{"schema":"https://ver.cy/schemas/card/1.0.0","id":"vr.tr.leucine-rich-repeat-protein-family","code":"thing-q935326","url":"https://ver.cy/models/thing/q935326/","name":"leucine-rich repeat proteins","alternateNames":["Leucine-rich repeat, protein family"],"kind":"thing","status":"published","version":"0.1.0-research.1","language":"en","classifiers":{"family":"Thing Registry","category":"Physical world and living systems","entryKind":"thing","plane":"PHY","domain":["PHY.MAT"],"industry":[],"navPath":"","tags":[],"facets":{}},"whatItIs":"Leucine-rich repeat proteins are proteins containing tandem arrays of repeats enriched in leucine and other hydrophobic residues that typically form a curved alpha/beta horseshoe fold supporting molecular recognition; this structural grouping encompasses multiple whole-protein families.","purpose":"Enable an agent to recognise leucine-rich repeat proteins, assess evidence for their repeat architecture and functional state, and select justified annotation or experimental actions.","scope":{"in":["Evidence that a protein contains leucine-rich repeats rather than merely a high proportion of leucine","Repeat boundaries, repeat count, sequence variation and interruptions within an LRR array","LRR domain conformation, terminal protection and structural integrity","Whole-protein architecture and localisation as context for interpreting the LRR region","Experimentally supported LRR-mediated interactions and effects of sequence changes"],"out":["Free leucine and its chemical or nutritional properties","Complete models of individual LRR-containing receptors, enzymes or other named protein families","Full signalling pathways and organism-level phenotypes associated with particular members","Non-LRR repeat families such as ankyrin and tetratricopeptide repeats","Manufacturing, formulation and regulatory classification of products containing an LRR protein"],"boundaries":[]},"distinguishingFeatures":["Require repeat-profile or structural evidence; leucine enrichment alone does not establish an LRR assignment.","Evaluate tandem organisation and compatible repeat boundaries rather than treating an isolated short sequence match as a confirmed LRR domain.","Where structural evidence exists, assess compatibility with the curved solenoid architecture of LRR domains. [Structure-Aware Annotation of Leucine-rich Repeat Domains](https://pmc.ncbi.nlm.nih.gov/articles/PMC10634995/)","Distinguish a repeat annotation from a whole-protein family assignment; these are different classification levels. [InterPro entry types](https://www.ebi.ac.uk/training/online/courses/interpro-functional-and-structural-analysis/what-is-an-interpro-entry/interpro-entry-types/)","Require member-specific evidence before assigning a ligand, receptor role or catalytic activity from the presence of LRRs."],"structure":{"bundles":[{"id":"lrr-identity-and-membership","name":"LRR identity and membership","description":"Establish what the registry entry denotes and what supports inclusion of a candidate protein.","layers":[{"id":"classification-boundary","name":"Classification boundary","description":"Separate repeat, domain and whole-protein classifications.","findings":[{"id":"registered-family-meaning","name":"Registered family meaning","description":"Record the intended breadth of the existing registry entry without creating an unsupported narrower family.","questions":[{"text":"Does the originating registry record denote an LRR repeat class, an LRR-containing protein grouping or a specific homologous family?","id":"registered-family-meaning-q01","kind":"definition"},{"text":"Which existing models already cover this concept or particular member families?","id":"registered-family-meaning-q02","kind":"boundary"}]}]},{"id":"membership-evidence","name":"Membership evidence","description":"Evaluate candidate LRR assignments against their underlying sequence and annotation methods.","findings":[{"id":"supported-lrr-assignment","name":"Supported LRR assignment","description":"Require interpretable evidence for repeats and retain uncertainty around isolated or conflicting matches.","questions":[{"text":"Which sequence accession, version and residue intervals were assessed?","id":"supported-lrr-assignment-q01","kind":"provenance"},{"text":"Which repeat profiles or structural observations support the assignment, and with what scores or confidence?","id":"supported-lrr-assignment-q02","kind":"measurement"},{"text":"Could the match reflect leucine enrichment, low complexity or a different repeat architecture?","id":"supported-lrr-assignment-q03","kind":"boundary"}]}]}]},{"id":"repeat-array-architecture","name":"Repeat array architecture","description":"Describe how individual LRR units are organised within the protein.","layers":[{"id":"repeat-segmentation","name":"Repeat segmentation","description":"Locate repeat units and represent alternative boundary interpretations.","findings":[{"id":"repeat-map","name":"Repeat map","description":"Maintain an evidence-backed repeat map rather than a count inferred solely from domain length.","questions":[{"text":"How many repeats are supported, and what are their individual residue intervals and lengths?","id":"repeat-map-q01","kind":"measurement"},{"text":"Where do sequence-based and structure-based repeat boundaries disagree?","id":"repeat-map-q02","kind":"boundary"}]}]},{"id":"array-variation","name":"Array variation","description":"Characterise atypical units and discontinuities in the array.","findings":[{"id":"insertions-and-divergent-repeats","name":"Insertions and divergent repeats","description":"Record insertions, deletions and divergent units without automatically treating them as annotation errors.","questions":[{"text":"Which repeat positions contain insertions, deletions or departures from the assigned repeat profile?","id":"insertions-and-divergent-repeats-q01","kind":"measurement"},{"text":"Does each atypical segment remain part of the LRR array, form a separate domain or remain unresolved?","id":"insertions-and-divergent-repeats-q02","kind":"boundary"}]}]}]},{"id":"lrr-fold-and-integrity","name":"LRR fold and integrity","description":"Assess the three-dimensional organisation and physical integrity of the LRR region.","layers":[{"id":"solenoid-geometry","name":"Solenoid geometry","description":"Evaluate structural support for the assigned LRR architecture.","findings":[{"id":"observed-or-predicted-fold","name":"Observed or predicted fold","description":"Keep experimental structures and predictions distinguishable when assessing repeat packing and array conformation.","questions":[{"text":"Which structure, chain and residue coverage support the LRR fold assignment?","id":"observed-or-predicted-fold-q01","kind":"provenance"},{"text":"Which portions of the repeat array are experimentally resolved, confidently predicted or structurally uncertain?","id":"observed-or-predicted-fold-q02","kind":"measurement"}]}]},{"id":"array-ends-and-stability","name":"Array ends and stability","description":"Assess terminal protection and condition-dependent folding.","findings":[{"id":"cap-preservation-and-folding","name":"Cap preservation and folding","description":"Treat cap assignments and folding requirements as member-specific evidence needed for construct interpretation.","questions":[{"text":"What supports the proposed N-terminal and C-terminal caps or alternative protection of the array ends?","id":"cap-preservation-and-folding-q01","kind":"provenance"},{"text":"Under the tested conditions, what measurements distinguish a folded LRR construct from an unfolded or aggregated preparation?","id":"cap-preservation-and-folding-q02","kind":"measurement"},{"text":"Which proposed truncations require additional folding checks before their binding results can be interpreted?","id":"cap-preservation-and-folding-q03","kind":"action"}]}]}]},{"id":"protein-context-and-recognition","name":"Protein context and recognition","description":"Connect the LRR region to its protein environment and demonstrated interactions.","layers":[{"id":"domain-and-cellular-context","name":"Domain and cellular context","description":"Record architecture and localisation that constrain interpretation of the repeats.","findings":[{"id":"lrr-context-map","name":"LRR context map","description":"Relate the LRR region to neighbouring domains and its supported cellular setting.","questions":[{"text":"Which domains, signal sequences or membrane-spanning segments flank the LRR region?","id":"lrr-context-map-q01","kind":"boundary"},{"text":"What evidence establishes the cellular compartment and membrane orientation, where relevant?","id":"lrr-context-map-q02","kind":"provenance"}]}]},{"id":"partner-and-interface","name":"Partner and interface","description":"Evaluate interactions attributed specifically to the LRR region.","findings":[{"id":"lrr-mediated-binding","name":"LRR-mediated binding","description":"Separate direct binding and mapped interfaces from whole-protein association or downstream responses.","questions":[{"text":"Which partner binds the tested LRR-containing construct, and what establishes a direct interaction?","id":"lrr-mediated-binding-q01","kind":"provenance"},{"text":"Which repeat residues or surfaces are implicated by structural or perturbation evidence?","id":"lrr-mediated-binding-q02","kind":"measurement"},{"text":"Can the observed association be assigned to the LRR region rather than a neighbouring domain or bridging molecule?","id":"lrr-mediated-binding-q03","kind":"boundary"}]}]}]},{"id":"variation-and-experimental-decisions","name":"Variation and experimental decisions","description":"Guide interpretation of LRR changes and selection of informative follow-up work.","layers":[{"id":"variant-interpretation","name":"Variant interpretation","description":"Assess substitutions and repeat changes in their structural and experimental context.","findings":[{"id":"variant-effect-separation","name":"Variant effect separation","description":"Keep measured effects separate from predictions about repeat packing or partner recognition.","questions":[{"text":"Does the variant alter a repeat core, cap, candidate binding surface or repeat count?","id":"variant-effect-separation-q01","kind":"boundary"},{"text":"What measurements separate altered affinity from altered abundance, localisation or folding?","id":"variant-effect-separation-q02","kind":"measurement"},{"text":"Which matched control would best distinguish these explanations?","id":"variant-effect-separation-q03","kind":"action"}]}]},{"id":"construct-and-annotation-decisions","name":"Construct and annotation decisions","description":"Turn unresolved LRR assignments and functional claims into bounded next steps.","findings":[{"id":"evidence-limited-next-action","name":"Evidence-limited next action","description":"Choose follow-up actions that address specific uncertainties and define when an annotation can be strengthened.","questions":[{"text":"Which construct boundaries preserve the supported LRR array and terminal protection?","id":"evidence-limited-next-action-q01","kind":"action"},{"text":"What additional evidence would justify confirming the repeat assignment or transferring a functional annotation to another member?","id":"evidence-limited-next-action-q02","kind":"action"},{"text":"Which conclusion remains limited to the tested isoform, construct, partner and assay conditions?","id":"evidence-limited-next-action-q03","kind":"boundary"}]}]}]},{"id":"evidence-and-external-alignment","name":"Evidence and external alignment","description":"What the world already says about this thing, gathered so the model can be checked against it.","layers":[{"id":"reported-evidence","name":"Reported evidence","description":"Findings from the breadth pass, kept separate from the structural claims.","findings":[{"id":"evidence-confidence-notes","name":"Check these first","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these check these first hold for the sense of Leucine-rich repeat, protein family this model covers, and on what evidence?","id":"evidence-confidence-notes-q01","kind":"provenance"}]},{"id":"evidence-kinds","name":"Kinds and varieties","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these kinds and varieties hold for the sense of Leucine-rich repeat, protein family this model covers, and on what evidence?","id":"evidence-kinds-q01","kind":"provenance"}]},{"id":"evidence-identifiers","name":"Identifiers and schemes","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these identifiers and schemes hold for the sense of Leucine-rich repeat, protein family this model covers, and on what evidence?","id":"evidence-identifiers-q01","kind":"provenance"}]},{"id":"evidence-real-world-use","name":"Real-world use","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these real-world use hold for the sense of Leucine-rich repeat, protein family this model covers, and on what evidence?","id":"evidence-real-world-use-q01","kind":"provenance"}]},{"id":"evidence-measurements","name":"Typical measurements","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these typical measurements hold for the sense of Leucine-rich repeat, protein family this model covers, and on what evidence?","id":"evidence-measurements-q01","kind":"provenance"}]},{"id":"evidence-failure-modes-and-hazards","name":"Failure modes and hazards","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these failure modes and hazards hold for the sense of Leucine-rich repeat, protein family this model covers, and on what evidence?","id":"evidence-failure-modes-and-hazards-q01","kind":"provenance"}]},{"id":"evidence-neighbours","name":"Neighbouring kinds and how to tell them apart","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these neighbouring kinds and how to tell them apart hold for the sense of Leucine-rich repeat, protein family this model covers, and on what evidence?","id":"evidence-neighbours-q01","kind":"provenance"}]}]}]}]},"agentConduct":{"may":["Describe leucine-rich repeats and the proteins that carry them from structural biology sources.","Annotate sequences with the motif using recognized databases and stated confidence."],"mustNot":["Present a predicted repeat as confirmed structure or function without evidence.","Claim a disease link for a carrier protein beyond the published evidence.","Help engineer immune or pathogen proteins to harm people, crops or animals."],"requiresHuman":["Publishing functional claims used in clinical or crop decisions."]},"ethics":{"considerations":["Many immune receptors in plants and animals are built from these repeats; errors misdirect research.","Work on immune receptors and pathogens can have dual-use stakes."],"affectedParties":["Researchers and database users","Patients and farmers who rely on the research"]},"owners":{"steward":"Nobody owns the concept; curated protein databases maintain its classification.","roles":[],"masterSystems":["Protein family and structure databases"]},"relations":[{"target":"Q8054","type":"parent","note":"registry parent class"}],"interaction":{"identity":{"applicability":"required","items":["Vercy registry: vr.tr.leucine-rich-repeat-protein-family","Wikidata: Q935326 (https://www.wikidata.org/wiki/Q935326)"]},"properties":{"applicability":"required","items":["Classification level: individual repeat | LRR domain | LRR-containing protein | demonstrated homologous family | unresolved","Reference protein identity: sequence accession and version, organism, isoform and construct relationship","LRR assignment support: sequence-profile supported | structure supported | both | disputed | insufficient","Repeat count and boundaries: number of repeats and residue intervals on a versioned sequence, with uncertainty","Repeat length distribution: amino acid residues per repeat","Terminal protection: N-terminal and C-terminal cap assignments recorded separately as supported | predicted | absent | unresolved","LRR structural state: folded | partly folded | unfolded | aggregated | unresolved, with conditions and method","Neighbouring domain architecture: ordered links to adjacent domains, signal sequences and membrane-spanning segments","Interaction evidence: partner identity, tested construct, assay, conditions and supporting source","Binding affinity: Kd in mol/L where measured, including uncertainty, stoichiometry and assay conditions"]},"recognition":{"applicability":"required","items":["Not visible; in structures it forms a curved horseshoe or solenoid of repeated units."]},"capabilities":{"applicability":"required","items":["Annotate candidate LRR arrays on a versioned protein sequence and flag ambiguous boundaries.","Compare LRR architectures while keeping repeat similarity separate from whole-protein homology.","Map variants onto candidate core, terminal-cap and interaction-surface positions.","Choose domain constructs that preserve supported repeat boundaries and terminal protection.","Prioritise structural or binding experiments that resolve a specific uncertainty about the LRR region.","Restrict functional annotation to the proteins, constructs and conditions supported by evidence."]},"hazards":{"applicability":"required","items":["Repeat-counting errors spread through automated annotation."]},"interfaces":{"applicability":"not-applicable","items":[]},"context":{"applicability":"required","items":["Leucine-rich repeats occur in proteins studied in molecular biology, including proteins involved in recognition, adhesion and immune responses.","Researchers examine their sequence repeats and curved structural scaffolds when annotating proteins or investigating molecular interactions.","The motif helps describe protein architecture but does not by itself establish a protein's function or membership in a single evolutionary family."]}},"sources":[{"title":"Wikidata item Q935326: Leucine-rich repeat, protein family","url":"https://www.wikidata.org/wiki/Q935326","note":"identity and sense of the item"},{"title":"Wikipedia: Leucine-rich repeat","url":"https://en.wikipedia.org/wiki/Leucine-rich_repeat","note":"general description of the item"}],"openQuestions":["What originating database identifier and definition establish the intended meaning of the registry's 'protein family' label?","Does an existing Vercy world model already cover this LRR concept and therefore need to be linked instead of duplicated?","Which repeat classifications and annotation resources should define membership, and how should conflicting assignments be adjudicated?","How should partial sequences, isolated candidate repeats and highly divergent arrays be represented without overstating membership?","Which proposed structural and functional characteristics are supported across the intended grouping, and which must remain restricted to particular member families?"],"resources":{"spec":"/models/things/publications/thing-q935326/spec.json"},"provenance":{"origin":"thing registry research (pass 2)","builtFrom":["models/things/publications/thing-q935326/spec.json"],"providers":["Codex"],"researchStatus":"unreviewed","generatedAt":"2026-09-12T10:56:25Z","builder":"tools/build_cards.py@1.0.0"},"completeness":{"sections":{"classifiers":"filled","whatItIs":"filled","purpose":"filled","distinguishingFeatures":"filled","structure":"filled","agentConduct":"filled","ethics":"filled","owners":"filled","relations":"filled","interaction.identity":"filled","interaction.properties":"filled","interaction.recognition":"filled","interaction.capabilities":"filled","interaction.hazards":"filled","interaction.interfaces":"not-applicable","interaction.context":"filled","sources":"filled"},"notes":{"_gate":"Published through the thing publication gate 1.0 on 2026-10-07T12:16:35+00:00: completeness 1.00; sense: Wikidata description; 2 live sources; review by codex: pass","interaction.interfaces":"No dedicated legal requirement or universal technical standard applies to the leucine-rich repeat motif itself."},"score":1.0}}