{"schema":"https://ver.cy/schemas/card/1.0.0","id":"vr.tr.isopentenyl-diphosphate-biosynthetic-process-methylerythrito","code":"thing-q21198649","url":"https://ver.cy/models/thing/q21198649/","name":"isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway","alternateNames":["isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway involved in terpenoid biosynthetic process"],"kind":"thing","status":"published","version":"0.1.0-research.1","language":"en","classifiers":{"family":"Thing Registry","category":"Activities and processes","entryKind":"thing","plane":"ACT","domain":["ACT.PRC"],"industry":[],"navPath":"","tags":[],"facets":{}},"whatItIs":"The methylerythritol 4-phosphate (MEP) pathway is a sequence of enzymatic reactions that converts pyruvate and glyceraldehyde 3-phosphate into the isoprenoid precursors isopentenyl diphosphate (IPP) and dimethylallyl diphosphate (DMAPP), operating in many bacteria and in the plastids of plants and various algae.","purpose":"Enable an agent to recognize MEP-pathway production of isopentenyl diphosphate, assess its activity in a specified biological system, and identify justified measurements or interventions.","scope":{"in":["Reaction continuity from precursor entry through MEP intermediates to IPP production.","Enzyme-function assignments and evidence for missing or alternative implementations.","Organism, compartment, physiological condition, and observation interval defining an instance.","Intermediate pools, pathway-specific flux, and associated DMAPP output.","Resource dependencies, competing precursor sources, and experimentally supported perturbation responses."],"out":["The broader class of IPP biosynthetic processes and its shared properties.","Mevalonate-pathway chemistry, except as an alternative source requiring attribution.","Standalone models of IPP, MEP, enzymes, genes, or organisms.","Downstream prenyl-chain elongation and synthesis of individual terpenoids.","General central-carbon metabolism and organelle transport mechanisms beyond their pathway interfaces."],"boundaries":[]},"distinguishingFeatures":["Require evidence for a route through MEP intermediates; IPP detection alone cannot distinguish the MEP and mevalonate routes. [KEGG terpenoid backbone biosynthesis](https://www.genome.jp/pathway/map00900)","Check continuity through DXP reductoisomerase, the intervening MEP reactions, and HMBPP synthesis and reduction. [KEGG M00096](https://www.kegg.jp/entry/M00096)","Distinguish terminal HMBPP conversion from IPP-DMAPP isomerization, which KEGG also includes in its broader C5 module. [KEGG M00096](https://www.kegg.jp/entry/M00096)","Treat gene annotation as evidence of potential capacity; require condition-specific biochemical evidence before classifying an instance as actively producing IPP.","Keep production of the C5 precursor distinct from downstream incorporation into larger isoprenoids. [KEGG terpenoid backbone biosynthesis](https://www.genome.jp/pathway/map00900)"],"structure":{"bundles":[{"id":"mep-route-identity","name":"MEP route identity","description":"Criteria for recognizing this specific route and delimiting its output.","layers":[{"id":"route-membership","name":"Route membership","description":"Evidence connecting the observed process to MEP chemistry.","findings":[{"id":"mep-specific-continuity","name":"MEP-specific continuity","description":"Record the conversions supporting route identity and explicitly mark unobserved links.","questions":[{"text":"Which observed reactions or labeled intermediates establish passage through MEP?","id":"mep-specific-continuity-q01","kind":"definition"},{"text":"Which experiment supports this assignment beyond detecting IPP or predicting homologous genes?","id":"mep-specific-continuity-q02","kind":"provenance"}]}]},{"id":"precursor-output-boundary","name":"Precursor output boundary","description":"Separate IPP formation from associated C5 interconversion and downstream use.","findings":[{"id":"terminal-output-accounting","name":"Terminal output accounting","description":"Represent terminal production and subsequent IPP-DMAPP interconversion separately so pathway boundaries remain explicit.","questions":[{"text":"Does the reported endpoint measure terminal-reaction IPP production, net IPP accumulation, or incorporation into downstream products?","id":"terminal-output-accounting-q01","kind":"boundary"},{"text":"How are associated DMAPP production and later isomerization accounted for?","id":"terminal-output-accounting-q02","kind":"measurement"}]}]}]},{"id":"reaction-chain-realization","name":"Reaction chain realization","description":"Organism-specific implementation of the reference reaction sequence.","layers":[{"id":"dxp-to-mep-entry","name":"DXP to MEP entry","description":"Define precursor supply and entry into MEP chemistry.","findings":[{"id":"entry-reaction-assignment","name":"Entry reaction assignment","description":"The reference module includes DXP synthase and DXP reductoisomerase; record their local implementation and precursor interfaces. [KEGG M00096](https://www.kegg.jp/entry/M00096)","questions":[{"text":"Which evidence establishes precursor delivery to DXP formation in this system?","id":"entry-reaction-assignment-q01","kind":"provenance"},{"text":"Which enzyme or demonstrated alternative carries out DXP-to-MEP conversion?","id":"entry-reaction-assignment-q02","kind":"definition"}]}]},{"id":"mep-to-hmbpp-continuity","name":"MEP to HMBPP continuity","description":"Assess the intervening conversions that connect MEP to the terminal substrate.","findings":[{"id":"intermediate-conversion-coverage","name":"Intermediate conversion coverage","description":"Map cytidylyltransferase, kinase, cyclodiphosphate synthase, and HMBPP synthase activities to local evidence. [KEGG M00096](https://www.kegg.jp/entry/M00096)","questions":[{"text":"Which intervening activities are demonstrated, predicted, or unresolved?","id":"intermediate-conversion-coverage-q01","kind":"provenance"},{"text":"Do fused proteins, alternative enzymes, or incomplete annotations explain apparent gaps?","id":"intermediate-conversion-coverage-q02","kind":"boundary"}]}]},{"id":"hmbpp-conversion","name":"HMBPP conversion","description":"Assess the terminal reaction and its measured products.","findings":[{"id":"terminal-reductase-evidence","name":"Terminal reductase evidence","description":"Record HMBPP reductase assignment and direct evidence for terminal product formation. [KEGG M00096](https://www.kegg.jp/entry/M00096)","questions":[{"text":"What supports catalytic activity of the assigned terminal reductase under the stated conditions?","id":"terminal-reductase-evidence-q01","kind":"provenance"},{"text":"Were IPP and DMAPP resolved and quantified separately in the terminal-reaction assay?","id":"terminal-reductase-evidence-q02","kind":"measurement"}]}]}]},{"id":"cellular-context-and-resources","name":"Cellular context and resources","description":"Location and enabling conditions for the pathway instance.","layers":[{"id":"compartmental-realization","name":"Compartmental realization","description":"Anchor the pathway to a specific biological location.","findings":[{"id":"colocation-and-exchange","name":"Colocation and exchange","description":"Record enzyme localization, metabolite accessibility, and any transport assumptions connecting reactions.","questions":[{"text":"Which organism, cell type, and compartment contain the claimed pathway instance?","id":"colocation-and-exchange-q01","kind":"definition"},{"text":"Which reaction connections require transport, and what evidence supports that exchange?","id":"colocation-and-exchange-q02","kind":"boundary"}]}]},{"id":"catalytic-resource-support","name":"Catalytic resource support","description":"Track the resources needed by the locally implemented reactions.","findings":[{"id":"resource-dependency-assessment","name":"Resource dependency assessment","description":"Record reaction-specific nucleotide, reducing-equivalent, cofactor, and electron-delivery requirements without assuming identical implementations across organisms.","questions":[{"text":"Which resource and cofactor requirements are experimentally established for the local enzymes?","id":"resource-dependency-assessment-q01","kind":"provenance"},{"text":"What measurements distinguish resource limitation from insufficient catalytic capacity?","id":"resource-dependency-assessment-q02","kind":"measurement"}]}]}]},{"id":"flux-and-route-attribution","name":"Flux and route attribution","description":"Evidence that this route contributes to IPP production and the size of that contribution.","layers":[{"id":"pool-versus-throughput","name":"Pool versus throughput","description":"Separate metabolite abundance from production rate.","findings":[{"id":"flux-measurement-validity","name":"Flux measurement validity","description":"Require a time basis, normalization, analytical specificity, and stated assumptions for inferred MEP throughput.","questions":[{"text":"Does the experiment measure a metabolite pool, turnover, or pathway-attributed production rate?","id":"flux-measurement-validity-q01","kind":"measurement"},{"text":"How do sampling, detection limits, and uncertainty affect the inferred flux?","id":"flux-measurement-validity-q02","kind":"measurement"}]}]},{"id":"alternative-source-separation","name":"Alternative source separation","description":"Resolve MEP contributions where other routes or imported precursors may contribute.","findings":[{"id":"ipp-origin-discrimination","name":"IPP origin discrimination","description":"Record evidence separating local MEP synthesis from mevalonate-derived or externally supplied precursor contributions.","questions":[{"text":"What tracing or perturbation evidence distinguishes MEP-derived IPP from other sources?","id":"ipp-origin-discrimination-q01","kind":"provenance"},{"text":"Could precursor exchange or mixed cell populations explain the apparent pathway contribution?","id":"ipp-origin-discrimination-q02","kind":"boundary"}]}]}]},{"id":"pathway-control-and-perturbation","name":"Pathway control and perturbation","description":"Context-specific evidence for altering MEP output and interpreting the consequences.","layers":[{"id":"control-point-assessment","name":"Control point assessment","description":"Connect changes in particular reactions to changes in pathway output.","findings":[{"id":"conditional-flux-control","name":"Conditional flux control","description":"Treat control by an entry, intermediate, or terminal reaction as a condition-specific hypothesis requiring perturbation evidence.","questions":[{"text":"Which targeted change altered MEP-attributed flux under matched conditions?","id":"conditional-flux-control-q01","kind":"provenance"},{"text":"What additional measurement would distinguish a catalytic bottleneck from altered substrate supply or product consumption?","id":"conditional-flux-control-q02","kind":"action"}]}]},{"id":"response-and-compensation","name":"Response and compensation","description":"Evaluate pathway-specific effects and possible compensation after intervention.","findings":[{"id":"perturbation-causal-assessment","name":"Perturbation causal assessment","description":"Link target engagement, intermediate changes, precursor output, and downstream effects while recording possible alternative explanations.","questions":[{"text":"What establishes that the intervention affected the intended MEP reaction?","id":"perturbation-causal-assessment-q01","kind":"provenance"},{"text":"Could alternative IPP supply, altered uptake, or general physiological impairment explain the response?","id":"perturbation-causal-assessment-q02","kind":"boundary"},{"text":"Which control or rescue observation would most directly test the proposed causal explanation?","id":"perturbation-causal-assessment-q03","kind":"action"}]}]}]},{"id":"evidence-and-external-alignment","name":"Evidence and external alignment","description":"What the world already says about this thing, gathered so the model can be checked against it.","layers":[{"id":"reported-evidence","name":"Reported evidence","description":"Findings from the breadth pass, kept separate from the structural claims.","findings":[{"id":"evidence-confidence-notes","name":"Check these first","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these check these first hold for the sense of isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway this model covers, and on what evidence?","id":"evidence-confidence-notes-q01","kind":"provenance"}]},{"id":"evidence-identifiers","name":"Identifiers and schemes","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these identifiers and schemes hold for the sense of isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway this model covers, and on what evidence?","id":"evidence-identifiers-q01","kind":"provenance"}]},{"id":"evidence-real-world-use","name":"Real-world use","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these real-world use hold for the sense of isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway this model covers, and on what evidence?","id":"evidence-real-world-use-q01","kind":"provenance"}]},{"id":"evidence-measurements","name":"Typical measurements","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these typical measurements hold for the sense of isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway this model covers, and on what evidence?","id":"evidence-measurements-q01","kind":"provenance"}]},{"id":"evidence-failure-modes-and-hazards","name":"Failure modes and hazards","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these failure modes and hazards hold for the sense of isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway this model covers, and on what evidence?","id":"evidence-failure-modes-and-hazards-q01","kind":"provenance"}]},{"id":"evidence-neighbours","name":"Neighbouring kinds and how to tell them apart","description":"Recalled without web access and unsourced; every item is a lead to verify.","questions":[{"text":"Which of these neighbouring kinds and how to tell them apart hold for the sense of isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway this model covers, and on what evidence?","id":"evidence-neighbours-q01","kind":"provenance"}]}]}]}]},"agentConduct":{"may":["Describe the MEP pathway's steps and enzymes from scientific sources.","Annotate genes and organisms as having the pathway when evidence supports it."],"mustNot":["Annotate an organism as having the pathway without evidence.","Confuse it with the mevalonate pathway that makes the same precursors.","Overstate early research on pathway inhibitors as proven medicines or herbicides."],"requiresHuman":["Releasing engineered organisms that carry modified versions of the pathway."]},"ethics":{"considerations":["The pathway is a target for antimalarial drugs and herbicides, whose claims need honest evidence."],"affectedParties":["Researchers","Patients awaiting new drugs"]},"owners":{"steward":"Nobody owns the process; biological databases curate its annotations.","roles":[],"masterSystems":["Gene and pathway annotation databases"]},"relations":[{"target":"Q14865379","type":"parent","note":"registry parent class"},{"target":"Q21438305","type":"parent","note":"registry parent class"},{"target":"Q22282900","type":"parent","note":"registry parent class"}],"interaction":{"identity":{"applicability":"required","items":["Vercy registry: vr.tr.isopentenyl-diphosphate-biosynthetic-process-methylerythrito","Wikidata: Q21198649 (https://www.wikidata.org/wiki/Q21198649)"]},"properties":{"applicability":"not-applicable","items":["Biological realization: Organism or strain, tissue or cell type, compartment, and native or engineered context","Reaction coverage: Each required conversion: experimentally supported, predicted, unresolved, or demonstrated unavailable","Activity assessment: Capacity only, activity demonstrated, activity below detection, or unresolved; qualified by conditions","MEP-attributed IPP production rate: nmol IPP per mg protein per minute, or another explicitly stated normalization; uncertainty required","Intermediate abundance: Concentration or normalized amount for identified DXP, MEP, downstream intermediates, and HMBPP","IPP-to-DMAPP output ratio: Molar ratio, with terminal-reaction output distinguished from the subsequent cellular pool ratio","Route attribution evidence: Annotation, enzyme assay, metabolite identification, isotope tracing, perturbation, or convergent evidence","Perturbation response: Change in pathway-attributed flux or intermediate abundance relative to a matched control, with exposure and duration"]},"recognition":{"applicability":"optional","items":["Drawn as a sequence of enzyme steps from pyruvate and glyceraldehyde 3-phosphate to isoprenoid precursors.","Found in most bacteria, plant plastids and malaria parasites, not in animals."]},"capabilities":{"applicability":"required","items":["Classify evidence as supporting MEP-pathway capacity, observed activity, or an unresolved assignment.","Identify gaps in the reaction chain and select evidence needed to resolve them.","Compare pathway-attributed IPP production across matched conditions.","Distinguish changed intermediate pools from changed biosynthetic flux.","Evaluate proposed perturbations against target engagement, resource dependencies, and alternative precursor supply.","Link the registered process to neighboring models of enzymes, metabolites, transport, and downstream synthesis."]},"hazards":{"applicability":"required","items":["Wrong annotations propagate across genome databases."]},"interfaces":{"applicability":"required","items":["The Gene Ontology Consortium provides the biological process classification for isopentenyl diphosphate biosynthesis through the methylerythritol 4-phosphate pathway."]},"context":{"applicability":"required","items":["This pathway occurs in many bacteria and in the plastids of plants and various algae, where it supplies precursors for isoprenoid synthesis.","It is studied in microbial physiology, plant metabolism and biotechnology to understand precursor production and its contribution to downstream compounds."]}},"sources":[{"title":"Wikidata item Q21198649: isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway","url":"https://www.wikidata.org/wiki/Q21198649","note":"identity and sense of the item"},{"title":"Wikipedia: Non-mevalonate pathway","url":"https://en.wikipedia.org/wiki/Non-mevalonate_pathway","note":"general description of the item"}],"openQuestions":["Should the registry boundary include precursor formation through DXP synthase, and how should it align with reference modules that also include IPP-DMAPP isomerization?","Which organism-specific alternative enzymes or fused activities must be supported before reaction coverage can be judged reliably?","Which compartments exchange intermediates or C5 precursors in the intended biological systems, and how much does that exchange affect route attribution?","Which resource dependencies and control points are experimentally established for each intended context rather than extrapolated from another organism?","What minimum combination of tracing, analytical resolution, and perturbation evidence should qualify an instance as actively producing IPP through the MEP pathway?"],"resources":{"spec":"/models/things/publications/thing-q21198649/spec.json"},"provenance":{"origin":"thing registry research (pass 2)","builtFrom":["models/things/publications/thing-q21198649/spec.json"],"providers":["Codex"],"researchStatus":"unreviewed","generatedAt":"2026-09-12T10:38:14Z","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 2026-10-07T10:10:28+00:00: completeness 1.00; sense: Wikidata description; 2 live sources; review by codex: pass","interaction.properties":"Plane ACT: no invented physical properties."},"score":1.0}}