{
  "vercy": "1.0-draft",
  "publication": {
    "status": "research-draft",
    "adjudicationStatus": "unreviewed",
    "publishableCanonical": false,
    "generatedAt": "2026-09-13T15:53:25Z",
    "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": "2026-10-06T12:00:00Z",
      "ingestedAt": "2026-10-06T07:35:10+00:00",
      "fields": [
        "agent_conduct",
        "ethics",
        "owners"
      ]
    },
    "gate": {
      "passed": true,
      "version": "1.0",
      "at": "2026-10-06T19:51:59+00:00",
      "evidence": [
        "completeness 1.00",
        "sense: Wikidata description",
        "2 live sources",
        "review by codex: pass"
      ]
    }
  },
  "metaModel": {
    "id": "THING-Q3381520",
    "registryId": "vr.tr.phosphotransferase",
    "name": "phosphotransferase",
    "version": "0.2.0-wave.4",
    "entryKind": "thing",
    "family": "Thing Registry",
    "domain": [
      "PHY.MAT"
    ],
    "status": "research-draft"
  },
  "canonicalUrl": "https://ver.cy/models/thing/q3381520/",
  "model": {
    "registry_id": "vr.tr.phosphotransferase",
    "name": "phosphotransferase",
    "purpose": "Let an agent explain phosphotransferases and their subclasses, relay mechanisms and biological roles from biochemistry sources, describe the enzymes the registry aliases name, and distinguish phosphotransferases from phosphatases, phosphorylases and the bacterial phosphotransferase sugar transport system.",
    "definition": "An enzyme of class EC 2.7 that transfers a phosphorus-containing group from a donor, usually ATP, to an acceptor, including kinases that transfer phosphate groups, such as gluconate kinase and dephospho-CoA kinase, and nucleotidyltransferases that transfer nucleotide groups, such as FMN adenylyltransferase and phosphatidate cytidylyltransferase, along with specialised families such as the KptA/Tpt1 tRNA phosphotransferases; phosphotransferases are central to signalling and metabolism.",
    "what_it_is_for": "Not applicable; an enzyme class.",
    "affordances": [
      "explain the class",
      "relay mechanisms and roles",
      "describe named enzymes",
      "distinguish related enzymes"
    ],
    "distinguishing_features": [
      "Group transfer",
      "Kinases and nucleotidyltransferases",
      "ATP donors",
      "Central to metabolism"
    ],
    "appearance": "Not a visible object; proteins.",
    "visual_identification": [
      "Enzymes transferring phosphorus-containing groups",
      "Kinases such as gluconate kinase and dephospho-CoA kinase; nucleotidyltransferases such as FMN adenylyltransferase and phosphatidate cytidylyltransferase; KptA/Tpt1",
      "Phosphatases remove phosphate; phosphorylases add inorganic phosphate; the PTS is a transport system"
    ],
    "physical_properties": [
      {
        "quantity": "EC class",
        "typical_range": "EC 2.7",
        "unit": "note",
        "note": ""
      },
      {
        "quantity": "human protein kinases",
        "typical_range": "about 500",
        "unit": "count",
        "note": "kinome"
      },
      {
        "quantity": "common donor",
        "typical_range": "ATP",
        "unit": "note",
        "note": ""
      }
    ],
    "families_and_kinds": [
      "protein kinases",
      "metabolic kinases such as gluconate and dephospho-CoA kinase",
      "nucleotidyltransferases such as FMN adenylyltransferase",
      "CDP-diacylglycerol synthases such as phosphatidate cytidylyltransferase",
      "RNA phosphotransferases such as KptA/Tpt1"
    ],
    "related_models": [
      {
        "relation": "is a kind of",
        "target": "transferase",
        "why": "in registry terms"
      },
      {
        "relation": "includes",
        "target": "kinase",
        "why": "as a major subclass"
      },
      {
        "relation": "is contrasted with",
        "target": "phosphatase",
        "why": "which removes phosphate"
      },
      {
        "relation": "uses",
        "target": "adenosine triphosphate",
        "why": "as a common donor"
      }
    ],
    "identifiers": [
      {
        "scheme": "EC",
        "value_or_pattern": "2.7",
        "note": "transferring phosphorus-containing groups"
      },
      {
        "scheme": "MeSH",
        "value_or_pattern": "D010770",
        "note": "Phosphotransferases"
      }
    ],
    "standards_and_regulation": [
      "IUBMB enzyme nomenclature"
    ],
    "failure_modes_and_hazards": [
      "Confusing phosphotransferases with phosphatases",
      "Registry aliases mixing subclasses and specific enzymes",
      "Confusing with the bacterial PTS"
    ],
    "in_scope": [],
    "out_of_scope": [],
    "characteristics": [],
    "agent_conduct": {
      "may": [
        "Explain phosphotransferases of EC 2.7 and their subclasses, citing enzyme nomenclature sources.",
        "Distinguish them from phosphatases and from the bacterial PTS."
      ],
      "must_not": [
        "Treat specific enzymes in the aliases as synonyms of the whole class.",
        "Give medical advice based on enzyme functions for a specific person.",
        "Invent EC numbers or enzyme activities."
      ],
      "requires_human": [
        "Changing curated enzyme classification records."
      ]
    },
    "ethics": {
      "considerations": [
        "Errors in enzyme classification propagate through databases and research.",
        "Kinase drugs are medical topics where individual advice needs a clinician."
      ],
      "affected_parties": [
        "Researchers and students",
        "Curators of biological databases"
      ]
    },
    "owners": {
      "steward": "Nobody owns the class; the international enzyme nomenclature committee maintains its classification.",
      "master_systems": [
        "Enzyme nomenclature lists of the international biochemistry union"
      ]
    }
  },
  "sources": [
    {
      "id": "wikidata",
      "title": "Wikidata item Q3381520: phosphotransferase",
      "url": "https://www.wikidata.org/wiki/Q3381520",
      "url_status": "live",
      "what_it_supports": "identity and sense of the item",
      "checked_by": "wikidata-api"
    },
    {
      "id": "wikipedia-en",
      "title": "Wikipedia: Phosphotransferase",
      "url": "https://en.wikipedia.org/wiki/Phosphotransferase",
      "url_status": "live",
      "what_it_supports": "general description of the item",
      "checked_by": "wikidata-api sitelink"
    }
  ],
  "structure": {
    "bundles": [
      {
        "id": "understand",
        "name": "Understand",
        "description": "What a phosphotransferase is.",
        "rationale": "Science.",
        "layers": [
          {
            "id": "definition",
            "name": "Definition",
            "description": "Definition.",
            "findings": [
              {
                "id": "definition-finding",
                "name": "Definition",
                "description": "Definition.",
                "questions": [
                  {
                    "text": "What is a phosphotransferase, and how does it differ from phosphatases, phosphorylases and the PTS?",
                    "kind": "definition"
                  },
                  {
                    "text": "Is the question about the class, a subclass, an enzyme or a disease link?",
                    "kind": "boundary"
                  }
                ]
              }
            ]
          },
          {
            "id": "enzymes",
            "name": "Enzymes",
            "description": "Named enzymes.",
            "findings": [
              {
                "id": "enzymes-finding",
                "name": "Enzymes",
                "description": "Enzymes.",
                "questions": [
                  {
                    "text": "What do gluconate kinase, dephospho-CoA kinase, FMN adenylyltransferase, phosphatidate cytidylyltransferase and Tpt1 do?",
                    "kind": "definition"
                  },
                  {
                    "text": "Which entry fits the specific enzyme?",
                    "kind": "action"
                  }
                ]
              }
            ]
          }
        ]
      },
      {
        "id": "biochemistry",
        "name": "Biochemistry",
        "description": "Mechanism.",
        "rationale": "Science.",
        "layers": [
          {
            "id": "classification",
            "name": "Classification",
            "description": "Classification.",
            "findings": [
              {
                "id": "classification-finding",
                "name": "Classification",
                "description": "Classification.",
                "questions": [
                  {
                    "text": "How is EC 2.7 subdivided by acceptor group?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Which references are standard?",
                    "kind": "provenance"
                  }
                ]
              }
            ]
          },
          {
            "id": "mechanism",
            "name": "Mechanism",
            "description": "Mechanism.",
            "findings": [
              {
                "id": "mechanism-finding",
                "name": "Mechanism",
                "description": "Mechanism.",
                "questions": [
                  {
                    "text": "How do kinases and nucleotidyltransferases catalyse group transfer?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Which sources are cited?",
                    "kind": "provenance"
                  }
                ]
              }
            ]
          }
        ]
      },
      {
        "id": "roles",
        "name": "Roles",
        "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 these enzymes play in coenzyme A, flavin and lipid synthesis?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Which entry fits coenzyme A biosynthesis?",
                    "kind": "action"
                  }
                ]
              }
            ]
          },
          {
            "id": "signalling",
            "name": "Signalling",
            "description": "Signalling and drugs.",
            "findings": [
              {
                "id": "signalling-finding",
                "name": "Signalling",
                "description": "Signalling.",
                "questions": [
                  {
                    "text": "How do protein kinases drive signalling, and how are they targeted by drugs?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Which entry fits kinase inhibitor?",
                    "kind": "action"
                  }
                ]
              }
            ]
          }
        ]
      },
      {
        "id": "context",
        "name": "Context",
        "description": "History.",
        "rationale": "Context.",
        "layers": [
          {
            "id": "history",
            "name": "History",
            "description": "History.",
            "findings": [
              {
                "id": "history-finding",
                "name": "History",
                "description": "History.",
                "questions": [
                  {
                    "text": "How were phosphotransferases discovered and classified?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Which entry fits the history of enzymology?",
                    "kind": "action"
                  }
                ]
              }
            ]
          },
          {
            "id": "pts",
            "name": "PTS",
            "description": "Bacterial PTS.",
            "findings": [
              {
                "id": "pts-finding",
                "name": "PTS",
                "description": "PTS.",
                "questions": [
                  {
                    "text": "What is the bacterial phosphotransferase system, and where is it covered?",
                    "kind": "provenance"
                  },
                  {
                    "text": "Which entry fits phosphotransferase system?",
                    "kind": "action"
                  }
                ]
              }
            ]
          }
        ]
      }
    ]
  },
  "openQuestions": [
    "Should kinase and nucleotidyltransferase be separate primary entries?",
    "How should biochemistry sources 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
  }
}