date: '2026-09-20' scope: Seven remaining featured TreeGrafter exemplars; all annotation rows including earlier NEW proposals genes: - gene: ECOLX/mcr-1 gene_file: genes/ECOLX/mcr-1/mcr-1-ai-review.yaml status: reviewed scope: full_gene outcome: changed annotation_count: 9 annotations: - term_id: GO:0005886 term_label: plasma membrane evidence_type: IEA original_reference_id: GO_REF:0000120 previous_action: ACCEPT action: ACCEPT outcome: retained rationale: Correct and specific cellular location; consistent with the experimental localization (PMID:27655155) and the UniProt 'Cell inner membrane' annotation. - term_id: GO:0009244 term_label: lipopolysaccharide core region biosynthetic process evidence_type: IEA original_reference_id: GO_REF:0000118 previous_action: MARK_AS_OVER_ANNOTATED action: MARK_AS_OVER_ANNOTATED outcome: retained rationale: '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.' - term_id: GO:0016020 term_label: membrane evidence_type: IEA original_reference_id: GO_REF:0000002 previous_action: MODIFY action: ACCEPT outcome: changed rationale: Membrane is a valid broad description of the experimentally supported plasma-membrane location. A more specific annotation does not make this InterPro annotation incorrect. - term_id: GO:0016772 term_label: transferase activity, transferring phosphorus-containing groups evidence_type: IEA original_reference_id: GO_REF:0000002 previous_action: MODIFY action: ACCEPT outcome: changed rationale: This broad transferase activity is chemically entailed by the established lipid A modification reaction and is a current GO ancestor of GO:0043838. Retain it alongside the more specific function. - term_id: GO:0016776 term_label: phosphotransferase activity, phosphate group as acceptor evidence_type: IEA original_reference_id: GO_REF:0000118 previous_action: MODIFY action: MODIFY outcome: changed rationale: 'Retain MODIFY as a refinement to GO:0043838, not a finding that phosphoethanolamine transfer is false. Existing reports disagree: Falcon treats the phosphate-acceptor wording as applicable, whereas OpenScientist emphasizes EC 2.7.8.43 and the substituted-phosphate branch. Current QuickGO places GO:0043838 under GO:0016780 and GO:0016772, not GO:0016776. The broad text alone does not establish a wrong substrate reaction or a wrong graft position.' - term_id: GO:0005886 term_label: plasma membrane evidence_type: EXP original_reference_id: PMID:27655155 previous_action: ACCEPT action: ACCEPT outcome: retained rationale: Experimental evidence for the bacterial inner (plasma) membrane location; this is the core cellular component for the enzyme. - term_id: GO:0043838 term_label: phosphatidylethanolamine:Kdo2-lipid A phosphoethanolamine transferase activity evidence_type: IDA original_reference_id: PMID:27655155 previous_action: NEW action: NEW outcome: retained rationale: Replaces the two over-general IEA MF terms with the specific, structurally and biochemically supported activity. Directly evidenced by the MCR-1 structure/mechanism papers and EC 2.7.8.43. - term_id: GO:0046677 term_label: response to antibiotic evidence_type: IMP original_reference_id: PMID:26603172 previous_action: NEW action: NEW outcome: retained rationale: The biological process in which MCR-1 participates is antibiotic (colistin) resistance via target modification; this is the accurate BP, replacing the mis-propagated GO:0009244. - term_id: GO:0008270 term_label: zinc ion binding evidence_type: IDA original_reference_id: PMID:27655155 previous_action: NEW action: NEW outcome: retained rationale: Structurally supported zinc binding at the active site; the zinc is mechanistically required and is more informative than the keyword-derived 'metal ion binding'. changes: - term_id: GO:0016020 previous_action: MODIFY action: ACCEPT - term_id: GO:0016772 previous_action: MODIFY action: ACCEPT evidence: existing_adjudications: - genes/ECOLX/mcr-1/mcr-1-hypotheses/function-hypothesis-go-0016776/falcon.md - genes/ECOLX/mcr-1/mcr-1-hypotheses/function-hypothesis-go-0016776/openscientist.md notes_file: genes/ECOLX/mcr-1/mcr-1-notes.md adjudication: needed: null duplicate_runs_launched: false validation: command: just validate ECOLX mcr-1 result: passed history_record: history/genes/ECOLX/mcr-1/2026-09-21T010056Z-codex-57d196.yaml history_validation: command: just validate-history history/genes/ECOLX/mcr-1/2026-09-21T010056Z-codex-57d196.yaml result: passed source_rows_preserved: true final_annotation_count: 9 - gene: SACEN/eryAIII gene_file: genes/SACEN/eryAIII/eryAIII-ai-review.yaml status: reviewed scope: full_gene outcome: changed annotation_count: 8 annotations: - term_id: GO:0004312 term_label: fatty acid synthase activity evidence_type: IEA original_reference_id: GO_REF:0000118 previous_action: MODIFY action: MODIFY outcome: changed rationale: The characterized assembly-line product is 6-deoxyerythronolide B, a macrolide polyketide. This supports a polyketide-synthase refinement of the fatty-acid-synthase assignment. Shared acyl-carrier/condensation chemistry is real; absence of DH/ER domains from this particular subunit is not, by itself, a universal discriminator of all fatty acid synthases. - term_id: GO:0004315 term_label: 3-oxoacyl-[acyl-carrier-protein] synthase activity evidence_type: IEA original_reference_id: GO_REF:0000002 previous_action: MODIFY action: MODIFY outcome: changed rationale: The current GO:0004315 definition specifies malonyl-ACP condensation. DEBS modules 5 and 6 use methylmalonyl-derived units during erythronolide assembly, so retain a substrate-aware refinement to polyketide synthase activity. The distinction is the defined reaction, not a rule excluding all PKS domains merely because the term is familiar from fatty-acid synthesis. - term_id: GO:0006633 term_label: fatty acid biosynthetic process evidence_type: IEA original_reference_id: GO_REF:0000120 previous_action: MODIFY action: MODIFY outcome: retained rationale: Wrong process. Replace with GO:1901115 (erythromycin biosynthetic process). - term_id: GO:0016740 term_label: transferase activity evidence_type: IEA original_reference_id: GO_REF:0000002 previous_action: ACCEPT action: ACCEPT outcome: retained rationale: Accurate (general) molecular function. - term_id: GO:0016746 term_label: acyltransferase activity evidence_type: IEA original_reference_id: GO_REF:0000002 previous_action: ACCEPT action: ACCEPT outcome: retained rationale: Correct component (AT-domain) molecular function. - term_id: GO:0031177 term_label: phosphopantetheine binding evidence_type: IEA original_reference_id: GO_REF:0000120 previous_action: ACCEPT action: ACCEPT outcome: retained rationale: Correct component (ACP-domain) molecular function. - term_id: GO:0033068 term_label: macrolide biosynthetic process evidence_type: IEA original_reference_id: GO_REF:0000117 previous_action: ACCEPT action: ACCEPT outcome: retained rationale: Accurate biological process. - term_id: GO:0047879 term_label: erythronolide synthase activity evidence_type: IEA original_reference_id: GO_REF:0000120 previous_action: ACCEPT action: ACCEPT outcome: retained rationale: Correct, specific molecular function for the DEBS subunit. changes: [] evidence: existing_adjudications: - genes/SACEN/eryAIII/eryAIII-hypotheses/function-hypothesis-go-0004312/falcon.md - genes/SACEN/eryAIII/eryAIII-hypotheses/function-hypothesis-go-0004312/openscientist.md notes_file: genes/SACEN/eryAIII/eryAIII-notes.md adjudication: needed: null duplicate_runs_launched: false validation: command: just validate SACEN eryAIII result: passed history_record: history/genes/SACEN/eryAIII/2026-09-21T010059Z-codex-ecf8a0.yaml history_validation: command: just validate-history history/genes/SACEN/eryAIII/2026-09-21T010059Z-codex-ecf8a0.yaml result: passed source_rows_preserved: true final_annotation_count: 8 - gene: NICAT/NaPMT3 gene_file: genes/NICAT/NaPMT3/NaPMT3-ai-review.yaml status: reviewed scope: full_gene outcome: changed annotation_count: 7 annotations: - term_id: GO:0003824 term_label: catalytic activity evidence_type: IEA original_reference_id: GO_REF:0000002 previous_action: MARK_AS_OVER_ANNOTATED action: ACCEPT outcome: changed rationale: Catalytic activity is an entailed broad molecular function of the accepted putrescine N-methyltransferase activity. Its generality is not over-annotation. - term_id: GO:0004766 term_label: spermidine synthase activity evidence_type: IEA original_reference_id: GO_REF:0000118 previous_action: REMOVE action: REMOVE outcome: changed rationale: PMT proteins evolved from spermidine synthase but now catalyze putrescine N-methylation in alkaloid biosynthesis. The target carries the PMT-specific IPR025803/PROSITE assignment and the SAM-dependent methylation reaction. The existing reports support a PMT-versus-SPDS functional divergence, not loss of catalytic function. - term_id: GO:0005829 term_label: cytosol evidence_type: IEA original_reference_id: GO_REF:0000118 previous_action: KEEP_AS_NON_CORE action: ACCEPT outcome: changed rationale: The TreeGrafter localization is compatible with the PMT family and there is no target-specific evidence of a different compartment. Less detailed study of PMT3 than PMT1 does not make the same enzymatic location non-core. - term_id: GO:0008295 term_label: spermidine biosynthetic process evidence_type: IEA original_reference_id: GO_REF:0000118 previous_action: REMOVE action: REMOVE outcome: retained rationale: PMT3 channels putrescine into alkaloid biosynthesis rather than spermidine biosynthesis. - term_id: GO:0009753 term_label: response to jasmonic acid evidence_type: IEA original_reference_id: GO_REF:0000117 previous_action: KEEP_AS_NON_CORE action: KEEP_AS_NON_CORE outcome: retained rationale: The annotation fits nicotine defense-pathway context but is less central than the catalytic and pathway assignments. - term_id: GO:0030750 term_label: putrescine N-methyltransferase activity evidence_type: IEA original_reference_id: GO_REF:0000120 previous_action: ACCEPT action: ACCEPT outcome: retained rationale: UniProt explicitly assigns the putrescine methyltransferase reaction to this root-expressed paralog. - term_id: GO:0042179 term_label: nicotine biosynthetic process evidence_type: IEA original_reference_id: GO_REF:0000041 previous_action: KEEP_AS_NON_CORE action: ACCEPT outcome: changed rationale: UniProt assigns PMT3 to the putrescine-to-N-methylputrescine step of nicotine biosynthesis; its PMT-specific InterPro signature and root expression support that inference. Uncertainty about relative flux contribution compared with PMT1 paralogs does not make the same pathway activity non-core. changes: - term_id: GO:0003824 previous_action: MARK_AS_OVER_ANNOTATED action: ACCEPT - term_id: GO:0005829 previous_action: KEEP_AS_NON_CORE action: ACCEPT - term_id: GO:0042179 previous_action: KEEP_AS_NON_CORE action: ACCEPT evidence: existing_adjudications: - genes/NICAT/NaPMT3/NaPMT3-hypotheses/function-hypothesis-go-0004766/falcon.md - genes/NICAT/NaPMT3/NaPMT3-hypotheses/function-hypothesis-go-0004766/openscientist.md notes_file: genes/NICAT/NaPMT3/NaPMT3-notes.md adjudication: needed: null duplicate_runs_launched: false validation: command: just validate NICAT NaPMT3 result: passed warnings: - General deep-research file not cited; existing focused reports and primary evidence are cited. history_record: history/genes/NICAT/NaPMT3/2026-09-21T010103Z-codex-5121e5.yaml history_validation: command: just validate-history history/genes/NICAT/NaPMT3/2026-09-21T010103Z-codex-5121e5.yaml result: passed source_rows_preserved: true final_annotation_count: 7 - gene: DOROP/ADAR2 gene_file: genes/DOROP/ADAR2/ADAR2-ai-review.yaml status: reviewed scope: full_gene outcome: changed annotation_count: 13 annotations: - term_id: GO:0003723 term_label: RNA binding evidence_type: IEA original_reference_id: GO_REF:0000120 previous_action: KEEP_AS_NON_CORE action: ACCEPT outcome: changed rationale: The broad RNA-binding term is entailed by directly supported dsRNA binding. It is part of the core substrate-recognition mechanism, not peripheral simply because a more specific binding annotation also exists. - term_id: GO:0003725 term_label: double-stranded RNA binding evidence_type: IEA original_reference_id: GO_REF:0000118 previous_action: ACCEPT action: ACCEPT outcome: retained rationale: dsRNA binding is a core molecular function of sqADAR2, demonstrated directly using recombinant protein with quantitative binding assays. The three dsRBD architecture of sqADAR2a is a defining and unique feature of this enzyme. This is at the right level of specificity for the binding function. - term_id: GO:0003726 term_label: double-stranded RNA adenosine deaminase activity evidence_type: IEA original_reference_id: GO_REF:0000118 previous_action: ACCEPT action: ACCEPT outcome: retained rationale: This is the defining catalytic activity of sqADAR2 and the most important molecular function annotation. It has been demonstrated directly using recombinant enzyme on multiple substrates, with quantitative activity data. The term is at exactly the right level of specificity. - term_id: GO:0004000 term_label: adenosine deaminase activity evidence_type: IEA original_reference_id: GO_REF:0000002 previous_action: MODIFY action: MODIFY outcome: retained rationale: GO:0004000 (adenosine deaminase activity) describes the deamination of free adenosine, which is the activity of ADA enzymes, not ADAR enzymes. ADAR2 specifically deaminates adenosine residues within double-stranded RNA. The correct term GO:0003726 is already annotated, so this annotation should be replaced to avoid confusion between ADA and ADAR activities. - term_id: GO:0005634 term_label: nucleus evidence_type: IEA original_reference_id: GO_REF:0000120 previous_action: ACCEPT action: ACCEPT outcome: retained rationale: Nuclear localization is well-supported for ADAR2 enzymes generally, as co-transcriptional editing of pre-mRNAs occurs in the nucleus. While sqADAR2 is also found in the cytoplasm, nuclear localization remains valid. - term_id: GO:0005730 term_label: nucleolus evidence_type: IEA original_reference_id: GO_REF:0000118 previous_action: UNDECIDED action: UNDECIDED outcome: changed rationale: Retain UNDECIDED because the available squid localization evidence resolves nucleus versus cytoplasm but not nucleolus. Vertebrate nucleolar localization can support a phylogenetic hypothesis; missing target-specific microscopy alone is not a refutation. An explicit comparison of nucleolar-targeting determinants would help assess this prediction. - term_id: GO:0005737 term_label: cytoplasm evidence_type: IEA original_reference_id: GO_REF:0000118 previous_action: ACCEPT action: ACCEPT outcome: retained rationale: Cytoplasmic localization is directly demonstrated in squid neurons, where sqADAR2 is found in the axoplasm and is catalytically active. This represents a significant finding that RNA editing occurs outside the nucleus in squid. The term is appropriate. - term_id: GO:0006382 term_label: adenosine to inosine editing evidence_type: IEA original_reference_id: GO_REF:0000118 previous_action: ACCEPT action: ACCEPT outcome: retained rationale: A-to-I editing is the defining biological process for sqADAR2. This is supported by extensive direct evidence from multiple studies using recombinant protein assays and transcriptome-wide editing profiling. The term is at exactly the right level of specificity. - term_id: GO:0006396 term_label: RNA processing evidence_type: IEA original_reference_id: GO_REF:0000120 previous_action: KEEP_AS_NON_CORE action: ACCEPT outcome: changed rationale: The broad process describes the same direct catalytic work as the accepted A-to-I editing annotation. Its generality is not evidence of a non-core role. - term_id: GO:0008251 term_label: tRNA-specific adenosine deaminase activity evidence_type: IEA original_reference_id: GO_REF:0000118 previous_action: REMOVE action: REMOVE outcome: changed rationale: 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 with tRNA editing activity. This is a phylogenetic transfer error likely due to the shared deaminase domain superfamily between ADARs and ADATs. The existing OpenScientist report supports the three-dsRBD architecture, while Falcon incorrectly labels C1JAR3 as the two-dsRBD sqADAR2b variant. The cached 786-aa sequence has three dsRNA-binding domains and is consistent with sqADAR2a. Functional divergence is supported, but no exact historical graft error is established from domain architecture alone. - term_id: GO:0016556 term_label: mRNA modification evidence_type: NAS original_reference_id: PMID:25569156 previous_action: NEW action: NEW outcome: retained rationale: mRNA modification (GO:0016556) captures the specific substrate class (mRNA) that sqADAR2 acts on. While GO:0006382 (adenosine to inosine editing) is the most specific process term, mRNA modification highlights that the primary biological role of sqADAR2 is to modify mRNAs encoding proteins, as opposed to editing structural RNAs or tRNAs. - term_id: GO:0008270 term_label: zinc ion binding evidence_type: NAS original_reference_id: PMID:37342458 previous_action: NEW action: NEW outcome: retained rationale: Zinc ion binding is an inherent property of the ADAR catalytic deaminase domain. The UniProt entry lists zinc binding as a keyword. While metal ion binding (GO:0046872) is annotated in the UniProt GO cross-references, the more specific zinc ion binding term better captures the biochemistry of the ADAR active site. - term_id: GO:1904115 term_label: axon cytoplasm evidence_type: NAS original_reference_id: PMID:32201888 previous_action: NEW action: NEW outcome: retained rationale: Axon cytoplasm localization is directly demonstrated for sqADAR2 in the squid giant axon system. This is a key finding that distinguishes sqADAR2 function from the canonical nuclear-only editing paradigm. The term GO:1904115 (axon cytoplasm) is more specific than GO:0005737 (cytoplasm) and accurately captures the demonstrated localization. changes: - term_id: GO:0003723 previous_action: KEEP_AS_NON_CORE action: ACCEPT - term_id: GO:0006396 previous_action: KEEP_AS_NON_CORE action: ACCEPT evidence: existing_adjudications: - genes/DOROP/ADAR2/ADAR2-hypotheses/function-hypothesis-go-0008251/falcon.md - genes/DOROP/ADAR2/ADAR2-hypotheses/function-hypothesis-go-0008251/openscientist.md notes_file: genes/DOROP/ADAR2/ADAR2-notes.md adjudication: needed: Nucleolar localization remains UNDECIDED; functional ADAR-vs-ADAT hypothesis already has two reports. duplicate_runs_launched: false validation: command: just validate DOROP ADAR2 result: passed warnings: - General deep-research file not cited; existing focused reports and primary evidence are cited. history_record: history/genes/DOROP/ADAR2/2026-09-21T010105Z-codex-a21475.yaml history_validation: command: just validate-history history/genes/DOROP/ADAR2/2026-09-21T010105Z-codex-a21475.yaml result: passed source_rows_preserved: true final_annotation_count: 13 - gene: NICAT/NaUGT1_candidate_UGT85A2_0 gene_file: genes/NICAT/NaUGT1_candidate_UGT85A2_0/NaUGT1_candidate_UGT85A2_0-ai-review.yaml status: reviewed scope: full_gene outcome: Gene-level nicotine function established from primary supplementary sequences and assays; report categorical refutation rejected with reproducible evidence. Alternative substrate activities remain unresolved. annotation_count: 6 annotations: - term_id: GO:0008194 term_label: UDP-glycosyltransferase activity evidence_type: IEA original_reference_id: GO_REF:0000002 previous_action: MODIFY action: ACCEPT outcome: changed rationale: UDP-glycosyltransferase activity is a valid broad parent of the accepted UDP-glucosyltransferase function. The more specific donor assignment does not invalidate this broad InterPro inference. - term_id: GO:0035251 term_label: UDP-glucosyltransferase activity evidence_type: IEA original_reference_id: GO_REF:0000117 previous_action: ACCEPT action: MODIFY outcome: retained rationale: GO:0050139 already exists for this exact reaction. The Cell 2026 NaUGT1 assay/perturbation primers map to the g26396 locus, and its primer-compatible extended ORF contains the complete A0A2H4GSI3 sequence. Independent tobacco UGT1 supplements explicitly map the assayed N-glucosyltransferase to a close homolog (466 identities across 485 alignment columns). This establishes gene-level function; the retrieved assays do not directly test the isolated 485-aa database form. Narrow the generic MF using the existing term rather than proposing a duplicate ontology term. - term_id: GO:0080043 term_label: quercetin 3-O-glucosyltransferase activity evidence_type: IEA original_reference_id: GO_REF:0000118 previous_action: REMOVE action: UNDECIDED outcome: changed rationale: Primary 2026 data support nicotinate N-glucosylation at the mapped g26396 locus, with a documented construct-boundary caveat. They do not assay every alternative acceptor. Neither the positive nicotine function nor sequence-family distance establishes that quercetin or 7-deoxyloganetic acid cannot also be glucosylated. The earlier reports wrongly used missing assays and automated homolog names as negative biochemical evidence. Retain the source assertion for substrate-panel adjudication rather than asserting a negative function. - term_id: GO:0080044 term_label: quercetin 7-O-glucosyltransferase activity evidence_type: IEA original_reference_id: GO_REF:0000118 previous_action: REMOVE action: UNDECIDED outcome: changed rationale: Primary 2026 data support nicotinate N-glucosylation at the mapped g26396 locus, with a documented construct-boundary caveat. They do not assay every alternative acceptor. Neither the positive nicotine function nor sequence-family distance establishes that quercetin or 7-deoxyloganetic acid cannot also be glucosylated. The earlier reports wrongly used missing assays and automated homolog names as negative biochemical evidence. Retain the source assertion for substrate-panel adjudication rather than asserting a negative function. - term_id: GO:0102970 term_label: 7-deoxyloganetic acid glucosyltransferase activity evidence_type: IEA original_reference_id: GO_REF:0000003 previous_action: MARK_AS_OVER_ANNOTATED action: UNDECIDED outcome: changed rationale: Primary 2026 data support nicotinate N-glucosylation at the mapped g26396 locus, with a documented construct-boundary caveat. They do not assay every alternative acceptor. Neither the positive nicotine function nor sequence-family distance establishes that quercetin or 7-deoxyloganetic acid cannot also be glucosylated. The earlier reports wrongly used missing assays and automated homolog names as negative biochemical evidence. Retain the source assertion for substrate-panel adjudication rather than asserting a negative function. - term_id: GO:0042179 term_label: nicotine biosynthetic process evidence_type: IDA original_reference_id: PMID:41928514 previous_action: NEW action: NEW outcome: reinstated_author_proposal_with_primary_evidence rationale: Reinstate the prior author proposal with primary biochemical evidence and verified gene-level identity rather than the earlier notes-only TAS. NaUGT1 itself catalyzes an on-pathway reaction, established by recombinant assay and pathway reconstruction, independently of knockout necessity evidence. Supplemental primers map to g26396; the inferred N-terminal extension relative to the cached protein is documented, and no unverified isoform identifier is invented. QuickGO confirms the process definition/parents and analogous annotations on PMT1, PMT3, QPT2 and A622. No redundant process ancestor/descendant or GO-CAM assignment exists on this target. changes: - term_id: GO:0008194 previous_action: MODIFY action: ACCEPT - term_id: GO:0080043 previous_action: REMOVE action: UNDECIDED - term_id: GO:0080044 previous_action: REMOVE action: UNDECIDED - term_id: GO:0102970 previous_action: MARK_AS_OVER_ANNOTATED action: UNDECIDED - term_id: GO:0042179 previous_action: NEW action: WITHDRAWN reason: Exact-target nicotine function remains unresolved; retain hypothesis/evidence in notes and suggested_questions pending focused mapping adjudication. evidence: existing_adjudications: - genes/NICAT/NaUGT1_candidate_UGT85A2_0/NaUGT1_candidate_UGT85A2_0-hypotheses/function-hypothesis-go-0080043/falcon.md - genes/NICAT/NaUGT1_candidate_UGT85A2_0/NaUGT1_candidate_UGT85A2_0-hypotheses/function-hypothesis-go-0080043/openscientist.md - genes/NICAT/NaUGT1_candidate_UGT85A2_0/NaUGT1_candidate_UGT85A2_0-hypotheses/naugt1-candidate-identity-and-nicotinate-glucosylation/openscientist.md notes_file: genes/NICAT/NaUGT1_candidate_UGT85A2_0/NaUGT1_candidate_UGT85A2_0-notes.md primary_references: - PMID:42151135 - PMID:41928514 - PMID:31611893 bioinformatics: genes/NICAT/NaUGT1_candidate_UGT85A2_0/NaUGT1_candidate_UGT85A2_0-bioinformatics/RESULTS.md adjudication: status: incorporated job_id: a85d6e42-5653-4e27-a7f7-7c4db18ffd6a verdict_assessment: DISPUTED; pathway-exclusion finding OVERTURNED by primary 2026 reconstitution. findings_incorporated: - Exact tobacco UGT1 mapping A0A1S3YWH6/Nitab4.5_0006222g0020 from original supplemental tables; assayed 479-aa sequence globally 96.08% identical to target across all 485 columns. - Cell NaUGT1 primers map to the same g26396 genomic locus; inferred 530-aa construct contains complete 485-aa target unchanged after 45-aa extension. - Report O-versus-N family exclusion and storage-only pathway model contradicted by two 2026 primaries; plant nicotinate N-GTs already characterized in PMID:31611893. - Artifact average linkage mislabeled neighbor joining; identity traceback terminal overhang issue; independently recomputed published construct instead. - The positive nicotinate reaction does not exclude promiscuous alternative substrates; three source-specific MF claims remain UNDECIDED. duplicate_runs_launched: false remaining_expert_questions: - Native initiation site and activity of isolated 485-aa form. - Quantified quercetin/iridoid substrate panel. validation: command: just validate NICAT NaUGT1_candidate_UGT85A2_0 result: passed warnings: - 'Uncited Falcon annotation support: primary 2026 evidence supersedes its unresolved mapping; report retained with DISPUTED assessment.' final_annotation_count: 6 history_record: history/genes/NICAT/NaUGT1_candidate_UGT85A2_0/2026-09-21T010107Z-codex-0fd609.yaml history_validation: command: just validate-history history/genes/NICAT/NaUGT1_candidate_UGT85A2_0/2026-09-21T010107Z-codex-0fd609.yaml result: passed source_rows_preserved: true followup_changes: - term_id: GO:0035251 from_action: ACCEPT action: MODIFY replacement: GO:0050139 reason: Exact existing MF verified; primary assays mapped to g26396. - term_id: GO:0042179 from_action: WITHDRAWN action: NEW reason: Reinstated using primary IDA and independently verified locus identity, preserving 485-aa construct caveat. - section: proposed_new_terms change: Removed duplicate nicotinate N-glucosyltransferase proposal; GO:0050139 already exists. followup_history_record: history/genes/NICAT/NaUGT1_candidate_UGT85A2_0/2026-09-21T025359Z-codex-4b25d4.yaml followup_history_validation: passed - gene: PSEPK/aceK gene_file: genes/PSEPK/aceK/aceK-ai-review.yaml status: reviewed scope: full_gene outcome: changed annotation_count: 10 annotations: - term_id: GO:0004721 term_label: phosphoprotein phosphatase activity evidence_type: IEA original_reference_id: GO_REF:0000118 previous_action: MODIFY action: ACCEPT outcome: changed rationale: Both existing adjudications support phosphoprotein phosphatase activity in substance. A more specific substrate term is useful in the core summary, but its availability does not make the TreeGrafter parent assertion biologically incorrect. - term_id: GO:0005524 term_label: ATP binding evidence_type: IEA original_reference_id: GO_REF:0000120 previous_action: MARK_AS_OVER_ANNOTATED action: ACCEPT outcome: changed rationale: The UniProt record explicitly annotates ATP-binding residues, and the characterized AceK structure contains ATP. This functional ligand interaction is real and core; coexistence with kinase activity is not over-annotation. - term_id: GO:0005737 term_label: cytoplasm evidence_type: IEA original_reference_id: GO_REF:0000120 previous_action: ACCEPT action: ACCEPT outcome: retained rationale: UniProt annotates the cytoplasmic location and this is consistent with the function of a soluble metabolic regulatory enzyme. - term_id: GO:0006006 term_label: glucose metabolic process evidence_type: IEA original_reference_id: GO_REF:0000002 previous_action: MARK_AS_OVER_ANNOTATED action: MARK_AS_OVER_ANNOTATED outcome: changed rationale: Glucose-versus-acetate growth changes the AceK/IDH regulatory state. That observation supports metabolic regulation but does not itself establish a glucose-specific metabolic pathway role, since TCA and glyoxylate partitioning also concerns other carbon sources. Retain the over-annotation judgment with this scope distinction, without claiming that AceK is inactive whenever cells grow on glucose. - term_id: GO:0006097 term_label: glyoxylate cycle evidence_type: IEA original_reference_id: GO_REF:0000104 previous_action: ACCEPT action: ACCEPT outcome: retained rationale: AceK enables flux through the glyoxylate shunt by inactivating IDH, partitioning isocitrate toward isocitrate lyase and malate synthase. This is a defining biological role of the enzyme. - term_id: GO:0006099 term_label: tricarboxylic acid cycle evidence_type: IEA original_reference_id: GO_REF:0000104 previous_action: ACCEPT action: ACCEPT outcome: retained rationale: By reactivating IDH (dephosphorylation), AceK restores TCA-cycle flux; by inactivating IDH (phosphorylation) it diverts flux to the glyoxylate bypass. This regulatory role makes the TCA cycle association appropriate. - term_id: GO:0008772 term_label: '[isocitrate dehydrogenase (NADP+)] kinase activity' evidence_type: IEA original_reference_id: GO_REF:0000120 previous_action: ACCEPT action: ACCEPT outcome: retained rationale: Matches the UniProt-annotated catalytic activity (EC 2.7.11.5) and the kinase half of the bifunctional enzyme. This is a central, specific core function. - term_id: GO:0016208 term_label: AMP binding evidence_type: IEA original_reference_id: GO_REF:0000118 previous_action: KEEP_AS_NON_CORE action: ACCEPT outcome: changed rationale: The E. coli AceK structure shows AMP at an interdomain allosteric site controlling the opposing catalytic activities. This provides positive family-level support for the TreeGrafter inference to the conserved P. putida AceK. An unmeasured target-specific binding constant is not sufficient reason to mark the inherited mechanism non-core. - term_id: GO:0016788 term_label: hydrolase activity, acting on ester bonds evidence_type: IEA original_reference_id: GO_REF:0000104 previous_action: MARK_AS_OVER_ANNOTATED action: ACCEPT outcome: changed rationale: Hydrolase activity acting on ester bonds is a valid broad function of the enzyme. Redundancy with substrate-specific phosphatase activity is not a biological error. - term_id: GO:0016791 term_label: phosphatase activity evidence_type: IEA original_reference_id: GO_REF:0000002 previous_action: MODIFY action: ACCEPT outcome: changed rationale: Phosphatase activity is entailed by the accepted specific phosphoprotein dephosphorylation reaction. Retain the correct InterPro parent term. changes: - term_id: GO:0004721 previous_action: MODIFY action: ACCEPT - term_id: GO:0005524 previous_action: MARK_AS_OVER_ANNOTATED action: ACCEPT - term_id: GO:0016208 previous_action: KEEP_AS_NON_CORE action: ACCEPT - term_id: GO:0016788 previous_action: MARK_AS_OVER_ANNOTATED action: ACCEPT - term_id: GO:0016791 previous_action: MODIFY action: ACCEPT evidence: existing_adjudications: - genes/PSEPK/aceK/aceK-hypotheses/function-hypothesis-go-0004721/falcon.md - genes/PSEPK/aceK/aceK-hypotheses/function-hypothesis-go-0004721/openscientist.md notes_file: genes/PSEPK/aceK/aceK-notes.md adjudication: needed: null duplicate_runs_launched: false validation: command: just validate PSEPK aceK result: passed warnings: - The specific phosphatase core term is not separately in existing_annotations; broad correct source annotations are retained. No redundant NEW was added. history_record: history/genes/PSEPK/aceK/2026-09-21T010110Z-codex-3e6fb9.yaml history_validation: command: just validate-history history/genes/PSEPK/aceK/2026-09-21T010110Z-codex-3e6fb9.yaml result: passed source_rows_preserved: true final_annotation_count: 10 - gene: PSEPK/ahpC gene_file: genes/PSEPK/ahpC/ahpC-ai-review.yaml status: reviewed scope: full_gene outcome: changed annotation_count: 13 annotations: - term_id: GO:0004601 term_label: peroxidase activity evidence_type: IEA original_reference_id: GO_REF:0000120 previous_action: MODIFY action: ACCEPT outcome: changed rationale: Peroxiredoxin activity is peroxidase activity. The broad parent does not become wrong because the catalytic subfamily is known. - term_id: GO:0005737 term_label: cytoplasm evidence_type: IEA original_reference_id: GO_REF:0000120 previous_action: ACCEPT action: ACCEPT outcome: changed rationale: The available evidence supports AhpC as a soluble cytoplasmic protein. - term_id: GO:0005829 term_label: cytosol evidence_type: IEA original_reference_id: GO_REF:0000118 previous_action: MODIFY action: ACCEPT outcome: changed rationale: The current cytosol definition excludes organelles but includes soluble proteins and protein complexes. It applies to bacteria; the existing cytoplasm annotation does not justify replacing this correct, more specific localization. - term_id: GO:0006979 term_label: response to oxidative stress evidence_type: IEA original_reference_id: GO_REF:0000120 previous_action: KEEP_AS_NON_CORE action: ACCEPT outcome: changed rationale: Direct peroxide reduction performs work in the oxidative-stress response. The more specific detoxification annotation is complementary and does not make this core protective role peripheral. - term_id: GO:0008379 term_label: thioredoxin peroxidase activity evidence_type: IEA original_reference_id: GO_REF:0000118 previous_action: MODIFY action: MODIFY outcome: changed rationale: QuickGO checked on 2026-09-20 marks GO:0008379 obsolete; preserve the source GOA identifier and refine its review to the active peroxiredoxin term. Independently, the existing reports support a typical AhpC/AhpF system and distinguish its immediate protein reductant from free thioredoxin. Their donor discussion does not undermine peroxide reduction, antioxidant activity or H2O2 catabolism. - term_id: GO:0016209 term_label: antioxidant activity evidence_type: IEA original_reference_id: GO_REF:0000002 previous_action: KEEP_AS_NON_CORE action: ACCEPT outcome: changed rationale: The broad antioxidant activity follows from the accepted peroxiredoxin reaction; it is the same core function at broader granularity. - term_id: GO:0016491 term_label: oxidoreductase activity evidence_type: IEA original_reference_id: GO_REF:0000002 previous_action: MODIFY action: ACCEPT outcome: changed rationale: This broad parent is chemically entailed by peroxiredoxin activity. It is acceptable alongside the specific function. - term_id: GO:0033554 term_label: cellular response to stress evidence_type: IEA original_reference_id: GO_REF:0000118 previous_action: KEEP_AS_NON_CORE action: ACCEPT outcome: changed rationale: The general stress-response annotation is supported by the direct antioxidant mechanism and OxyR-associated response. Broadness alone does not turn that response into a non-core function. - term_id: GO:0042744 term_label: hydrogen peroxide catabolic process evidence_type: IEA original_reference_id: GO_REF:0000118 previous_action: MODIFY action: ACCEPT outcome: changed rationale: Hydrogen peroxide is among the substrates explicitly listed in the UniProt reaction/function annotation. Activity toward additional organic hydroperoxides does not invalidate the specific H2O2 catabolic process or require generalizing it. - term_id: GO:0045454 term_label: cell redox homeostasis evidence_type: IEA original_reference_id: GO_REF:0000118 previous_action: KEEP_AS_NON_CORE action: ACCEPT outcome: changed rationale: Peroxide reduction directly limits oxidative burden as part of the antioxidant system. This is a supported broad process, not merely an unrelated phenotype. - term_id: GO:0051920 term_label: peroxiredoxin activity evidence_type: IEA original_reference_id: GO_REF:0000120 previous_action: ACCEPT action: ACCEPT outcome: changed rationale: This term captures the core catalytic identity of the protein without overcommitting to donor-specific chemistry at the single-gene-product level. - term_id: GO:0098869 term_label: cellular oxidant detoxification evidence_type: IEA original_reference_id: GO_REF:0000120 previous_action: ACCEPT action: ACCEPT outcome: changed rationale: The process term aligns with both the known chemistry of the enzyme and the regulatory/physiological evidence from P. putida. - term_id: GO:0102039 term_label: NADH-dependent peroxiredoxin activity evidence_type: IEA original_reference_id: GO_REF:0000120 previous_action: MODIFY action: MODIFY outcome: changed rationale: The coupled AhpCF system is NADH-dependent, as recognized by both existing reports. AhpC directly reduces peroxide while AhpF supplies electrons from NADH. Retain the donor-independent single-subunit refinement to peroxiredoxin activity; this is a gene-product scope distinction, not a claim that NADH-dependent AhpCF physiology is absent. Whether GO:0102039 is conventionally assigned to the catalytic AhpC subunit itself remains a useful curation second opinion. changes: - term_id: GO:0004601 previous_action: MODIFY action: ACCEPT - term_id: GO:0005829 previous_action: MODIFY action: ACCEPT - term_id: GO:0006979 previous_action: KEEP_AS_NON_CORE action: ACCEPT - term_id: GO:0016209 previous_action: KEEP_AS_NON_CORE action: ACCEPT - term_id: GO:0016491 previous_action: MODIFY action: ACCEPT - term_id: GO:0033554 previous_action: KEEP_AS_NON_CORE action: ACCEPT - term_id: GO:0042744 previous_action: MODIFY action: ACCEPT - term_id: GO:0045454 previous_action: KEEP_AS_NON_CORE action: ACCEPT evidence: existing_adjudications: - genes/PSEPK/ahpC/ahpC-hypotheses/function-hypothesis-go-0008379/falcon.md - genes/PSEPK/ahpC/ahpC-hypotheses/function-hypothesis-go-0008379/openscientist.md notes_file: genes/PSEPK/ahpC/ahpC-notes.md adjudication: needed: 'Optional curation scope check: GO:0102039 on AhpC catalytic subunit versus full AhpCF system; existing reports already discuss donor mechanism.' duplicate_runs_launched: false validation: command: just validate PSEPK ahpC result: passed history_record: history/genes/PSEPK/ahpC/2026-09-21T010113Z-codex-6e4a4a.yaml history_validation: command: just validate-history history/genes/PSEPK/ahpC/2026-09-21T010113Z-codex-6e4a4a.yaml result: passed source_rows_preserved: true final_annotation_count: 13 validation: all_source_fields: Compared all original non-NEW annotation metadata against HEAD; unchanged. original_rows_reviewed: 66 final_annotation_rows: 65 withdrawn_author_proposals: 1 history_records: All seven scaffolded by just new-history with actor-name codex and passed just validate-history. gene_reviews: All seven pass just validate; advisory warnings documented per gene.