id: F4JLB7
gene_symbol: F4JLB7
taxon:
  id: NCBITaxon:3702
  label: Arabidopsis thaliana
status: COMPLETE
description: >-
  F4JLB7 is a 450-residue LRR-containing receptor-like protein without a protein kinase domain. Kinase
  activity is incompatible with this architecture, while participation in phosphorylation remains unresolved.
source_documents:
  - genes/ARATH/F4JLB7/F4JLB7-uniprot.txt
  - genes/ARATH/F4JLB7/F4JLB7-goa.tsv
  - genes/ARATH/F4JLB7/F4JLB7-hypotheses/prediction-kinase-activity/openscientist.md
predictions:
  - source_method: ProtNLM2
    source_version: UniProt 2024_06 pilot
    predicted_term:
      id: GO:0016310
      label: phosphorylation
    predicted_term_type: GO_BP
    review:
      assessment: UNC
      confidence_score: 1
      summary: >-
        The OpenScientist investigation integrates LRR domain architecture, catalytic-motif analysis,
        and predicted structure to argue against intrinsic protein kinase activity. Those findings do
        not exclude participation in phosphorylation through an associated kinase or signaling complex.
        The cached IBA signaling receptor annotation is compatible with such a role, but does not establish
        it. No target-specific pathway evidence establishes or excludes participation in phosphorylation,
        so this biological-process prediction remains uncertain.
      supported_by:
        - reference_id:
            file: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:ARATH/F4JLB7/F4JLB7-uniprot.txt
          supporting_text: >-
            ID   F4JLB7_ARATH            Unreviewed;       450 AA. ... DR   GO; GO:0005886; C:plasma membrane;
            IBA:GO_Central. ... DR   GO; GO:0038023; F:signaling receptor activity; IBA:GO_Central. ...
            DR   InterPro; IPR001611; Leu-rich_rpt. ... DR   InterPro; IPR032675; LRR_dom_sf. ... DR   Pfam;
            PF00560; LRR_1; 3. ... DR   Pfam; PF13855; LRR_8; 1. ... FT   SIGNAL          1..22
  - source_method: ProtNLM2
    source_version: UniProt 2024_06 pilot
    predicted_term:
      id: GO:0016301
      label: kinase activity
    predicted_term_type: GO_MF
    review:
      assessment: NPI
      error_type: DOMAIN_ARCHITECTURE_MISMATCH
      confidence_score: 0
      summary: >-
        The OpenScientist investigation strongly supports rejection of kinase activity: it integrates
        LRR-only domain assignments, a sequence scan finding no ordered kinase catalytic motifs, and
        an AlphaFold model assessed as an LRR fold without a kinase lobe. These complementary findings
        argue against a protein kinase catalytic domain in the 450-residue target, rather than merely
        noting the absence of a kinase annotation in UniProt. The report also explains why the ERECTA
        FunFam match supports a shared LRR region without transferring the kinase's catalytic activity.
        The rejection rests on this combined architecture and analysis evidence, not on absence of a
        single short motif; it is a computational assessment without a direct biochemical assay.
        The kinase prediction is therefore NPI; participation in a
        phosphorylation pathway is a separate question.
      supported_by:
        - reference_id:
            file: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:ARATH/F4JLB7/F4JLB7-uniprot.txt
          supporting_text: >-
            ID   F4JLB7_ARATH            Unreviewed;       450 AA. ... DR   GO; GO:0005886; C:plasma membrane;
            IBA:GO_Central. ... DR   GO; GO:0038023; F:signaling receptor activity; IBA:GO_Central. ...
            DR   InterPro; IPR001611; Leu-rich_rpt. ... DR   InterPro; IPR032675; LRR_dom_sf. ... DR   Pfam;
            PF00560; LRR_1; 3. ... DR   Pfam; PF13855; LRR_8; 1. ... FT   SIGNAL          1..22
references:
  - id: file:ARATH/F4JLB7/F4JLB7-hypotheses/prediction-kinase-activity/openscientist.md
    title: 'OpenScientist investigation: F4JLB7 kinase activity'
    reference_review:
      relevance: HIGH
      review_notes: >-
        Substantive computational synthesis directly addressing the kinase prediction. Domain assignments
        and the ERECTA FunFam entry agree with the cached UniProt cross-references. Motif and structural
        findings contribute to the combined case against protein kinase activity; motif absence alone
        is insufficient to exclude all kinase mechanisms. The available artifacts contain the final
        report in HTML and PDF, without executed analysis code. The proposed phosphorylation rejection
        exceeds the evidence against intrinsic catalysis. The report's proposed frequency-bias mechanism
        and gene-symbol carry-over are hypotheses, not established causes of the prediction.
  - id: file:ARATH/F4JLB7/F4JLB7-uniprot.txt
    title: F4JLB7-uniprot.txt