{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-13T02:04:23Z", "providers": [ "Claude" ], "breadth": "written by Claude from model knowledge without web access - no source was read, every claim is a lead to verify", "pass": 2, "wave": 3, "engine": "claude", "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T10:00:00Z", "ingestedAt": "2026-10-06T07:06:04+00:00", "fields": [ "agent_conduct", "ethics", "owners" ] }, "gate": { "passed": true, "version": "1.0", "at": "2026-10-07T10:10:29+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q2609152", "registryId": "vr.tr.acyltransferases", "name": "acyltransferases", "version": "0.2.0-wave.3", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q2609152/", "model": { "registry_id": "vr.tr.acyltransferases", "name": "acyltransferases", "purpose": "Let an agent explain acyltransferases and their classification, relay subclasses and examples from enzyme databases, describe roles in metabolism, epigenetics and biosynthesis, and distinguish acyltransferases from acylases and lyases.", "definition": "A class of enzymes that transfer acyl groups from a donor such as acyl-CoA to an acceptor molecule, classified as EC 2.3 and including aminoacyltransferases, acetyltransferases such as histone acetyltransferases, lipoyl and octanoyl transferases, polyketide synthases such as lovastatin nonaketide synthase, citramalate synthase and phosphate butyryltransferase; acyltransferases are central to fatty acid and lipid metabolism, protein modification, natural product biosynthesis and gene regulation.", "what_it_is_for": "Transferring acyl groups in metabolism and biosynthesis.", "affordances": [ "explain the class and subclasses", "relay examples and nomenclature", "describe metabolic and regulatory roles", "distinguish from related enzymes" ], "distinguishing_features": [ "Acyl group transfer", "Acyl-CoA donors common", "Subclasses by group transferred", "Roles in lipids and epigenetics" ], "appearance": "Not visible; proteins shown as structural models.", "visual_identification": [ "EC 2.3 enzymes transferring acyl groups", "Acetyltransferases, aminoacyltransferases, polyketide synthases and others", "Acylases and hydrolases cleave acyl groups; lyases form bonds without transfer" ], "physical_properties": [ { "quantity": "Molecular mass", "unit": "kDa", "typical_range": "", "note": "Determine mass from the protein sequence or mass spectrometry and specify whether it describes a subunit or an assembled complex." }, { "quantity": "Hydrodynamic radius", "unit": "nm", "typical_range": "", "note": "Determine effective size in solution using a suitable diffusion measurement under stated solvent conditions." }, { "quantity": "Isoelectric point", "unit": "pH units", "typical_range": "", "note": "Measure the pH of zero net electrical charge by isoelectric focusing or report a sequence-based estimate." }, { "quantity": "Thermal unfolding midpoint", "unit": "deg C", "typical_range": "", "note": "Determine the midpoint of an observed unfolding transition using calorimetry or spectroscopy under stated solution conditions." } ], "families_and_kinds": [ "EC 2.3.1 acyltransferases transferring groups other than aminoacyl, including acetyltransferases", "EC 2.3.2 aminoacyltransferases", "EC 2.3.3 acyl groups converted to alkyl on transfer, such as citramalate synthase", "histone acetyltransferases", "polyketide synthases such as lovastatin nonaketide synthase", "lipoyl and octanoyl transferases", "phosphate acyltransferases such as phosphate butyryltransferase" ], "related_models": [ { "relation": "is a kind of", "target": "transferase, transferring acyl groups", "why": "in registry terms" }, { "relation": "is classified as", "target": "EC 2.3", "why": "in the Enzyme Commission system" }, { "relation": "uses", "target": "acyl-CoA", "why": "as a common donor" }, { "relation": "acts in", "target": "fatty acid metabolism", "why": "among other pathways" } ], "identifiers": [ { "scheme": "EC number", "value_or_pattern": "2.3.-.-", "note": "" }, { "scheme": "Gene Ontology", "value_or_pattern": "GO:0016746", "note": "acyltransferase activity" } ], "standards_and_regulation": [ "IUBMB enzyme nomenclature", "Regulation of enzyme inhibitors as drugs" ], "failure_modes_and_hazards": [ "Misclassifying enzymes", "Outdated nomenclature", "Confusing acyltransferases with acylases" ], "in_scope": [], "out_of_scope": [], "characteristics": [], "agent_conduct": { "may": [ "Explain acyltransferase classes and their biological roles with EC numbers.", "Report enzyme data from curated databases with source." ], "must_not": [ "Present research findings on these enzymes as proven treatments.", "Misassign EC classifications or merge distinct enzymes.", "Give dosing or self-treatment advice based on enzyme activity." ], "requires_human": [ "Using enzyme findings to advise on a patient's treatment." ] }, "ethics": { "considerations": [ "Overstated research claims about enzymes in disease mislead patients.", "Accurate classification underpins drug development and safety." ], "affected_parties": [ "Researchers", "Patients awaiting therapies" ] }, "owners": { "steward": "Nobody owns the class; the enzyme nomenclature committee assigns EC numbers.", "master_systems": [ "Enzyme nomenclature lists" ] } }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q2609152: acyltransferases", "url": "https://www.wikidata.org/wiki/Q2609152", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Acyltransferase", "url": "https://en.wikipedia.org/wiki/Acyltransferase", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "understand", "name": "Understand", "description": "What acyltransferases are.", "rationale": "Science.", "layers": [ { "id": "definition", "name": "Definition", "description": "Definition and subclasses.", "findings": [ { "id": "definition-finding", "name": "Definition", "description": "Definition.", "questions": [ { "text": "What is an acyltransferase, and what subclasses exist?", "kind": "definition" }, { "text": "Is the enzyme an acyltransferase, an acylase or a lyase?", "kind": "boundary" } ] } ] }, { "id": "mechanism", "name": "Mechanism", "description": "Mechanisms.", "findings": [ { "id": "mechanism-finding", "name": "Mechanism", "description": "Mechanism.", "questions": [ { "text": "How do acyltransferases transfer acyl groups from acyl-CoA and other donors?", "kind": "definition" }, { "text": "Which entry fits the specific enzyme?", "kind": "action" } ] } ] } ] }, { "id": "biology", "name": "Biology", "description": "Biological roles.", "rationale": "Science.", "layers": [ { "id": "metabolism", "name": "Metabolism", "description": "Metabolism.", "findings": [ { "id": "metabolism-finding", "name": "Metabolism", "description": "Metabolism.", "questions": [ { "text": "What roles do acyltransferases play in lipid, fatty acid and amino acid metabolism?", "kind": "provenance" }, { "text": "Which entry fits the specific pathway?", "kind": "action" } ] } ] }, { "id": "regulation", "name": "Regulation", "description": "Protein acetylation and epigenetics.", "findings": [ { "id": "regulation-finding", "name": "Regulation", "description": "Regulation.", "questions": [ { "text": "How do histone and protein acetyltransferases regulate gene expression?", "kind": "provenance" }, { "text": "Which references are standard?", "kind": "provenance" } ] } ] } ] }, { "id": "apply", "name": "Apply", "description": "Applications.", "rationale": "Application.", "layers": [ { "id": "biosynthesis", "name": "Biosynthesis", "description": "Natural products.", "findings": [ { "id": "biosynthesis-finding", "name": "Biosynthesis", "description": "Biosynthesis.", "questions": [ { "text": "How do polyketide synthases and related acyltransferases build natural products such as lovastatin?", "kind": "provenance" }, { "text": "Which entry fits polyketide synthase?", "kind": "action" } ] } ] }, { "id": "drugs", "name": "Drugs", "description": "Drug targets.", "findings": [ { "id": "drugs-finding", "name": "Drugs", "description": "Drugs.", "questions": [ { "text": "Which acyltransferases are drug targets, with findings attributed?", "kind": "provenance" }, { "text": "Which sources are cited?", "kind": "provenance" } ] } ] } ] }, { "id": "context", "name": "Context", "description": "Nomenclature and history.", "rationale": "Context.", "layers": [ { "id": "nomenclature", "name": "Nomenclature", "description": "Nomenclature.", "findings": [ { "id": "nomenclature-finding", "name": "Nomenclature", "description": "Nomenclature.", "questions": [ { "text": "How does the EC system organise acyltransferases, and how are new enzymes named?", "kind": "provenance" }, { "text": "Which entry fits enzyme nomenclature?", "kind": "action" } ] } ] }, { "id": "history", "name": "History", "description": "History.", "findings": [ { "id": "history-finding", "name": "History", "description": "History.", "questions": [ { "text": "How were acyltransferases and acyl-CoA discovered, including Lipmann work on coenzyme A?", "kind": "provenance" }, { "text": "Which entry fits the history of biochemistry?", "kind": "action" } ] } ] } ] } ] }, "openQuestions": [ "Should histone acetyltransferase be a separate primary entry?", "How should enzyme databases be linked?", "The registry entry has merged aliases naming specific enzymes; should they be split off?" ], "statistics": { "bundles": 4, "layers": 8, "findings": 8, "questions": 16 } }