family_id: PANTHER:PTHR48004 family_name: OS01G0149700 PROTEIN preferred_name: Plant leucine-rich-repeat receptor-like proteins summary: The retrieved family includes plant receptor-like proteins RLP19 and PII-2. Extracellular leucine-rich repeats provide a recognition surface; receptor-associated signaling can occur without an intrinsic protein kinase domain. functional_coherence: UNKNOWN coherence_reason: >- F4JLB7, RLP19 and PII-2 support extracellular LRR receptor-like architecture, but a recognition surface alone does not establish a common ligand, catalytic reaction or partner-mediated signaling mechanism. The F4JLB7 sequence lacks a complete kinase domain; an associated kinase could in principle mediate signaling, but no such target mechanism is established. The unresolved coherence concerns what shared activity the architecture performs, not the ratio of cached entries to a metadata protein count. subfamilies: - label: F4JLB7 LRR receptor-like protein description: Both classification snapshots place F4JLB7 in the same parent family; its exact subfamily is unresolved. F4JLB7 is an LRR receptor-like sequence, and its OpenScientist domain analysis finds no kinase domain. Kinase activity is therefore contradicted for that sequence; participation in phosphorylation-mediated signaling is a separate unresolved question. Ligand recognition and partner kinases require member-specific evidence. representative_members: - id: UniProtKB:F4JLB7 gene_symbol: F4JLB7 organism: Arabidopsis thaliana gene_review: genes/ARATH/F4JLB7/F4JLB7-ai-review.yaml term_assessments: - assessed_term: id: GO:0016310 label: phosphorylation scope: UNRESOLVED scope_reason: An extracellular LRR receptor-like protein can regulate a phosphorylation pathway through a partner kinase without itself phosphorylating a substrate. F4JLB7 lacks the kinase domain in the sequence/domain analysis, but no partner-dependent phosphorylation mechanism is established for it. The family evidence therefore does not support a universal phosphorylation-process grant or a universal negative. supported_by: - reference_id: file:genes/ARATH/F4JLB7/F4JLB7-hypotheses/prediction-kinase-activity/openscientist.md supporting_text: no protein-kinase Pfam (PF00069) and no InterPro protein-kinase domain is present anywhere in the sequence. - reference_id: file:genes/ARATH/F4JLB7/F4JLB7-uniprot.txt supporting_text: DR InterPro; IPR001611; Leu-rich_rpt. - reference_id: file:genes/ARATH/F4JLB7/F4JLB7-uniprot.txt supporting_text: DR InterPro; IPR032675; LRR_dom_sf. - reference_id: file:genes/ARATH/F4JLB7/F4JLB7-uniprot.txt supporting_text: DR Pfam; PF00560; LRR_1; 3. - reference_id: file:genes/ARATH/F4JLB7/F4JLB7-uniprot.txt supporting_text: DR Pfam; PF13855; LRR_8; 1. - assessed_term: id: GO:0016301 label: kinase activity scope: UNRESOLVED scope_reason: >- F4JLB7 has an LRR solenoid without a complete protein-kinase domain or an ordered catalytic motif arrangement; isolated DFG-like strings do not establish a kinase active site. This refutes intrinsic kinase activity for that sequence. The evidence does not define a family-wide kinase or non-kinase mechanism, or a supported catalytically distinct subfamily boundary, so the target-level result is not promoted to a universal NOT_APPLICABLE judgment. supported_by: - reference_id: file:genes/ARATH/F4JLB7/F4JLB7-hypotheses/prediction-kinase-activity/openscientist.md supporting_text: Second, a **direct motif scan** of the sequence recovered 9 canonical LRR cores but found no ordered kinase catalytic triad; the isolated "DFG" (position 149, inside PEDFGSV) and a "GNGFHG" hit (position 186) are coincidental tripeptides embedded within the LRR solenoid, not part of a folded catalytic cleft. - reference_id: file:genes/ARATH/F4JLB7/F4JLB7-uniprot.txt supporting_text: DR InterPro; IPR001611; Leu-rich_rpt. - reference_id: file:genes/ARATH/F4JLB7/F4JLB7-uniprot.txt supporting_text: DR InterPro; IPR032675; LRR_dom_sf. - reference_id: file:genes/ARATH/F4JLB7/F4JLB7-uniprot.txt supporting_text: DR Pfam; PF00560; LRR_1; 3. - reference_id: file:genes/ARATH/F4JLB7/F4JLB7-uniprot.txt supporting_text: DR Pfam; PF13855; LRR_8; 1. references: - id: file:genes/ARATH/F4JLB7/F4JLB7-hypotheses/prediction-kinase-activity/openscientist.md - id: file:genes/ARATH/F4JLB7/F4JLB7-uniprot.txt - id: file:interpro/panther/PTHR48004/PTHR48004-entries.csv - id: file:interpro/panther/PTHR48004/PTHR48004-paint.tsv - id: file:projects/PROTNLM_EVALUATION/family-curation/PANTHER-classification-conflicts-2026-10-02.md title: 'PANTHER classification conflicts: eight exact accession assignments observed on 2026-10-02' review_status: IN_PROGRESS reviewed_by: codex review_date: '2026-10-02' notes: |- ARATH/F4JLB7: requested accession F4JLB7; current record F4JLB7; sequence length 450; source cohort ARGO50. Family boundaries were assessed using the fetched member set and the cited domain, literature and analytical evidence. Gene-review verdicts and ARBA assertions are not independent validation. PANTHER subfamily labels and membership are recorded from the frozen UniProt records and panther.obo; they do not by themselves prove functional uniformity within a subfamily. PAINT rows were inspected as ancestral assertions, but node placement is not adjudicated without the relevant descendant tree/alignment. No residue requirement is encoded without a verified sequence-version anchor. A target-level refutation is not a family-wide NOT_APPLICABLE judgment. Exact protein-name-only predictions are treated as family-identification hypotheses rather than invented GO predictions. Placement evidence (2026-10-02) | Protein / source | Frozen UniProt placement (historical observation) | Official PANTHER 19.0 row | |---|---|---| | F4JLB7 (arabidopsis / 15922) | PTHR48004:SF58 — OS01G0162200 PROTEIN | PTHR48004:SF38 | Both observations support this parent; only numbered subfamily placement is unresolved. Both observed classification sources place F4JLB7 in PTHR48004, while SF58 versus SF38 remains unresolved. Its frozen 2026 UniProt record combines RIC7 naming with a 450-residue LRR sequence, sequence version 1 since 2011. The alternative name is not evidence for a CRIB-effector mechanism or accession sequence drift. The cached PAINT table has no F4JLB7 seed or SF38/SF58 bridge. OpenScientist sequence/domain analysis finds an LRR solenoid, no complete protein-kinase domain and no ordered catalytic motif arrangement; isolated DFG-like strings are not a kinase active site. Intrinsic kinase activity is contradicted for this sequence, but an extracellular LRR protein could in principle regulate phosphorylation through a partner kinase. No such F4JLB7 partner-dependent mechanism is established. RLP19 and PII-2 illustrate receptor-like architecture in the retrieved cohort; ligand recognition and partners require member-specific evidence. Current UNRESOLVED term reasons below govern the family; they are not historical or universal negative claims. The table records source observations, not live membership declarations. Complete earlier descriptors and assessments are preserved at https://github.com/ai4curation/ai-gene-review/blob/e82261ba811dadbb944cd3770e7fdd2889ec69a4/interpro/panther/PTHR48004/PTHR48004-review.yaml. Current structured term assessments are authoritative; duplicate historical copies have been removed from these notes. Persistent provenance: file:projects/PROTNLM_EVALUATION/family-curation/PANTHER-classification-conflicts-2026-10-02.md. Diagnostic run 36943928592, compact artifact 11201891369, SHA256 9861e63fc8279e570e57ad56d639c36edafeac62809ee9867681a27175707136. Official sequence-file dates, exact row labels, URLs and verification limits are retained in that report. Full raw-body hashes remain runner-recorded rather than locally recomputed. No PAINT-node placement or replacement family is inferred. Review remains IN_PROGRESS. Bounded comparator audit (2026-10-02): source run 36956025748, compact artifact 11205408249, SHA256 7df7b0367d5d10dc5be4c919adc9af3a89ea3e057ba788fc4b067eaa0d926931. All 17 outcomes were authenticated; the 15 matching rows were replayed locally against the unchanged parser. The two whole-file NO_MATCH results are runner observations. The persistent report records all 17 targets, original labels and source dates. Complete source-body hashes are runner-recorded, not independently recomputed locally. Classification observations do not establish evolutionary cause or complete family coverage.