{ "vercy": "1.0-draft", "publication": { "status": "research-draft", "adjudicationStatus": "unreviewed", "publishableCanonical": false, "generatedAt": "2026-09-13T19:53:26Z", "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": 4, "engine": "claude", "enrichment": { "pass": 3, "engine": "claude", "producedAt": "2026-10-06T10:00:00Z", "ingestedAt": "2026-10-06T07:34:29+00:00", "fields": [ "agent_conduct", "ethics", "owners" ] }, "gate": { "passed": true, "version": "1.0", "at": "2026-10-06T19:52:00+00:00", "evidence": [ "completeness 1.00", "sense: Wikidata description", "2 live sources", "review by codex: pass" ] } }, "metaModel": { "id": "THING-Q4746164", "registryId": "vr.tr.amidohydrolases", "name": "amidohydrolases", "version": "0.2.0-wave.4", "entryKind": "thing", "family": "Thing Registry", "domain": [ "PHY.MAT" ], "status": "research-draft" }, "canonicalUrl": "https://ver.cy/models/thing/q4746164/", "model": { "registry_id": "vr.tr.amidohydrolases", "name": "amidohydrolases", "purpose": "Let an agent explain amidohydrolases, relay classification, mechanisms and biological roles from enzymology sources, describe the enzymes the registry aliases name as examples, and distinguish amidohydrolases from peptidases, the structural amidohydrolase superfamily and other hydrolases.", "definition": "A group of hydrolase enzymes, classified mainly in EC 3.5.1, that cleave carbon-nitrogen bonds other than peptide bonds in linear amides, such as protein-glutamine glutaminase, streptothricin hydrolase that confers antibiotic resistance, N-acetylglucosamine-6-phosphate deacetylase in amino sugar metabolism, N-carbamoylputrescine amidase in polyamine synthesis, the bacterial chemoreceptor glutamine deamidase CheD and formyltetrahydrofolate deformylase in folate metabolism; the amidohydrolase superfamily is also a structural grouping with a shared metal-binding fold.", "what_it_is_for": "Not applicable; an enzyme class.", "affordances": [ "explain classification", "relay mechanisms and roles", "describe named enzymes", "distinguish related enzymes" ], "distinguishing_features": [ "Non-peptide C-N bonds", "Diverse substrates", "Metabolic roles", "Some medical uses" ], "appearance": "Not a visible object; proteins.", "visual_identification": [ "Enzymes hydrolysing non-peptide amide bonds", "Protein-glutamine glutaminase, streptothricin hydrolase, GlcNAc-6-P deacetylase, N-carbamoylputrescine amidase, CheD, formyltetrahydrofolate deformylase", "Peptidases cleave peptide bonds; the amidohydrolase superfamily is a structural fold; other hydrolases act on esters or glycosides" ], "physical_properties": [ { "quantity": "EC subclass", "typical_range": "3.5.1", "unit": "code", "note": "linear amides" }, { "quantity": "examples", "typical_range": "urease, asparaginase, amidases", "unit": "list", "note": "" }, { "quantity": "superfamily feature", "typical_range": "TIM-barrel with metal centre", "unit": "note", "note": "structural grouping" } ], "families_and_kinds": [ "amidases", "deacetylases", "deamidases", "deformylases", "antibiotic-inactivating hydrolases", "therapeutic enzymes such as asparaginase" ], "related_models": [ { "relation": "is a kind of", "target": "hydrolase", "why": "in registry terms" }, { "relation": "is classified in", "target": "Enzyme Commission number", "why": "EC 3.5.1" }, { "relation": "includes", "target": "asparaginase", "why": "" }, { "relation": "is contrasted with", "target": "peptidase", "why": "" } ], "identifiers": [ { "scheme": "EC", "value_or_pattern": "3.5.1", "note": "linear amide hydrolases" } ], "standards_and_regulation": [ "IUBMB enzyme nomenclature" ], "failure_modes_and_hazards": [ "Confusing EC class and structural superfamily", "Treating specific enzymes as synonyms", "Registry aliases naming individual enzymes" ], "in_scope": [], "out_of_scope": [], "characteristics": [], "agent_conduct": { "may": [ "Explain amidohydrolases, their EC 3.5.1 classification and biological roles from enzymology sources.", "Relay examples of these enzymes in metabolism and industry with citations.", "Distinguish amidohydrolases from peptidases and other hydrolases." ], "must_not": [ "Present an enzyme supplement as a treatment for disease without evidence.", "Give laboratory procedures for handling enzymes to a person without lab safety training.", "Assign a function to an enzyme that its database entry does not support.", "Confuse individual enzyme names within the group." ], "requires_human": [ "Using enzyme data to decide a patient's treatment." ] }, "ethics": { "considerations": [ "Misattributed enzyme functions can mislead research and teaching.", "Enzyme products are marketed with health claims that need honest checking." ], "affected_parties": [ "Students and researchers", "Patients", "Consumers of supplements" ] }, "owners": { "steward": "Nobody owns the enzyme group; enzyme nomenclature committees maintain its classification.", "master_systems": [ "Enzyme nomenclature databases" ] } }, "sources": [ { "id": "wikidata", "title": "Wikidata item Q4746164: amidohydrolases", "url": "https://www.wikidata.org/wiki/Q4746164", "url_status": "live", "what_it_supports": "identity and sense of the item", "checked_by": "wikidata-api" }, { "id": "wikipedia-en", "title": "Wikipedia: Amidohydrolase", "url": "https://en.wikipedia.org/wiki/Amidohydrolase", "url_status": "live", "what_it_supports": "general description of the item", "checked_by": "wikidata-api sitelink" } ], "structure": { "bundles": [ { "id": "understand", "name": "Understand", "description": "What amidohydrolases are.", "rationale": "Science.", "layers": [ { "id": "definition", "name": "Definition", "description": "Definition.", "findings": [ { "id": "definition-finding", "name": "Definition", "description": "Definition.", "questions": [ { "text": "What are amidohydrolases, and how do they differ from peptidases, the structural superfamily and other hydrolases?", "kind": "definition" }, { "text": "Is the question about enzymology, a specific enzyme, medicine or industry?", "kind": "boundary" } ] } ] }, { "id": "named", "name": "Named enzymes", "description": "Named enzymes.", "findings": [ { "id": "named-finding", "name": "Named enzymes", "description": "Named enzymes.", "questions": [ { "text": "What do protein-glutamine glutaminase, streptothricin hydrolase, GlcNAc-6-P deacetylase, N-carbamoylputrescine amidase, CheD and formyltetrahydrofolate deformylase do?", "kind": "definition" }, { "text": "Which entry fits the specific enzyme?", "kind": "action" } ] } ] } ] }, { "id": "biochemistry", "name": "Biochemistry", "description": "Biochemistry.", "rationale": "Science.", "layers": [ { "id": "mechanism", "name": "Mechanism", "description": "Mechanism.", "findings": [ { "id": "mechanism-finding", "name": "Mechanism", "description": "Mechanism.", "questions": [ { "text": "How do amidohydrolases catalyse amide bond hydrolysis?", "kind": "provenance" }, { "text": "Which references are standard?", "kind": "provenance" } ] } ] }, { "id": "classification", "name": "Classification", "description": "Classification.", "findings": [ { "id": "classification-finding", "name": "Classification", "description": "Classification.", "questions": [ { "text": "How does the EC system classify amidohydrolases?", "kind": "provenance" }, { "text": "Which sources are cited?", "kind": "provenance" } ] } ] } ] }, { "id": "applications", "name": "Applications", "description": "Applications.", "rationale": "Application.", "layers": [ { "id": "medicine", "name": "Medicine", "description": "Medicine.", "findings": [ { "id": "medicine-finding", "name": "Medicine", "description": "Medicine.", "questions": [ { "text": "How is asparaginase used in leukaemia treatment?", "kind": "provenance" }, { "text": "Which entry fits asparaginase?", "kind": "action" } ] } ] }, { "id": "industry", "name": "Industry", "description": "Food and industry.", "findings": [ { "id": "industry-finding", "name": "Industry", "description": "Industry.", "questions": [ { "text": "How is protein-glutaminase used in food processing?", "kind": "provenance" }, { "text": "Which entry fits industrial enzymes?", "kind": "action" } ] } ] } ] }, { "id": "context", "name": "Context", "description": "Microbiology.", "rationale": "Context.", "layers": [ { "id": "resistance", "name": "Resistance", "description": "Antibiotic resistance.", "findings": [ { "id": "resistance-finding", "name": "Resistance", "description": "Resistance.", "questions": [ { "text": "How do hydrolases such as streptothricin hydrolase inactivate antibiotics?", "kind": "provenance" }, { "text": "Which entry fits antimicrobial resistance?", "kind": "action" } ] } ] }, { "id": "chemotaxis", "name": "Chemotaxis", "description": "Chemotaxis.", "findings": [ { "id": "chemotaxis-finding", "name": "Chemotaxis", "description": "Chemotaxis.", "questions": [ { "text": "How does CheD modify chemoreceptors in bacterial chemotaxis?", "kind": "provenance" }, { "text": "Which entry fits chemotaxis?", "kind": "action" } ] } ] } ] } ] }, "openQuestions": [ "Should the named enzymes be separate entries?", "How should BRENDA and ExplorEnz 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 } }