{"schema":"https://ver.cy/schemas/card/1.0.0","id":"vr.tr.protein-catabolic-process","code":"thing-q14876077","url":"https://ver.cy/models/thing/q14876077/","name":"protein catabolic process","alternateNames":["epidermal growth factor catabolic process","low-density lipoprotein particle receptor catabolic process","glycoprotein catabolic process","hemoglobin catabolic process","lipoprotein catabolic process","proteasomal protein catabolic process","insulin catabolic process","mitochondrial protein catabolic process","protein catabolic process in the vacuole","histone catabolic process","rhodopsin catabolic process","PSII associated light-harvesting complex II catabolic process"],"kind":"thing","status":"published","version":"0.2.0-wave.5","language":"en","classifiers":{"family":"Thing Registry","category":"Activities and processes","entryKind":"thing","plane":"ACT","domain":["ACT.PRC"],"industry":[],"navPath":"","tags":[],"facets":{}},"whatItIs":"The chemical reactions and pathways resulting in the breakdown of a protein by destruction of its native, active configuration, with or without hydrolysis of peptide bonds (Gene Ontology GO:0030163); in eukaryotes mainly through the ubiquitin-proteasome system and lysosomal or vacuolar pathways, and in bacteria through ATP-dependent proteases.","purpose":"Let an agent explain protein breakdown pathways, find Gene Ontology annotations, and relate protein degradation to physiology and disease with sources.","scope":{"in":[],"out":[],"boundaries":[]},"distinguishingFeatures":["The ubiquitin-proteasome system degrades most short-lived proteins.","Autophagy delivers proteins and organelles to lysosomes.","Denaturation without hydrolysis also counts as catabolism in the GO definition."],"structure":{"bundles":[{"id":"pathway","name":"Pathway","description":"Which route.","layers":[{"id":"route","name":"Route","description":"Proteasome or lysosome.","findings":[{"id":"route","name":"Route","description":"Pathway and machinery.","questions":[{"text":"Which pathway degrades the protein?","kind":"provenance"},{"text":"What evidence shows it?","kind":"provenance"}]}]},{"id":"signal","name":"Signal","description":"Degrons and tags.","findings":[{"id":"signal","name":"Signal","description":"Tag.","questions":[{"text":"Which signal targets it, such as ubiquitin chains?","kind":"provenance"},{"text":"Which enzymes add it?","kind":"provenance"}]}]}]},{"id":"annotation","name":"Annotation","description":"Databases.","layers":[{"id":"go-terms","name":"GO terms","description":"Ontology.","findings":[{"id":"go-term","name":"GO term","description":"ID and evidence.","questions":[{"text":"Which GO terms apply?","kind":"provenance"},{"text":"With which evidence codes?","kind":"provenance"}]}]},{"id":"protein-records","name":"Protein records","description":"UniProt.","findings":[{"id":"record","name":"Record","description":"Organism, the substrate protein degraded, and proteins that take part in degradation, kept distinct.","questions":[{"text":"Which protein is degraded?","kind":"provenance"},{"text":"Which record describes it?","kind":"provenance"}]}]}]},{"id":"physiology","name":"Physiology","description":"Roles.","layers":[{"id":"regulation","name":"Regulation","description":"Turnover.","findings":[{"id":"turnover","name":"Turnover","description":"Half-life.","questions":[{"text":"What is the protein's half-life?","kind":"measurement"},{"text":"In which cells?","kind":"provenance"}]}]},{"id":"disease","name":"Disease","description":"Failure.","findings":[{"id":"disease-link","name":"Disease link","description":"Condition and evidence.","questions":[{"text":"Which diseases involve failed degradation?","kind":"provenance"},{"text":"What evidence?","kind":"provenance"}]}]}]},{"id":"methods","name":"Methods","description":"Measurement.","layers":[{"id":"assays","name":"Assays","description":"Turnover assays.","findings":[{"id":"assay","name":"Assay","description":"Method.","questions":[{"text":"How was degradation measured?","kind":"provenance"},{"text":"With which controls?","kind":"provenance"}]}]},{"id":"drugs","name":"Drugs","description":"Pharmacology.","findings":[{"id":"drug","name":"Drug","description":"Agent and target.","questions":[{"text":"Which drugs act on these pathways?","kind":"provenance"},{"text":"At which step?","kind":"provenance"}]}]}]}]},"agentConduct":{"may":["explain processes and point to databases"],"mustNot":["give medical advice"],"requiresHuman":[]},"ethics":{"considerations":["accuracy"],"affectedParties":["researchers","students"]},"owners":{"steward":"nobody; a biological process","roles":[],"masterSystems":["Gene Ontology"]},"relations":[{"target":"Q14864262","type":"parent","note":"registry parent class"},{"target":"Q22274829","type":"parent","note":"registry parent class"},{"target":"Q22276126","type":"parent","note":"registry parent class"},{"target":"catabolic process","type":"related","note":"metabolism"},{"target":"proteasome","type":"related","note":"machinery"},{"target":"lysosome","type":"related","note":"organelle"},{"target":"Gene Ontology","type":"related","note":"annotation"}],"interaction":{"identity":{"applicability":"required","items":["Vercy registry: vr.tr.protein-catabolic-process","Wikidata: Q14876077 (https://www.wikidata.org/wiki/Q14876077)","Gene Ontology: GO:0030163 protein catabolic process"]},"properties":{"applicability":"not-applicable","items":[]},"recognition":{"applicability":"optional","items":["Not visible; measured by protein turnover experiments"]},"capabilities":{"applicability":"required","items":["explain main degradation pathways","give Gene Ontology terms","relate degradation to disease and drugs with sources","describe experimental methods"]},"hazards":{"applicability":"required","items":["Protein aggregation diseases when degradation fails"]},"interfaces":{"applicability":"required","items":["Gene Ontology definitions"]},"context":{"applicability":"required","items":["Removing damaged or unneeded proteins, regulating protein levels and recycling amino acids.","ubiquitin-dependent and ubiquitin-independent proteasomal degradation","ER-associated degradation (ERAD)","lysosomal, vacuolar and autophagic degradation","organellar and bacterial protease degradation","non-proteolytic denaturation"]}},"sources":[{"title":"Q14876077","url":"https://www.wikidata.org/wiki/Q14876077","note":"identity of the registry item, labels and sitelinks"},{"title":"Proteolysis","url":"https://en.wikipedia.org/wiki/Proteolysis","note":"protein breakdown"},{"title":"GO:0030163 - protein catabolic process","url":"https://www.pombase.org/term/GO%3A0030163","note":"Identifier, definition including loss of native configuration without peptide-bond hydrolysis, and parent terms."},{"title":"Protein Degradation","url":"https://www.ncbi.nlm.nih.gov/books/NBK9957/","note":"Eukaryotic degradation pathways, ubiquitin targeting, lysosomes, autophagy and protein turnover."},{"title":"Regulated Proteolysis in Bacteria","url":"https://pmc.ncbi.nlm.nih.gov/articles/PMC6013389/","note":"Bacterial protein degradation through ATP-dependent proteases including Lon, ClpXP and FtsH."},{"title":"Protein degrons and degradation: Exploring substrate recognition and pathway selection in plants","url":"https://pubmed.ncbi.nlm.nih.gov/38701343/","note":"Plant degradation pathways, substrate signals, autophagy and organellar proteases."},{"title":"Introduction to GO annotations","url":"https://www.geneontology.org/docs/go-annotations/","note":"Meaning of biological process annotations, gene product participation, references and evidence codes."}],"openQuestions":["The registry merges many substrate-specific catabolic processes; they should be separate entries."],"resources":{"spec":"/models/things/publications/thing-q14876077/spec.json"},"provenance":{"origin":"thing registry research (pass 2)","builtFrom":["models/things/publications/thing-q14876077/spec.json"],"providers":["Claude"],"researchStatus":"unreviewed","generatedAt":"2026-10-22T10:18:19Z","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":"not-applicable","interaction.recognition":"filled","interaction.capabilities":"filled","interaction.hazards":"filled","interaction.interfaces":"filled","interaction.context":"filled","sources":"filled"},"notes":{"_gate":"Published through the thing publication gate 1.0 on 2026-10-22T10:34:33+00:00: completeness 1.00; sense: Wikidata description; 7 live sources; review by codex: pass","interaction.properties":"A process has no physical properties; half-lives are recorded under physiology."},"score":1.0}}