identifier: traitmech:000077 label: urease activity definition: A physiological enzyme-activity phenotype in which a cell produces urease, which hydrolyzes urea to ammonia and carbon dioxide, typically raising local pH; it is the basis of the diagnostic urease test. definition_source: DOI:10.1128/mr.59.3.451-480.1995 trait_category: PHYSIOLOGY term_kind: CLASS mapping_status: REVIEWED parent_traits: - METPO:1000059 synonyms: - synonym_text: urease-positive synonym_type: RELATED_SYNONYM source: DOI:10.1128/mr.59.3.451-480.1995 evidence: - reference: DOI:10.1128/mr.59.3.451-480.1995 notes: Mobley, Island & Hausinger review the molecular biology of microbial ureases that hydrolyze urea to ammonia and carbon dioxide. - reference: DOI:10.1128/mr.53.1.85-108.1989 notes: Mobley & Hausinger review the significance and regulation of microbial ureases. canonical_examples: - taxon_id: NCBITaxon:1474 taxon_label: Sporosarcina pasteurii note: "Most-used organism for microbially induced calcite precipitation; copious constitutive urease (formerly Bacillus pasteurii)." reference: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6979283/ causal_graphs: - graph_id: urease_activity_urea_hydrolysis title: Urease-catalyzed urea hydrolysis description: Evidence-backed causal sketch linking urease to hydrolysis of urea into ammonia, the basis of the urease test. nodes: - node_id: urease_activity_trait label: urease activity node_type: TRAIT grounding: traitmech:000077 description: Possession of urease. - node_id: urease label: urease node_type: GENE_OR_PROTEIN description: Nickel metalloenzyme hydrolyzing urea. grounding: UniProtKB:A0A090IGX8 - node_id: urease_function label: urease activity node_type: MOLECULAR_FUNCTION grounding: GO:0009039 description: Hydrolysis of urea to ammonia and carbon dioxide. - node_id: urea label: urea node_type: CHEMICAL grounding: CHEBI:16199 description: Substrate hydrolyzed by urease. - node_id: ammonia label: ammonia node_type: CHEMICAL grounding: CHEBI:16134 description: Product that raises local pH. - node_id: hydroxide label: hydroxide node_type: CHEMICAL description: Hydroxide ion produced by urea hydrolysis, raising local pH. grounding: CHEBI:16234 - node_id: carbon_dioxide label: carbon dioxide node_type: CHEMICAL description: CO2 product of urea hydrolysis; feeds carbonate chemistry. grounding: CHEBI:16526 - node_id: ph_quality label: pH node_type: QUALITY description: Local pH, increased by urease-driven alkalinization. - node_id: carbonic_anhydrase_function label: carbonic anhydrase activity node_type: MOLECULAR_FUNCTION description: Hydration of CO2 to bicarbonate. grounding: GO:0004089 - node_id: bicarbonate label: bicarbonate node_type: CHEMICAL description: Bicarbonate produced from CO2 hydration by carbonic anhydrase. grounding: CHEBI:17544 - node_id: calcium_carbonate_precipitation label: calcium carbonate precipitation node_type: BIOLOGICAL_PROCESS description: Precipitation of CaCO3 mineral, influenced by buffering chemistry. edges: - subject: urease predicate: enables object: urease_function description: Urease carries out urea hydrolysis. evidence: - reference: DOI:10.1128/mr.59.3.451-480.1995 notes: Mobley, Island & Hausinger review microbial ureases. predicate_id: RO:0002327 - subject: urease_function predicate: consumes object: urea description: The urease reaction consumes urea. evidence: - reference: DOI:10.1128/mr.59.3.451-480.1995 notes: Supports urea as the hydrolysis substrate. predicate_id: biolink:consumes - subject: urease_function predicate: produces object: ammonia description: Urea hydrolysis produces ammonia. evidence: - reference: DOI:10.1128/mr.53.1.85-108.1989 notes: Mobley & Hausinger support ammonia release from urea hydrolysis. predicate_id: METPO:2000202 - subject: urease_function predicate: manifests as object: urease_activity_trait description: Urease enzymatic activity manifests as the observable urease-activity phenotype scored by the diagnostic urease test. evidence: - reference: DOI:10.1128/mr.59.3.451-480.1995 notes: Urease activity (urea-to-ammonia hydrolysis raising local pH) is the assayable phenotype used to score urease-positive organisms. predicate_id: METPO:2007400 - subject: urease_function predicate: produces object: hydroxide description: Urea hydrolysis produces hydroxide, mechanistically explaining alkalinization. evidence: - reference: DOI:10.24263/2304-974x-2024-13-2-10 notes: (NH2)2CO + 2H2O + urease -> 2 NH4+ + 2 OH- + CO2 + urease. predicate_id: METPO:2000202 - subject: urease_function predicate: produces object: carbon_dioxide description: Urea hydrolysis produces carbon dioxide. evidence: - reference: DOI:10.24263/2304-974x-2024-13-2-10 notes: (NH2)2CO + 2H2O + urease -> 2 NH4+ + 2 OH- + CO2 + urease. predicate_id: METPO:2000202 - subject: urease_function predicate: increases object: ph_quality description: Urea hydrolysis (NH4+/OH- production) increases local pH, the basis of the urease test color change. evidence: - reference: DOI:10.1021/acs.est.3c06617 notes: Urea hydrolysis produces NH4+ and OH-, causing a pH increase. predicate_id: RO:0002213 - subject: carbon_dioxide predicate: is substrate of object: carbonic_anhydrase_function description: CO2 from urea hydrolysis is hydrated by carbonic anhydrase. evidence: - reference: DOI:10.1021/acs.est.3c06617 notes: Hydration of CO2 to HCO3- by carbonic anhydrase. - subject: carbonic_anhydrase_function predicate: increases object: bicarbonate description: Carbonic anhydrase hydrates CO2, increasing bicarbonate. evidence: - reference: DOI:10.1021/acs.est.3c06617 notes: Increase in [HCO3-] following the hydration of CO2 to HCO3- by CA. predicate_id: RO:0002213 - subject: carbonic_anhydrase_function predicate: affects object: calcium_carbonate_precipitation description: CA-driven buffering enhances solubility trapping and affects the CaCO3 phase formed. evidence: - reference: DOI:10.1021/acs.est.3c06617 notes: CA physiologically promotes buffering, which enhances solubility trapping and affects the phase of the CaCO3 mineral formed. curation_history: - timestamp: '2026-06-04T00:00:00Z' curator: claude action: PROPOSED_FROM_RESEARCH changes: Proposed candidate PHYSIOLOGY trait (urease activity) from literature research to fill the enzyme-activity-phenotype gap. llm_assisted: true - timestamp: '2026-06-08T13:00:00Z' curator: claude action: CURATED_CAUSAL_GRAPH changes: Added evidence-backed causal graph (urease urea hydrolysis) with GO/CHEBI node groundings and RO/METPO/biolink predicate groundings; promoted PROPOSED to REVIEWED. llm_assisted: true - timestamp: '2026-06-14T06:38:16Z' curator: claude action: GROUND_CAUSAL_NODES changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (UniProtKB:A0A090IGX8×1). llm_assisted: true - timestamp: '2026-06-16T00:00:00Z' curator: claude action: FIX_ORPHAN_NODE changes: Connected the previously-orphaned urease_activity_trait node via a 'manifests as' (METPO:2007400) edge from urease_function, so the molecular function links to the observable trait. llm_assisted: true - timestamp: '2026-06-23T00:00:00Z' curator: claude action: ENRICH_CAUSAL_GRAPH changes: Added 6 evidence-backed generic edges (6 new nodes) from the deep-research report. llm_assisted: true - timestamp: '2026-06-24T17:21:15Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 4 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202×2, RO:0002213×2). llm_assisted: true - timestamp: '2026-06-24T17:21:20Z' curator: claude action: GROUND_CAUSAL_NODES changes: Grounded 1 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:16526×1). llm_assisted: true - timestamp: '2026-06-24T17:23:35Z' curator: claude action: GROUND_CAUSAL_NODES changes: Grounded 3 causal-node grounding field(s) via mappings/node_grounding.tsv (CHEBI:16234×1, GO:0004089×1, CHEBI:17544×1). llm_assisted: true