--- provider: openscientist model: openscientist-autonomous cached: false start_time: '2026-07-09T04:55:42.436855' end_time: '2026-07-09T05:20:36.412887' duration_seconds: 1493.98 template_file: templates/gene_hypothesis_deep_research.md template_variables: organism: WHEAT gene: F6LAX4 gene_symbol: LOC123103357 uniprot_accession: F6LAX4 taxon_id: NCBITaxon:4565 taxon_label: Triticum aestivum focus_type: computational_prediction hypothesis_slug: prediction-animal-specific-terms hypothesis_text: ProtNLM2 predicts several animal-specific terms for the Triticum aestivum (wheat) ARM-repeat protein F6LAX4 -- neuron projection (GO:0043005), neuronal cell body (GO:0043025), protein antigen binding (GO:1990405), chromosome centromeric region (GO:0000775), chromosome segregation (GO:0007059), and protein heterodimerization activity (GO:0046982). Independently determine the protein's identity from its domain architecture (ARM/HEAT-repeat solenoid) and orthology -- in particular whether it is the protein phosphatase 2A (PP2A) scaffold (A/PR65) subunit -- and assess whether these predicted terms are appropriate for a wheat protein, given that plants have no neurons and no adaptive immune system. Determine whether the predictions are supported or are cross-kingdom / taxon-inappropriate misassignments transferred from mammalian orthologs. term_context: '- Term: neuron projection (GO:0043005)' reference_context: No specific reference context supplied. source_file: '' source_selector: '' source_context_yaml: "hypothesis: ProtNLM2 predicts several animal-specific terms\ \ for the Triticum aestivum (wheat) ARM-repeat\n protein F6LAX4 -- neuron projection\ \ (GO:0043005), neuronal cell body (GO:0043025), protein antigen binding\n (GO:1990405),\ \ chromosome centromeric region (GO:0000775), chromosome segregation (GO:0007059),\ \ and protein\n heterodimerization activity (GO:0046982). Independently determine\ \ the protein's identity from its domain\n architecture (ARM/HEAT-repeat solenoid)\ \ and orthology -- in particular whether it is the protein phosphatase\n 2A (PP2A)\ \ scaffold (A/PR65) subunit -- and assess whether these predicted terms are appropriate\ \ for\n a wheat protein, given that plants have no neurons and no adaptive immune\ \ system. Determine whether\n the predictions are supported or are cross-kingdom\ \ / taxon-inappropriate misassignments transferred\n from mammalian orthologs.\n\ focus_type: computational_prediction\nterm_id: GO:0043005\nterm_label: neuron\ \ projection\ncontext: []\nreference_id: []" provider_config: timeout: 3600 max_retries: 3 parameters: allowed_domains: [] max_iterations: 3 use_hypotheses: false investigation_mode: autonomous poll_interval: 30 timeout: 7200 save_artifacts: true artifact_max_bytes: 5242880 artifact_count: 2 artifact_sources: openscientist_artifacts_zip: 2 artifacts: - filename: final_report.html path: openscientist_artifacts/final_report.html media_type: text/html source: openscientist_artifacts_zip data_storage_id: null description: OpenScientist final report - filename: final_report.pdf path: openscientist_artifacts/final_report.pdf media_type: application/pdf source: openscientist_artifacts_zip data_storage_id: null description: OpenScientist final report --- ## Question # AIGR Gene Hypothesis Deep Research You are evaluating one focused gene curation hypothesis for AI Gene Review. This is not a general gene overview. Use the seed hypothesis and source context below to search for evidence that supports, refutes, narrows, or competes with the proposed curation decision. ## Target Gene - **Organism code:** WHEAT - **Taxon:** Triticum aestivum (NCBITaxon:4565) - **Gene directory:** F6LAX4 - **Gene symbol:** LOC123103357 - **UniProt accession:** F6LAX4 ## Focus - **Focus type:** computational_prediction - **Hypothesis slug:** prediction-animal-specific-terms - **Source file:** - **Source selector:** ## Seed Hypothesis ProtNLM2 predicts several animal-specific terms for the Triticum aestivum (wheat) ARM-repeat protein F6LAX4 -- neuron projection (GO:0043005), neuronal cell body (GO:0043025), protein antigen binding (GO:1990405), chromosome centromeric region (GO:0000775), chromosome segregation (GO:0007059), and protein heterodimerization activity (GO:0046982). Independently determine the protein's identity from its domain architecture (ARM/HEAT-repeat solenoid) and orthology -- in particular whether it is the protein phosphatase 2A (PP2A) scaffold (A/PR65) subunit -- and assess whether these predicted terms are appropriate for a wheat protein, given that plants have no neurons and no adaptive immune system. Determine whether the predictions are supported or are cross-kingdom / taxon-inappropriate misassignments transferred from mammalian orthologs. ## Term and Decision Context - Term: neuron projection (GO:0043005) ## Reference Context No specific reference context supplied. ## Source Context YAML ```yaml hypothesis: ProtNLM2 predicts several animal-specific terms for the Triticum aestivum (wheat) ARM-repeat protein F6LAX4 -- neuron projection (GO:0043005), neuronal cell body (GO:0043025), protein antigen binding (GO:1990405), chromosome centromeric region (GO:0000775), chromosome segregation (GO:0007059), and protein heterodimerization activity (GO:0046982). Independently determine the protein's identity from its domain architecture (ARM/HEAT-repeat solenoid) and orthology -- in particular whether it is the protein phosphatase 2A (PP2A) scaffold (A/PR65) subunit -- and assess whether these predicted terms are appropriate for a wheat protein, given that plants have no neurons and no adaptive immune system. Determine whether the predictions are supported or are cross-kingdom / taxon-inappropriate misassignments transferred from mammalian orthologs. focus_type: computational_prediction term_id: GO:0043005 term_label: neuron projection context: [] reference_id: [] ``` ## Research Objective Build a focused report that helps a curator decide whether this hypothesis should affect the gene review. Address the focus type directly: 1. For an existing GO annotation decision, evaluate whether the current action is justified, too strong, too weak, or should change. 2. For a proposed replacement or new GO term, evaluate whether the term is biologically supported, too broad, too narrow, or missing key qualifiers. 3. For a computational prediction, evaluate whether the prediction is correct, less precise than existing knowledge, uncertain, or likely wrong because of paralog overannotation, frequency bias, pathway context, or in vitro-only activity. 4. For a core-function hypothesis, evaluate whether the proposed activity, process, and location represent the gene product's primary function rather than a downstream effect, pleiotropic phenotype, or context-specific role. 5. For a function-assignment hypothesis, evaluate whether the gene product directly has the stated GO term/function. Treat the prior review action, if any, as intentionally blinded unless it appears in the supplied context. Use primary literature whenever possible. Prefer PMID citations and include DOI citations when no PMID is available. Treat reviews and database records as orientation unless they contain directly relevant synthesized evidence that is clearly labeled as review-level or database-level support. Evaluate the hypothesis from the supplied seed context, primary literature, and publicly accessible bioinformatics resources. Local `*-bioinformatics` analyses, when they already exist in the repository, are intentionally withheld from this prompt so the report can be compared against them after the run. Do not rely on literature alone. Where the hypothesis is decidable by computation, actually run the analysis and keep it as provenance rather than only reasoning about it. Match the analysis to the question, for example: - membrane topology / localization: compute a hydropathy profile and predicted transmembrane segments from the sequence, and locate signal peptides and targeting/sorting motifs (e.g. dileucine, acidic-cluster, NLS); compare against UniProt topology features and AlphaFold geometry. - catalytic / binding activity: check whether the specific active-site, metal-binding, or motif residues are present and correctly spaced (in sequence and, where useful, structure) and compare to characterized family members. - DNA-binding / regulatory: examine the binding-domain class, obligate partners, and known binding-motif / PWM signatures. - family / paralog questions: use domain (Pfam/InterPro), orthology, and conservation comparisons to distinguish subfamilies. Use resources you can actually access programmatically (UniProt, AlphaFold DB, InterPro, sequence computation, public APIs). If a resource is web-only or you cannot run a check, say so plainly instead of guessing — never fabricate a result, and an inconclusive or "could not run" analysis is an acceptable and useful outcome. Report all computational results conservatively and prefer recording the underlying analysis (code, computed values, table, or plot) as provenance. ## Required Output ### Executive Judgment Give a concise verdict: supported, partially supported, unresolved, weakly supported, over-annotated, or refuted. Explain the reasoning and the most important caveats. ### Evidence Matrix Create a table with one row per important evidence item: - Citation (PMID preferred) - Evidence type (direct assay, mutant phenotype, localization, interaction, structural/evolutionary, computational, review/database) - Supports / refutes / qualifies / competing - Claim tested - Key finding - Organism, tissue, cell type, or assay context - Confidence and limitations ### GO Curation Implications State the likely curation action as a lead requiring curator verification. If GO terms are involved, explain whether the evidence supports an MF, BP, or CC term, and whether the term should be retained, removed, generalized, made more specific, or treated as non-core. Avoid using "protein binding" as a final recommendation unless no more informative term is supported. ### Mechanistic Scope Describe the immediate molecular or cellular function being tested. Separate direct gene-product activity from downstream phenotypes, pathway consequences, developmental outcomes, disease manifestations, or effects inferred only from loss of function. ### Conflicts and Alternatives Identify evidence that conflicts with the seed hypothesis or suggests an alternative interpretation, including paralog confusion, organism-specific differences, isoform-specific findings, experimental artifacts, or database carry-over. ### Knowledge Gaps List explicit uncertainties that matter for curation. For each gap, state what was checked, why the gap matters, and what evidence or experiment would resolve it. ### Discriminating Tests Recommend concrete assays, perturbations, datasets, or comparative analyses that would most efficiently distinguish this hypothesis from alternatives. ### Curation Leads Provide candidate updates for the review, clearly labeled as leads requiring curator verification. Include candidate references with exact snippets to verify, candidate replacement or new GO terms, possible action changes, suggested questions, and suggested experiments. If the provider supports artifacts, save provenance for any analysis you run — the executed code together with its output (computed values, plot, or table), not just a summary figure — alongside artifact-friendly tables such as an evidence matrix, GO decision table, or comparison table. Genuine computed provenance is more valuable than a hand-drawn summary, and you must not synthesize a figure that implies an analysis you did not actually run. These artifacts are important provenance for hypothesis-level review. ## Output # AIGR Deep-Research Report — F6LAX4 (WHEAT, LOC123103357) **Focus:** computational_prediction · slug `prediction-animal-specific-terms` **Primary term in focus:** GO:0043005 *neuron projection* (CC) **Question:** Are the ProtNLM2 animal-specific predictions for wheat F6LAX4 appropriate, or are they cross-kingdom / taxon-inappropriate misassignments? Independently determine whether F6LAX4 is the PP2A scaffold (A/PR65) subunit. --- ## Executive Judgment **Verdict: REFUTED (over-annotated) for the animal-context terms; the underlying protein identity in the seed hypothesis is SUPPORTED.** F6LAX4 is, with high confidence, the **wheat orthologue of the protein phosphatase 2A (PP2A) 65 kDa scaffold / structural "A" subunit (PR65 / PPP2R1)**. This is established independently by (i) UniProt naming it "Protein phosphatase 2A structural subunit", (ii) its ARM/HEAT-repeat α-α solenoid domain architecture (InterPro IPR051023 *PP2A_Regulatory_Subunit_A*, PANTHER PTHR10648:SF4, Pfam PF02985/PF22646), and (iii) computed orthology — **85–90 % global identity to the three Arabidopsis PP2A A subunits** (RCN1/A1, A2, A3) and **56–59 % to human PR65 α/β**, the exact conservation signature of this deeply conserved scaffold. Given this identity, the ProtNLM2 predictions divide into two groups: - **Taxon-inappropriate (REFUTE):** *neuron projection* (GO:0043005), *neuronal cell body* (GO:0043025) — plants have **no neurons**; *protein antigen binding* (GO:1990405) — plants have **no adaptive immune system / antibodies**. These are text-transfer artifacts from the extensive mammalian PP2A/PR65 neuronal literature. They must not be asserted on a wheat protein. - **Conserved but indirect / imprecise (QUALIFY, do not assert on this subunit):** *chromosome centromeric region* (GO:0000775) and *chromosome segregation* (GO:0007059) describe a genuine, eukaryote-conserved Shugoshin–PP2A cohesion-protection function, but that role is mediated by the **B56 regulatory subunit** binding Shugoshin — not by the A scaffold intrinsically — so for the A subunit these are holoenzyme-context, non-core terms with no direct wheat evidence. *Protein heterodimerization activity* (GO:0046982) mis-describes the scaffold, which nucleates an **A–B–C heterotrimer**; the informative MF is protein-phosphatase regulator/PP2A-complex scaffolding, already captured by the existing IBA annotations. **Most important caveat:** F6LAX4 is a TrEMBL (unreviewed) entry with no wheat-specific experimental characterization; the identity call rests on strong sequence/domain orthology (computational + database), and the "conserved-but-indirect" mitotic terms cannot be positively excluded as PP2A-complex functions — they are simply not supportable for the *scaffold subunit* on current evidence. --- ## Evidence Matrix | Citation | Evidence type | Supports/Refutes/Qualifies | Claim tested | Key finding | Context | Confidence & limitations | |---|---|---|---|---|---|---| | UniProt F6LAX4 (database) | review/database | Supports | Protein identity = PP2A A subunit | Submission name "Protein phosphatase 2A structural subunit"; 587 aa; existing IBA GO: PP2A complex GO:0000159, phosphatase regulator GO:0019888, cytoplasm/cytosol/nucleus | Triticum aestivum, gene LOC123103357 | High for naming; TrEMBL (unreviewed), no wheat wet-lab data | | InterPro/Pfam/PANTHER (database) | structural/evolutionary | Supports | Domain architecture = ARM/HEAT solenoid scaffold | IPR051023 PP2A_Regulatory_Subunit_A; PTHR10648:SF4; PF02985; PROSITE PS50077 HEAT ×12; Gene3D ARM-like solenoid | Sequence-based | High; signature-based | | This report — global NW identity (computational) | computational | Supports | F6LAX4 is the plant PP2A A ortholog | 85.0 % vs Ath RCN1/A1, 89.8 % vs A2, 88.6 % vs A3; 58.9 %/56.0 % vs human PR65 α/β; human vs Ath baseline 59.0 % | 6 UniProt sequences | High; simple match/mismatch NW, not BLOSUM, but margins are large | | PMID 20133745 | structural | Supports | PR65 is a HEAT-repeat α-α solenoid PP2A scaffold | "PR65 is the two-layered (alpha-alpha solenoid) HEAT-repeat … scaffold of protein phosphatase PP2A" | Biophysics of human PR65 | High | | PMID 38820156 | structural/computational | Supports | PR65 scaffolds the heterotrimeric PP2A | "PR65 is the HEAT repeat scaffold subunit of the heterotrimeric protein phosphatase 2A (PP2A)" | MD + optical tweezers, human PR65 | High | | PMID 37290287 | mutant phenotype / review | Supports | Plant PP2A A subunit (RCN1) is a real, growth/development regulator | RCN1 = "a regulatory A1 subunit isoform of Arabidopsis PP2A"; rcn1 mutants alter UPR/ER-stress sensitivity | Arabidopsis, plant | High for plant orthology & function class | | PMID 26888284 / 28165500 | mutant phenotype | Supports (function class) | Plant PP2A-A scaffolds developmental signaling | RCN1/PP2A regulates PIN auxin-transporter polarity & recycling with PINOID antagonism | Arabidopsis | High for plant scaffold role | | PMID 33973335 | interaction/structural | Qualifies | Centromere/segregation role is via B56, not A scaffold | "shugoshin proteins are universal protectors of centromeric cohesin"; "a highly conserved pocket on the B56 regulatory subunit is required for hSgo1 binding" | Human somatic cells | High; maps GO:0000775/0007059 to B56, not A | | Botanical fact (plants lack neurons & adaptive immunity) | review/first-principles | Refutes | Animal-context terms invalid in wheat | No neurons → GO:0043005/0043025 impossible; no antibodies → GO:1990405 impossible | Triticum aestivum | High | | This report — AlphaFold + Kabsch superposition (computational) | structural/computational | Supports | F6LAX4 3D fold = PR65 HEAT solenoid | F6LAX4 AF pLDDT=90.4; local 60-res-window Kabsch CA-RMSD to Ath RCN1 median **0.29 Å**, to human PR65 median **0.92 Å**; global RMSD (2.8/4.5 Å) inflated only by solenoid hinge-bending | AlphaFold DB v6 models | High; local repeat-level fold identity is unambiguous | | UniProt F6LAX4 GO set (database) | review/database | Qualifies | Are ProtNLM terms already curated? | Curated GO = only 5 IBA terms; intersection with 6 ProtNLM terms = ∅ → action is "reject prediction," not "remove annotation" | Triticum aestivum | High | | This report — PPP catalytic-motif scan (computational) | computational | Supports | F6LAX4 is A scaffold, not catalytic C subunit | F6LAX4 lacks all PPP metal-binding motifs (GDxHG, GDxVDRG, GNHE, RGNHE); positive control PPP2CA (P67775) has all four | Sequence-based | High; excludes catalytic-subunit alternative | --- ## Structural Confirmation (added Iteration 2) AlphaFold DB models were retrieved for F6LAX4 (global pLDDT 90.4, an elongated, confidently modeled HEAT-repeat solenoid), Arabidopsis RCN1 (Q38845, pLDDT 93.0) and human PR65α (P30153, pLDDT 94.9). A Kabsch superposition of Cα atoms over identical-residue anchors gives an elevated *global* RMSD (F6LAX4↔RCN1 2.82 Å; F6LAX4↔human PR65 4.46 Å), but a sliding 60-residue **local** window RMSD is near-zero (median **0.29 Å** vs RCN1, **0.92 Å** vs human PR65). This pattern — individually superimposable repeats but hinge-bent ends — is the structural signature of the elastic PR65 α-α solenoid (PMID 20133745) and independently confirms the scaffold identity. Provenance: `/tmp/aigr/AF-*.pdb`, superposition code in the executed analysis log. --- ## Family Disambiguation & Annotation-Status Check (added Iteration 3) Two curator-relevant confirmations: 1. **The ProtNLM2 terms are NOT curated GO annotations.** UniProt's curated GO set for F6LAX4 is exactly five IBA/GO_Central terms — cytoplasm (GO:0005737), cytosol (GO:0005829), nucleus (GO:0005634), PP2A complex (GO:0000159), protein phosphatase regulator activity (GO:0019888). The intersection with the six ProtNLM2 predictions is **empty**. The correct curation action is therefore **"reject / do not import the prediction,"** not "remove an existing annotation." 2. **F6LAX4 is the non-catalytic A scaffold, not the catalytic C subunit.** A motif scan finds **none** of the PPP-phosphatase catalytic metal-binding signatures (GDxHG, GDxVDRG, GNHE, RGNHE) in F6LAX4 (587 aa), whereas the genuine PP2A catalytic subunit human PPP2CA (P67775, 309 aa) contains **all four**. This excludes the main competing family assignment (catalytic subunit) and is consistent with the scaffold role. --- ## GO Curation Implications (leads — require curator verification) | Term | Aspect | ProtNLM2 predicted | Recommended curator action | |---|---|---|---| | GO:0043005 neuron projection | CC | yes | **Do not annotate / reject.** Taxon-inappropriate (no neurons in plants). Flag as ProtNLM cross-kingdom error. | | GO:0043025 neuronal cell body | CC | yes | **Do not annotate / reject.** Same rationale. | | GO:1990405 protein antigen binding | MF | yes | **Do not annotate / reject.** No adaptive immunity/antibodies in plants. | | GO:0000775 chromosome centromeric region | CC | yes | **Do not assert on this subunit.** Conserved Sgo–PP2A function is B56-mediated; non-core for the A scaffold; no wheat evidence. | | GO:0007059 chromosome segregation | BP | yes | **Do not assert on this subunit.** Holoenzyme/B56-context; indirect for the scaffold. | | GO:0046982 protein heterodimerization activity | MF | yes | **Replace with more informative scaffold term** (e.g., protein phosphatase 2A binding / structural constituent of PP2A holoenzyme). Heterodimerization mis-describes an A–B–C heterotrimer scaffold. | | GO:0000159 protein phosphatase type 2A complex | CC | (existing IBA) | **Retain.** Correct and plant-appropriate. | | GO:0019888 protein phosphatase regulator activity | MF | (existing IBA) | **Retain.** Correct core MF for the A scaffold. | | GO:0005737/0005829/0005634 cyto/cytosol/nucleus | CC | (existing IBA) | **Retain.** Consistent with plant PP2A. | Net: the existing IBA annotations already capture the correct core function; the ProtNLM2 additions add nothing valid and three are actively wrong. --- ## Mechanistic Scope Immediate molecular function of F6LAX4: it is the **structural (A) scaffold subunit of the PP2A holoenzyme** — a rigid-yet-elastic α-α solenoid of ~15 HEAT repeats that simultaneously binds the catalytic (C) subunit and a variable regulatory (B/B56/B''/B''') subunit, thereby determining substrate specificity of a Ser/Thr phosphatase. It has **no catalytic activity itself** and no intrinsic DNA-, antigen-, or neuron-related activity. Downstream/holoenzyme-context phenomena (auxin-transport polarity, ethylene signaling, ER-stress/UPR in plants; Tau dephosphorylation, cohesion protection in animals) are properties of *specific PP2A holoenzymes*, not of the isolated scaffold, and must be separated from the scaffold's direct GO annotation. --- ## Conflicts and Alternatives - **Paralog/ortholog confusion (the actual error source):** ProtNLM2 transferred descriptors from mammalian PR65/PP2A entries whose partner holoenzymes act in neurons and immune cells. The wheat sequence is a bona fide ortholog (56–59 % to human), so a naive language model reuses mammalian tissue/organelle vocabulary. - **Subunit confusion:** the centromere/segregation terms belong to **PP2A-B56 + Shugoshin**, i.e., the *regulatory* subunit, not the A scaffold. Assigning them to the A subunit conflates holoenzyme function with scaffold function. - **No competing identity hypothesis survives:** 85–90 % identity to three independent Arabidopsis A subunits rules out any non-PP2A-A assignment. The alternative that this is a generic ARM/HEAT protein (e.g., importin, karyopherin) is excluded by the PP2A-A-specific InterPro/PANTHER family and by orthology. --- ## Knowledge Gaps 1. **No wheat experimental data.** Checked: UniProt (TrEMBL, PE=3 "inferred from homology"), literature. Matters because all functional claims are homology-based. Resolved by: wheat PP2A pulldown/complex-MS, or a wheat rcn1-like mutant. 2. **Which wheat PP2A A homoeolog/paralog is this?** Hexaploid wheat has A/B/D homoeologs and multiple A-subunit genes; LOC123103357 is one copy. Checked: single UniProt entry only. Matters for gene-level annotation propagation. Resolved by: wheat genome synteny / homoeolog mapping. 3. **Does wheat PP2A participate in Sgo-mediated cohesion (GO:0000775/0007059)?** Checked: no wheat-specific paper found; conserved in animals/fungi and reported in plants via SGO1. Matters only if a curator considers those terms. Resolved by: wheat/cereal meiosis cohesion studies (SGO1–PP2A-B56). --- ## Discriminating Tests - **Orthology/phylogeny (done, decisive):** global identity to Arabidopsis A subunits (85–90 %) vs catalytic subunits (would be <25 %) confirms scaffold, not catalytic, identity. - **AlphaFold geometry:** predict/inspect the AlphaFold model of F6LAX4 for the characteristic hooked HEAT-repeat solenoid and superpose on human PR65 (PDB 1B3U) — expected low RMSD over the solenoid. - **Holoenzyme co-IP MS in wheat:** recovery of PP2A C and B/B56 subunits (not neuronal or immune proteins) would positively confirm scaffold function and simultaneously refute the animal-context terms. - **Motif check for B56/Sgo pocket:** the Sgo-binding pocket is on B56, absent from the A subunit — confirming the centromere terms do not map to F6LAX4. --- ## Curation Leads (require curator verification) - **Reject** GO:0043005, GO:0043025, GO:1990405 on F6LAX4 as ProtNLM2 cross-kingdom errors (organism = plant; no neurons, no adaptive immunity). - **Do not propagate** GO:0000775 / GO:0007059 to the A scaffold subunit; if any PP2A-complex mitotic annotation is desired, it belongs to the B56 subunit with a wheat/plant reference. - **Replace** GO:0046982 with an informative scaffold MF (protein phosphatase 2A binding / structural constituent of PP2A holoenzyme) rather than generic heterodimerization. - **Retain** existing IBA terms GO:0000159, GO:0019888, GO:0005737/0005829/0005634. - **Candidate references & exact snippets to verify:** - PMID 20133745 — "PR65 is the two-layered (alpha-alpha solenoid) HEAT-repeat … scaffold of protein phosphatase PP2A." - PMID 38820156 — "PR65 is the HEAT repeat scaffold subunit of the heterotrimeric protein phosphatase 2A (PP2A)." - PMID 37290287 — RCN1 "a regulatory A1 subunit isoform of Arabidopsis PP2A" (plant ortholog exists; function class = growth/development/signaling). - PMID 33973335 — "a highly conserved pocket on the B56 regulatory subunit is required for hSgo1 binding and cohesion protection" (centromere terms map to B56, not A). - **Suggested question for curators:** should AIGR add a taxon-constraint QC rule flagging animal-only CC/MF terms (neuron*, antibody/antigen) predicted on Viridiplantae proteins? - **Suggested experiment:** wheat PP2A affinity-MS to positively identify holoenzyme partners and close the "no wheat data" gap. --- ## Provenance / Artifacts - Orthology identity matrix (global Needleman–Wunsch, computed this run): `/tmp/aigr/orthology_identity.csv` - Per-term verdict table: `/tmp/aigr/protnlm_term_verdicts.csv` - Sequences retrieved from UniProt REST: F6LAX4, P30153, P30154, Q38845, Q38950, Q38951. *Computational note:* identities were computed with a simple match/mismatch (+1/−1, gap −2) global alignment rather than a BLOSUM-scored aligner; the plant-vs-plant (85–90 %) versus cross-kingdom (56–59 %) separation is large and robust to scoring scheme, so the ortholog assignment is not sensitive to alignment parameters. ## Artifacts - [OpenScientist final report](openscientist_artifacts/final_report.html) - [OpenScientist final report](openscientist_artifacts/final_report.pdf)