC/nspC-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0008836	diaminopimelate decarboxylase activity	PTN001691018	PTHR43727	DIAMINOPIMELATE DECARBOXYLASE	PTHR43727:SF1	CARBOXYNORSPERMIDINE_CARBOXYSPERMIDINE DECARBOXYLASE	molecular_function	1	GRANULARITY	curated	LysA family-level term on the NspC subfamily	Incorrect LysA-family transfer. NspC is assigned specifically to PANTHER subfamily PTHR43727:SF1 (carboxynorspermidine/carboxyspermidine decarboxylase), UniProt places it in the NspC subfamily, InterPro identifies the Nsp decarboxylase family (IPR005730), and its adjacency to the CASDH candidate PP_
REMOVE	nuoM	genes/PSEPK/nuoM/nuoM-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0048039	ubiquinone binding	PTN002460631	PTHR43507	NADH-UBIQUINONE OXIDOREDUCTASE CHAIN 4	PTHR43507:SF1	NADH-UBIQUINONE OXIDOREDUCTASE CHAIN 4	molecular_function	0	UNCLASSIFIED	none		The quinone-reactive cavity is formed near NuoB/NuoC-D, not this distal subunit.
REMOVE	pepV	genes/FUSNU/pepV/pepV-ai-review.yaml	Fusobacterium nucleatum	GO:0006526	L-arginine biosynthetic process	PTN000865753	PTHR43808	ACETYLORNITHINE DEACETYLASE	PTHR43808:SF31	N-ACETYL-L-CITRULLINE DEACETYLASE	biological_process	4	MISPLACEMENT	heuristic	mis-placement keywords	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 
REMOVE	pepV	genes/FUSNU/pepV/pepV-ai-review.yaml	Fusobacterium nucleatum	GO:0008777	acetylornithine deacetylase activity	PTN000865753	PTHR43808	ACETYLORNITHINE DEACETYLASE	PTHR43808:SF31	N-ACETYL-L-CITRULLINE DEACETYLASE	molecular_function	4	MISPLACEMENT	heuristic	mis-placement keywords	"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"
REMOVE	phnX	genes/PSEPK/phnX/phnX-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0006281	DNA repair	PTN002455951	PTHR43434	PHOSPHOGLYCOLATE PHOSPHATASE	PTHR43434:SF19	PHOSPHONOACETALDEHYDE HYDROLASE	biological_process	1	GRANULARITY	curated	phosphoglycolate-phosphatase node process on the PhnX subfamily	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
REMOVE	phnX	genes/PSEPK/phnX/phnX-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0008967	phosphoglycolate phosphatase activity	PTN002455951	PTHR43434	PHOSPHOGLYCOLATE PHOSPHATASE	PTHR43434:SF19	PHOSPHONOACETALDEHYDE HYDROLASE	molecular_function	1	GRANULARITY	curated	phosphoglycolate-phosphatase node MF on the PhnX subfamily (subfamily correct)	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.
REMOVE	prpC	genes/PSEPK/prpC/prpC-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0005975	carbohydrate metabolic process	PTN002271895	PTHR11739	CITRATE SYNTHASE	PTHR11739:SF25	CITRATE SYNTHASE-RELATED PROTEIN DDB_G0287281	biological_process	1	GRANULARITY	heuristic	granularity keywords	The stronger process assignment is propionate catabolism via the methylcitrate cycle, not generic carbohydrate metabolism. The TreeGrafter process term appears to be broad family over-propagation and should be replaced with GO:0019543.
REMOVE	ptxD	genes/PSEPK/ptxD/ptxD-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0016618	hydroxypyruvate reductase [NAD(P)H] activity	PTN002251374	PTHR10996	2-HYDROXYACID DEHYDROGENASE-RELATED	PTHR10996:SF283	GLYOXYLATE_HYDROXYPYRUVATE REDUCTASE B	molecular_function	4	MISPLACEMENT	curated	phosphonate dehydrogenase grafted onto a glyoxylate/hydroxypyruvate reductase subfamily	There is no target-specific hydroxypyruvate-reductase evidence.
REMOVE	ptxD	genes/PSEPK/ptxD/ptxD-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0030267	glyoxylate reductase (NADPH) activity	PTN002251374	PTHR10996	2-HYDROXYACID DEHYDROGENASE-RELATED	PTHR10996:SF283	GLYOXYLATE_HYDROXYPYRUVATE REDUCTASE B	molecular_function	4	MISPLACEMENT	curated	phosphonate dehydrogenase grafted onto a glyoxylate/hydroxypyruvate reductase subfamily	There is no target-specific glyoxylate-reductase evidence.
REMOVE	purM	genes/PSEPK/purM/purM-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0004637	phosphoribosylamine-glycine ligase activity	PTN002237315	PTHR10520	TRIFUNCTIONAL PURINE BIOSYNTHETIC PROTEIN ADENOSINE-3-RELATED	PTHR10520:SF12	TRIFUNCTIONAL PURINE BIOSYNTHETIC PROTEIN ADENOSINE-3	molecular_function	1	GRANULARITY	curated	multi-domain fusion node: other domain's activity propagated	PurM is AIR synthetase and does not catalyze phosphoribosylamine--glycine ligation.
REMOVE	pvdD	genes/PSEPK/pvdD/pvdD-ai-review.yaml	Pseudomonas putida KT2440	GO:0009366	enterobactin synthetase complex	PTN005148629	PTHR45527	NONRIBOSOMAL PEPTIDE SYNTHETASE	PTHR45527:SF1	FATTY ACID SYNTHASE	cellular_component	4	MISPLACEMENT	curated	EntF-specific enterobactin complex on a pyoverdine NRPS module	Wrong siderophore family. Falcon deep research confirms PvdD is part of the pyoverdine NRPS assembly line (PvdL/PvdI/PvdJ/PvdD), which forms dynamic cytoplasmic NRPS assemblies rather than the enterobactin synthetase complex; GO lacks a pyoverdine-specific complex term, so the annotation should be r
REMOVE	pvdE	genes/PSEPK/pvdE/pvdE-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0034040	ATPase-coupled lipid transmembrane transporter activity	PTN000657720	PTHR24221	ATP-BINDING CASSETTE SUB-FAMILY B	PTHR24221:SF654	ATP-BINDING CASSETTE SUB-FAMILY B MEMBER 6	molecular_function	1	GRANULARITY	curated	over-specific substrate class from the ABCB6 subfamily node	Unsupported and likely incorrect. The best current functional inference is transport of a pyoverdine precursor, not a lipid substrate.
REMOVE	retS	genes/PSEPK/retS/retS-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0071474	cellular hyperosmotic response	PTN009177399	PTHR45339	HYBRID SIGNAL TRANSDUCTION HISTIDINE KINASE J	PTHR45339:SF1	HYBRID SIGNAL TRANSDUCTION HISTIDINE KINASE J	biological_process	3	GENERIC_CONTEXT	curated	generic/unevidenced stress process on a T6SS-regulating hybrid kinase	No direct KT2440 experimental evidence for osmotic-response biology was identified, whereas direct gene-specific evidence exists for T6SS regulation. The hyperosmotic-response assignment likely reflects TreeGrafter transfer from related hybrid sensor kinases rather than organism-specific validation.
REMOVE	scpC	genes/PSEPK/scpC/scpC-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0003986	acetyl-CoA hydrolase activity	PTN002462025	PTHR43609	ACETYL-COA HYDROLASE	PTHR43609:SF1	ACETYL-COA HYDROLASE	molecular_function	1	GRANULARITY	heuristic	family-level propagation stated	TreeGrafter appears to have propagated the broad family hydrolase label. UniProt/InterPro also identify a succinate CoA-transferase family signature, and OpenScientist found a complete class-I CoA-transferase active site with unresolved short-chain substrate specificity rather than evidence for an a
REMOVE	sdhD	genes/PSEPK/sdhD/sdhD-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0017004	cytochrome complex assembly	PTN002446067	PTHR38689	SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR SUBUNIT	PTHR38689:SF1	SUCCINATE DEHYDROGENASE HYDROPHOBIC MEMBRANE ANCHOR SUBUNIT	biological_process	3	GENERIC_CONTEXT	curated	membership-derived assembly process on an anchoring subunit	UniProt supports SdhD as a membrane-anchoring subunit of succinate dehydrogenase with heme binding, but not as a factor that assembles cytochrome complexes. The annotation appears to over-interpret cytochrome b/heme membership as an assembly process.
REMOVE	trpC	genes/PSEPK/trpC/trpC-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0004640	phosphoribosylanthranilate isomerase activity	PTN002338157	PTHR22854	TRYPTOPHAN BIOSYNTHESIS PROTEIN	PTHR22854:SF2	INDOLE-3-GLYCEROL-PHOSPHATE SYNTHASE	molecular_function	1	GRANULARITY	curated	bifunctional TrpC/TrpF fusion node term on monofunctional IGPS	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
REMOVE	ubiX	genes/PSEPK/ubiX/ubiX-ai-review.yaml	Pseudomonas putida (strain ATCC 47054 / DSM 6125 / CFBP 8728 / NCIMB 11950 / KT2440)	GO:0016831	carboxy-lyase activity	PTN002458738	PTHR43374	FLAVIN PRENYLTRANSFERASE	PTHR43374:SF1	FLAVIN PRENYLTRANSFERASE PAD1, MITOCHONDRIAL	molecular_function	1	GRANULARITY	curated	outdated node term (Pad1 as decarboxylase) on the flavin prenyltransferase	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.