date: '2026-09-20' scope: TreeGrafter exemplars assigned to this review batch; includes every annotation in each gene genes: - gene: DESVH/Q72DT2 annotation_count: 7 all_annotations_reviewed: true annotations: - term_id: GO:0000104 term_label: succinate dehydrogenase activity evidence_type: IEA original_reference_id: GO_REF:0000118 previous_action: REMOVE action: REMOVE outcome: changed rationale: AprA has the APS-reductase substrate chemistry, AprA-specific domain assignment and sulfate-reduction pathway context, rather than succinate dehydrogenation. Existing OpenScientist and Falcon reports corroborate this distinction. Their assertion that a covalent FAD-binding histidine is universally necessary for all SDH/FRD catalysis is stronger than needed here and is not used as decisive proof. The incorrect function is established independently of whether the historical PANTHER graft position or ancestral term mapping caused it. - term_id: GO:0005886 term_label: plasma membrane evidence_type: IEA original_reference_id: GO_REF:0000118 previous_action: MODIFY action: ACCEPT outcome: changed rationale: Exact-strain membrane-preparation and reciprocal purification evidence supports a peripheral Qmo-associated pool. The broad GO term includes associated proteins. - term_id: GO:0009055 term_label: electron transfer activity evidence_type: IEA original_reference_id: GO_REF:0000118 previous_action: MARK_AS_OVER_ANNOTATED action: ACCEPT outcome: changed rationale: The current GO:0009055 definition includes directed electron transfer resulting in redox transformation during enzymatic reactions. AprB supplies the upstream Fe-S relay, but AprA performs FAD-dependent reduction of APS itself. Absence of Fe-S clusters in AprA does not exclude this broad molecular function; the prior review incorrectly restricted the term to carrier subunits. - term_id: GO:0009061 term_label: anaerobic respiration evidence_type: IEA original_reference_id: GO_REF:0000118 previous_action: MODIFY action: MODIFY outcome: retained rationale: 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. - term_id: GO:0050660 term_label: flavin adenine dinucleotide binding evidence_type: IEA original_reference_id: GO_REF:0000118 previous_action: ACCEPT action: ACCEPT outcome: retained rationale: FAD binding is well-established for AprA based on domain architecture (FAD-binding_2 domain) and functional characterization. The FAD cofactor is central to the catalytic mechanism of APS reduction. - term_id: GO:0009973 term_label: adenylyl-sulfate reductase activity evidence_type: IEA original_reference_id: GO_REF:0000003 previous_action: ACCEPT action: ACCEPT outcome: retained rationale: This is the primary molecular function of AprA, strongly supported by multiple lines of evidence including EC classification, domain architecture (IPR011803 AprA, TIGR02061), UniProt annotation, and extensive literature. - term_id: GO:0016491 term_label: oxidoreductase activity evidence_type: IEA original_reference_id: GO_REF:0000120 previous_action: ACCEPT action: ACCEPT outcome: retained rationale: While accurate, this is a high-level parent term that is redundant with the more specific GO:0009973. The annotation is technically correct based on the catalytic function of AprA in reducing APS. notes_file: genes/DESVH/Q72DT2/Q72DT2-notes.md gene_file: genes/DESVH/Q72DT2/Q72DT2-ai-review.yaml status: reviewed scope: full_gene outcome: changed changes: - term_id: GO:0009055 previous_action: MARK_AS_OVER_ANNOTATED action: ACCEPT - term_id: GO:0005886 previous_action: MODIFY action: ACCEPT intermediate_action: UNDECIDED evidence: existing_adjudications: - genes/DESVH/Q72DT2/Q72DT2-hypotheses/function-hypothesis-go-0000104/falcon.md - genes/DESVH/Q72DT2/Q72DT2-hypotheses/function-hypothesis-go-0000104/openscientist.md - genes/DESVH/Q72DT2/Q72DT2-hypotheses/function-hypothesis-go-0005886/openscientist.md notes_file: genes/DESVH/Q72DT2/Q72DT2-notes.md primary_localization: PMID:23842468 term_check: projects/TREEGRAFTER/rereview-2026-09-20/apra-membrane-term-check.json adjudication: status: incorporated provider: openscientist provider_job_id: 81dccdeb-fe21-441f-ac3c-3c52ef5efa6e final_action: ACCEPT second_opinion: [] findings: Membrane-preparation evidence supports the Qmo-associated pool. The report restriction of GO:0005886 to intrinsic membrane proteins is inconsistent with its definition and ancestry; exact graft topology and unavailable sequence CSV are not adopted. validation: command: just validate DESVH Q72DT2 result: passed warnings: - 'Advisory: core cytoplasm location has no original annotation row; no redundant NEW proposal added.' history_record: history/genes/DESVH/Q72DT2/2026-09-21T004740Z-claude-code-d72ad9.yaml history_validation: command: just validate-history history/genes/DESVH/Q72DT2/2026-09-21T004740Z-claude-code-d72ad9.yaml result: passed - gene: PSEPK/fcs annotation_count: 3 all_annotations_reviewed: true annotations: - term_id: GO:0006631 term_label: fatty acid metabolic process evidence_type: IEA original_reference_id: GO_REF:0000118 previous_action: MODIFY action: MODIFY outcome: changed rationale: 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 funnel into the beta-ketoadipate pathway. The correct biological process is ferulate catabolic process (GO:1901067). - term_id: GO:0031956 term_label: medium-chain fatty acid-CoA ligase activity evidence_type: IEA original_reference_id: GO_REF:0000118 previous_action: MODIFY action: MODIFY outcome: changed rationale: 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-CoA synthase activity (GO:0050563) is already annotated and is the appropriate replacement. Plaggenborg et al. (PMID:12764569) directly tested the KT2440 enzyme. Both existing adjudication reports support the aromatic-substrate assignment, but neither a narrow BLAST score advantage nor the PANTHER subfamily label proves the actual graft point was wrong. - term_id: GO:0050563 term_label: trans-feruloyl-CoA synthase activity evidence_type: IEA original_reference_id: GO_REF:0000003 previous_action: ACCEPT action: ACCEPT outcome: changed rationale: This is the precise, EC-based annotation for feruloyl-CoA synthetase (ATP + CoA + trans-ferulate -> feruloyl-CoA + AMP + diphosphate). It is consistent with the protein name, the AMP-binding/ANL domain architecture, and pathway evidence placing Fcs (PP_3356) at the ferulate -> feruloyl-CoA activation step in P. putida KT2440. Represents the core function of the gene. notes_file: genes/PSEPK/fcs/fcs-notes.md gene_file: genes/PSEPK/fcs/fcs-ai-review.yaml status: reviewed scope: full_gene outcome: changed changes: [] evidence: existing_adjudications: - genes/PSEPK/fcs/fcs-hypotheses/function-hypothesis-go-0031956/falcon.md - genes/PSEPK/fcs/fcs-hypotheses/function-hypothesis-go-0031956/openscientist.md notes_file: genes/PSEPK/fcs/fcs-notes.md adjudication: second_opinion: [] validation: command: just validate PSEPK fcs result: passed warnings: [] history_record: history/genes/PSEPK/fcs/2026-09-21T004740Z-claude-code-444077.yaml history_validation: command: just validate-history history/genes/PSEPK/fcs/2026-09-21T004740Z-claude-code-444077.yaml result: passed - gene: OCTVU/OCTS1 annotation_count: 5 all_annotations_reviewed: true annotations: - term_id: GO:0004364 term_label: glutathione transferase activity evidence_type: IEA original_reference_id: GO_REF:0000118 previous_action: MARK_AS_OVER_ANNOTATED action: MARK_AS_OVER_ANNOTATED outcome: changed rationale: Retain MARK_AS_OVER_ANNOTATED for propagation of an ancestral detoxifying GST function to a structural lens protein. Residual in-vitro catalysis is real and is not erased by this decision; its physiological importance for OCTS1 has not been demonstrated. The OctS4 study supports the family mechanism of enhanced GSH stabilization and reduced electrophilic-substrate catalysis, while the exact OCTS1-specific kinetic magnitude and residue effects remain inferred. Existing adjudications agree on structural co-option, but their categorical absence-of-function and essential-tryptophan language exceeds what is needed for this judgment. - term_id: GO:0006749 term_label: glutathione metabolic process evidence_type: IEA original_reference_id: GO_REF:0000118 previous_action: MARK_AS_OVER_ANNOTATED action: MARK_AS_OVER_ANNOTATED outcome: changed rationale: 'Retain the challenge to a physiological glutathione-metabolism assignment: the evidence supports a structural lens role and conserved GSH interaction, but does not establish appreciable OCTS1-specific glutathione turnover in vivo. The reported residual catalysis and homolog experiments are acknowledged rather than treated as absence of all chemistry.' - term_id: GO:0005212 term_label: structural constituent of eye lens evidence_type: TAS original_reference_id: PMID:7639695 previous_action: NEW action: NEW outcome: retained rationale: This is the primary molecular function of OCTS1. The protein has been co-opted from an ancestral GST enzyme to serve as a structural/refractive lens protein. Multiple studies confirm lens-specific expression and structural role. Although present in UniProt via keyword mapping, it is not in the GOA export and should be formally annotated. This is the most important annotation for this protein. - term_id: GO:0043295 term_label: glutathione binding evidence_type: ISS original_reference_id: PMID:27499004 previous_action: NEW action: NEW outcome: changed rationale: Retain the conservative GSH-binding proposal as an inferred conserved property of closely related S-crystallins. The 43-fold Km difference is an apparent kinetic parameter from OctS4, not a directly measured OCTS1 binding dissociation constant. A target-specific assay is still needed to establish OCTS1 affinity and stabilization quantitatively. - term_id: GO:0007601 term_label: visual perception evidence_type: NAS original_reference_id: PMID:17293312 previous_action: NEW action: NEW outcome: changed rationale: S-crystallins supply the refractive structure that focuses incoming light, which is direct structural participation in visual perception. A QuickGO comparator query on 2026-09-20 found the same process annotation on the lens structural proteins CRYAA (experimental) and CRYBA1 (IBA/NAS), supporting this use of the term. The squid radial-gradient evidence is homolog-level support for the octopus lens protein, not an OCTS1-specific perturbation assay. notes_file: genes/OCTVU/OCTS1/OCTS1-notes.md gene_file: genes/OCTVU/OCTS1/OCTS1-ai-review.yaml status: reviewed scope: full_gene outcome: changed changes: - field: author-proposed GO:0043295 evidence_type previous: IDA value: ISS reason: 2016 experiments tested OctS4 and its Q108F mutant; OCTS1 support is by homology. - field: description, core_functions and reference findings reason: Qualified homolog evidence and corrected nonverbatim quotations using cached full text. evidence: existing_adjudications: - genes/OCTVU/OCTS1/OCTS1-hypotheses/function-hypothesis-go-0004364/falcon.md - genes/OCTVU/OCTS1/OCTS1-hypotheses/function-hypothesis-go-0004364/openscientist.md notes_file: genes/OCTVU/OCTS1/OCTS1-notes.md adjudication: second_opinion: [] validation: command: just validate OCTVU OCTS1 result: passed warnings: - Available general deep-research files are not cited; focused existing adjudications and primary literature are cited. history_record: history/genes/OCTVU/OCTS1/2026-09-21T004740Z-claude-code-d15659.yaml history_validation: command: just validate-history history/genes/OCTVU/OCTS1/2026-09-21T004740Z-claude-code-d15659.yaml result: passed - gene: 9POAL/NCGR_LOCUS1270 annotation_count: 13 all_annotations_reviewed: true annotations: - term_id: GO:0042132 term_label: fructose 1,6-bisphosphate 1-phosphatase activity evidence_type: IEA original_reference_id: GO_REF:0000120 previous_action: ACCEPT action: ACCEPT outcome: retained rationale: Core enzymatic activity. Strong domain-based evidence from multiple sources (InterPro, PANTHER, HAMAP, Pfam PF00316). This is the primary molecular function of the protein. - term_id: GO:0016791 term_label: phosphatase activity evidence_type: IEA original_reference_id: GO_REF:0000002 previous_action: MARK_AS_OVER_ANNOTATED action: ACCEPT outcome: changed rationale: The specific FBPase activity does not invalidate this independently sourced broad InterPro annotation. ACCEPT reflects the same core catalytic function at broader granularity. - term_id: GO:0042578 term_label: phosphoric ester hydrolase activity evidence_type: IEA original_reference_id: GO_REF:0000002 previous_action: MARK_AS_OVER_ANNOTATED action: ACCEPT outcome: changed rationale: The broad InterPro activity is entailed by the defining enzymatic reaction. Coexistence with the more specific GO:0042132 is not over-annotation. - term_id: GO:0005975 term_label: carbohydrate metabolic process evidence_type: IEA original_reference_id: GO_REF:0000002 previous_action: MARK_AS_OVER_ANNOTATED action: ACCEPT outcome: changed rationale: The Calvin cycle supplies physiological context but does not make carbohydrate metabolic process false or peripheral. The enzyme itself catalyzes the reaction; this is not an indirect phenotype-based assignment. - term_id: GO:0005985 term_label: sucrose metabolic process evidence_type: IEA original_reference_id: GO_REF:0000117 previous_action: MODIFY action: UNDECIDED outcome: changed rationale: Chloroplast FBPase supplies and regulates carbon partitioning, whereas the best-established sucrose-synthesis reactions use the cytosolic paralog. Supplying precursors alone is not sufficient participation, but a different main compartment is not a negative functional assay. The named TreeGrafter reference is itself a chloroplast-associated sorghum protein, so the previous automatic cytosolic-paralog explanation is unproven. Preserve uncertainty about the actual physiological process boundary. - term_id: GO:0005986 term_label: sucrose biosynthetic process evidence_type: IEA original_reference_id: GO_REF:0000118 previous_action: REMOVE action: UNDECIDED outcome: retained rationale: The dominant Calvin-cycle role and separation from cytosolic FBPase are supported, but the previous absolute exclusion and claimed paralog misgraft were not established. Current PTN004269459 is the sorghum A0A1B6QP66 leaf, annotated to chloroplast/Calvin cycle and 96.85% identical across the full global alignment. Rice cytosolic-FBPase perturbation shows that paralog contributes to sucrose synthesis; it does not prove that all conditional contributions of this chloroplast homolog are absent. Direct pathway participation still needs clarification rather than being inferred simply from exported carbon. - term_id: GO:0006000 term_label: fructose metabolic process evidence_type: IEA original_reference_id: GO_REF:0000118 previous_action: MARK_AS_OVER_ANNOTATED action: UNDECIDED outcome: changed rationale: The report correctly separates fructose from its phosphorylated derivatives in the is_a hierarchy, but absence of an ancestor relation does not make pathways disjoint or require direct free-fructose turnover by every enzyme. QuickGO explicitly assigns this term to human FBP1/FBP2 with TAS and Dictyostelium fbp with IDA, and the F6P-process definition names fructose metabolism. Those comparators refute a blanket exclusion while not proving this chloroplast enzyme contributes to every fructose pathway. Retain UNDECIDED pending physiological and curator-scope clarification. - term_id: GO:0006002 term_label: fructose 6-phosphate metabolic process evidence_type: IEA original_reference_id: GO_REF:0000118 previous_action: MARK_AS_OVER_ANNOTATED action: ACCEPT outcome: changed rationale: GO:0006002 covers chemical reactions involving F6P without requiring a cytosolic location. Chloroplast Calvin-cycle chemistry therefore satisfies the term. The previous review incorrectly treated absent pathway specificity as over-annotation. - term_id: GO:0006094 term_label: gluconeogenesis evidence_type: IEA original_reference_id: GO_REF:0000118 previous_action: REMOVE action: UNDECIDED outcome: changed rationale: GO:0006094 describes glucose formation from noncarbohydrate precursors and does not impose the prior asserted cytosolic-only location. Chloroplast targeting and redox regulation distinguish this enzyme from the canonical cytosolic paralog, but neither is a direct demonstration of loss of all gluconeogenic participation. Shared FBPase chemistry alone also does not establish the complete pathway role. The named TreeGrafter reference is a close chloroplast-associated sorghum homolog; the actual query insertion and lineage-specific loss have not been established. - term_id: GO:0030388 term_label: fructose 1,6-bisphosphate metabolic process evidence_type: IEA original_reference_id: GO_REF:0000120 previous_action: KEEP_AS_NON_CORE action: ACCEPT outcome: changed rationale: This substrate-centered process directly describes the work performed by the enzyme and is core. Calvin-cycle context is complementary; it does not relegate FBP metabolism to a non-core function. - term_id: GO:0005737 term_label: cytoplasm evidence_type: IEA original_reference_id: GO_REF:0000118 previous_action: REMOVE action: ACCEPT outcome: changed rationale: GO:0005737 includes subcellular structures outside the nucleus and plasma membrane, including plastids. The previous REMOVE conflated cytoplasm with cytosol. Retain this broad localization while retaining the separate challenge to GO:0005829 cytosol. - term_id: GO:0005829 term_label: cytosol evidence_type: IEA original_reference_id: GO_REF:0000118 previous_action: REMOVE action: UNDECIDED outcome: changed rationale: The predicted transit sequence, conserved redox-regulatory insertion and close chloroplast homologs strongly support stromal localization. They do not by themselves establish exclusive import or exclude a conditional cytosolic pool. The source PTN leaf maps to the closely matching chloroplast-associated sorghum homolog, contradicting the assumption that TreeGrafter necessarily selected a cytosolic paralog. Retain the compartment conflict as UNDECIDED rather than asserting a demonstrated negative localization. - term_id: GO:0009507 term_label: chloroplast evidence_type: IEA original_reference_id: GO_REF:0000044 previous_action: MODIFY action: MODIFY outcome: retained rationale: Correct but could be more specific. The enzyme operates in the chloroplast stroma (GO:0009570), which is the site of the Calvin cycle reactions. Stromal localization is supported by immunolocalization of the related cpFBPaseII and by the enzyme's pH-dependent regulation (active at stromal alkaline pH ~8.0 in light). notes_file: genes/9POAL/NCGR_LOCUS1270/NCGR_LOCUS1270-notes.md gene_file: genes/9POAL/NCGR_LOCUS1270/NCGR_LOCUS1270-ai-review.yaml status: reviewed scope: full_gene outcome: Focused report incorporated critically; actual chloroplast source identity checked and unsupported categorical pathway/location exclusions relaxed. changes: - term_id: GO:0016791 previous_action: MARK_AS_OVER_ANNOTATED action: ACCEPT - term_id: GO:0042578 previous_action: MARK_AS_OVER_ANNOTATED action: ACCEPT - term_id: GO:0005975 previous_action: MARK_AS_OVER_ANNOTATED action: ACCEPT - term_id: GO:0006000 previous_action: MARK_AS_OVER_ANNOTATED action: UNDECIDED - term_id: GO:0006002 previous_action: MARK_AS_OVER_ANNOTATED action: ACCEPT - term_id: GO:0030388 previous_action: KEEP_AS_NON_CORE action: ACCEPT - term_id: GO:0005737 previous_action: REMOVE action: ACCEPT evidence: existing_adjudications: [] notes_file: genes/9POAL/NCGR_LOCUS1270/NCGR_LOCUS1270-notes.md bioinformatics: genes/9POAL/NCGR_LOCUS1270/NCGR_LOCUS1270-bioinformatics/RESULTS.md adjudication: status: incorporated job_id: 896d9254-bf61-4541-9b32-71fc7f2e7fc6 report: file:9POAL/NCGR_LOCUS1270/NCGR_LOCUS1270-hypotheses/function-hypothesis-go-0006000/openscientist.md verdict_assessment: 'DISPUTED: no is_a relation does not establish disjointness or require free-fructose substrate; same-enzyme curated comparators and actual source identity were omitted.' remaining_expert_questions: - Physiological process boundaries for fructose/sucrose/gluconeogenesis. - Conditional cytosolic pool and actual TreeGrafter query insertion. duplicate_runs_launched: false validation: command: just validate 9POAL NCGR_LOCUS1270 result: PASS warnings: - Nonblocking core Calvin-cycle coverage warning. history_record: history/genes/9POAL/NCGR_LOCUS1270/2026-09-21T004741Z-claude-code-29de6b.yaml history_validation: command: just validate-history history/genes/9POAL/NCGR_LOCUS1270/2026-09-21T004741Z-claude-code-29de6b.yaml result: passed followup_changes: - term_id: GO:0005985 from_action: MODIFY action: UNDECIDED - term_id: GO:0005986 from_action: REMOVE action: UNDECIDED - term_id: GO:0006094 from_action: REMOVE action: UNDECIDED - term_id: GO:0005829 from_action: REMOVE action: UNDECIDED followup_history_record: history/genes/9POAL/NCGR_LOCUS1270/2026-09-21T030225Z-codex-35c425.yaml followup_history_validation: 'PASS: just validate-history history/genes/9POAL/NCGR_LOCUS1270/2026-09-21T030225Z-codex-35c425.yaml' validation: gene_reviews: All four passed just validate; OCTS1 has one advisory deep-research citation warning. history_records: All four passed just validate-history. scope: All 28 annotation rows across four genes were assessed; includes three existing NEW proposals for OCTS1.