identifier: METPO:1000476 label: pH delta mid2 definition: A pH delta phenotype with a growth-supporting pH breadth of approximately 3–4 pH units, characteristic of organisms with broad pH-tolerance breadth. definition_source: DOI:10.1038/nrmicro2549 trait_category: ENVIRONMENT term_kind: CLASS mapping_status: REVIEWED parent_traits: - METPO:1000232 synonyms: - synonym_text: pHd_3_4 synonym_type: RELATED_SYNONYM source: metpo.owl evidence: - reference: DOI:10.1038/nrmicro2549 snippet: pH homeostasis notes: pH-homeostasis review supports broad pH-homeostasis flexibility as the basis of generalist pH-tolerance physiology. causal_graphs: - graph_id: ph_delta_mid2_broad_breadth title: pH-delta-mid2 broad-breadth pH homeostasis description: DOI-backed graph linking broad pH-homeostasis flexibility to a pH growth breadth of approximately 3–4 pH units. nodes: - node_id: ph_delta_mid2_trait label: pH delta mid2 node_type: TRAIT grounding: METPO:1000476 description: pH growth-supporting breadth approximately 3–4 pH units. - node_id: ph_delta label: pH delta node_type: TRAIT grounding: METPO:1000232 description: Breadth of the growth-supporting external pH range. - node_id: broad_ph_homeostasis label: broad pH-homeostasis flexibility node_type: BIOLOGICAL_PROCESS description: Strong capacity to remodel proton extrusion, K+/H+ antiport, and envelope buffering across a broad pH span. - node_id: external_ph_stress label: external pH stress node_type: ENVIRONMENTAL_FACTOR description: Deviation of external pH that perturbs proton motive force balance. - node_id: pmf_component_balance label: PMF component balance node_type: BIOLOGICAL_PROCESS description: Balance of proton motive force components (delta-pH and delta-psi). - node_id: respiratory_proton_pumps label: proton-pumping respiratory complexes node_type: GENE_OR_PROTEIN description: Primary respiratory-chain proton pumps that establish the PMF. - node_id: pmf_generation label: proton motive force generation node_type: BIOLOGICAL_PROCESS description: Generation of proton motive force across the membrane. - node_id: f1fo_atpase label: F1Fo-ATPase node_type: GENE_OR_PROTEIN description: Proton-coupled F1Fo-ATP synthase functioning as a proton pump. - node_id: proton_translocation_homeostasis label: proton translocation for pH homeostasis node_type: BIOLOGICAL_PROCESS description: Active proton translocation that maintains cytoplasmic pH homeostasis. - node_id: na_h_antiporter_activity label: Na+/H+ antiporter activity node_type: MOLECULAR_FUNCTION description: Cation/proton antiport that imports H+ and extrudes Na+. - node_id: alkaline_ph_homeostasis label: alkaline pH homeostasis node_type: BIOLOGICAL_PROCESS description: Maintenance of cytoplasmic pH under alkaline external conditions. - node_id: glutamate_decarboxylase_system label: glutamate decarboxylase system node_type: PATHWAY description: Proton-consuming glutamate decarboxylase (gad/GadB) acid-resistance system. - node_id: intracellular_proton label: intracellular H+ node_type: CHEMICAL description: Cytoplasmic protons whose concentration sets cytoplasmic pH. - node_id: cytoplasmic_buffers label: cytoplasmic buffering molecules node_type: CHEMICAL description: Small molecules (polyamines, amino acids, phosphate) providing passive pH buffering. - node_id: cytoplasmic_ph_buffering label: cytoplasmic pH buffering node_type: BIOLOGICAL_PROCESS description: Passive buffering of cytoplasmic pH by small molecules. edges: - subject: broad_ph_homeostasis predicate: produces object: ph_delta_mid2_trait description: Broad pH-homeostasis flexibility yields a 3–4 pH-unit pH-delta breadth. evidence: - reference: DOI:10.1038/nrmicro2549 snippet: pH homeostasis notes: Supports broad pH-homeostasis flexibility as the basis of a broad breadth. predicate_id: METPO:2000202 - subject: ph_delta_mid2_trait predicate: is a object: ph_delta description: pH delta mid2 is a quantitative bin of the pH-delta phenotype. evidence: - reference: DOI:10.1016/j.tim.2007.02.005 snippet: proton motive force notes: Supports the 3–4 unit breadth as a value within the pH-delta distribution. predicate_id: rdfs:subClassOf - subject: external_ph_stress predicate: alters object: pmf_component_balance description: External pH stress alters the balance/orientation of PMF components (delta-pH, delta-psi). evidence: - reference: DOI:10.1038/nrmicro2549 notes: Relative magnitudes and even orientation of PMF components change with external pH; under strong pH stress a component can reverse orientation. - subject: respiratory_proton_pumps predicate: generates object: pmf_generation description: Primary respiratory-chain proton pumps generate the proton motive force. evidence: - reference: DOI:10.1038/nrmicro2549 notes: Primary proton pumps (respiratory chain pumps) generate PMF; broad mechanism across bacteria. predicate_id: biolink:produces - subject: f1fo_atpase predicate: contributes to object: proton_translocation_homeostasis description: Proton-coupled F1Fo-ATPase contributes to proton translocation supporting pH homeostasis. evidence: - reference: DOI:10.1038/nrmicro2549 notes: Proton-coupled ATPases are a primary strategy; F1-F0 ATPase proton pump is an active pH-homeostasis mechanism. predicate_id: RO:0002326 - subject: na_h_antiporter_activity predicate: supports object: alkaline_ph_homeostasis description: Na+/H+ antiporter activity imports H+ and extrudes Na+ to support alkaline pH homeostasis. evidence: - reference: DOI:10.1038/nrmicro2549 notes: Cation/proton antiporters are transcriptionally up-regulated for inward proton transport under alkaline stress. - subject: glutamate_decarboxylase_system predicate: consumes object: intracellular_proton description: The glutamate decarboxylase system consumes intracellular protons during decarboxylation. evidence: - reference: DOI:10.3390/antibiotics12091474 notes: Glutamate decarboxylase (GadB with its antiporter) is a proton-consuming acid-tolerance mechanism (GDAR), broadly curated in Gram-negatives. predicate_id: biolink:consumes - subject: cytoplasmic_buffers predicate: buffers object: cytoplasmic_ph_buffering description: Small molecules (polyamines, amino acids, phosphate) passively buffer cytoplasmic pH. evidence: - reference: DOI:10.3390/antibiotics12091474 notes: Passive buffering of cytoplasmic pH is provided by small molecules (amino acids, proteins, polyamines, polyphosphate, inorganic phosphate). curation_history: - timestamp: '2026-05-05T01:35:46.839415+00:00' curator: seed_from_metpo action: SEEDED_FROM_METPO changes: imported from data/raw/metpo.owl (CLASS) llm_assisted: false - timestamp: '2026-05-13T10:00:00-07:00' curator: claude action: CURATED_CAUSAL_GRAPH changes: Added DOI-backed definition and causal graph linking broad pH-homeostasis flexibility to the broad-breadth pH-delta-mid2 bin. llm_assisted: true - timestamp: '2026-05-20T03:35:30Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 2 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (METPO:2000202×1, rdfs:subClassOf×1). llm_assisted: true - timestamp: '2026-06-23T00:00:00Z' curator: claude action: ENRICH_CAUSAL_GRAPH changes: Added 6 evidence-backed generic edges (12 new nodes) from the deep-research report. llm_assisted: true - timestamp: '2026-06-24T17:21:10Z' curator: claude action: GROUND_CAUSAL_PREDICATES changes: Grounded 3 causal-edge predicate_id field(s) via mappings/predicate_grounding.tsv (biolink:produces×1, RO:0002326×1, biolink:consumes×1). llm_assisted: true