id: MODULE:oxygenic_photosynthesis title: Oxygenic photosynthesis module description: >- A taxon-neutral decomposition of oxygenic photosynthesis as a recursively decomposable module. The module separates the thylakoid light reactions (light harvesting, water oxidation at photosystem II, the cytochrome b6f complex, photosystem I, mobile electron carriers, ferredoxin-NADP+ reductase, and the ATP synthase) from carbon fixation by the Calvin-Benson-Bassham reductive pentose-phosphate cycle, and adds optional photoprotection/electron balancing, the inorganic carbon-concentrating mechanism, and chlorophyll supply. It is phrased as functions, complexes, and pathway segments rather than a fixed gene list so it can represent cyanobacterial, algal, and plant implementations. Anoxygenic photosynthesis (single reaction center, non-water electron donors) is explicitly out of scope. status: DRAFT evidence: - source_id: file:modules/photosynthesis-deep-research-falcon.md title: Photosynthesis module deep research (falcon) statement: >- Module-targeted falcon deep research (generated from this module's outline) used to cross-check component coverage, variants, and failure modes. Machine-generated citations are not yet manually adjudicated. - source_id: file:terms/photosynthesis/photosynthesis-deep-research-falcon.md title: Photosynthesis concept deep research (falcon) statement: >- Falcon deep-research synthesis used to set module boundaries and the module-by-module component breakdown across Arabidopsis, Synechocystis, and Chlamydomonas (core vs accessory vs regulatory factors). - source_id: file:terms/photosynthesis/photosynthesis-notes.md title: Photosynthesis concept notes statement: Manually authored, GO- and PubMed-verified concept notes underpinning this module. - source_id: GO:0015979 title: photosynthesis statement: The module is grounded in the GO biological-process term for photosynthesis. - source_id: PMID:21499260 title: "Crystal structure of oxygen-evolving photosystem II at a resolution of 1.9 Å." statement: >- Defines the PSII D1/D2 reaction center, CP43/CP47 inner antennae, and the Mn4CaO5 water-oxidation cluster stabilized by the extrinsic OEC proteins. - source_id: PMID:11418848 title: "Three-dimensional structure of cyanobacterial photosystem I at 2.5 A resolution" statement: >- Defines the PsaA/PsaB reaction-center heterodimer and the terminal Fe-S clusters carried by PsaC. - source_id: PMID:18294858 title: Structure and function of Rubisco statement: >- Supports Rubisco as the major carboxylating enzyme of the CBB cycle and its competing oxygenase side-reaction. - source_id: PMID:33761918 title: A new type of flexible CP12 protein in the marine diatom Thalassiosira pseudonana statement: >- Supports CP12 as a redox-controlled scaffold that forms a PRK-GAPDH-CP12 ternary complex regulating the CBB cycle. - source_id: PMID:37549282 title: NTRC regulates CP12 to activate Calvin-Benson cycle during cold acclimation statement: >- Supports redox (NTRC/thioredoxin)-dependent assembly/disassembly of the PRK-CP12-GAPDH supracomplex gating CBB-cycle activity. notes: >- Identifiers are grounded only where verified against the local GO term cache, GOlr, or UniProt; descriptors without a `term` are deliberate (no confident identifier yet) rather than oversights. Representative UniProt members are concrete orienting examples, not exhaustive or species-restricting claims. module: id: oxygenic_photosynthesis label: Oxygenic photosynthesis module_type: BIOLOGICAL_PROCESS concepts: - preferred_term: oxygenic photosynthesis term: id: GO:0015979 label: photosynthesis description: >- Light-driven oxidation of water and reduction of CO2 to organic carbon, releasing O2. Comprises coupled light reactions and carbon fixation. context: taxa: - preferred_term: cyanobacteria - preferred_term: eukaryotic algae - preferred_term: land plants cellular_components: - preferred_term: photosynthetic membrane term: id: GO:0034357 label: photosynthetic membrane parts: - order: 1 role: light reactions (electron transport and photophosphorylation) node: id: light_reactions label: Thylakoid light reactions module_type: BIOLOGICAL_PROCESS concepts: - preferred_term: photosynthesis, light reaction term: id: GO:0019684 label: photosynthesis, light reaction - preferred_term: photosynthetic electron transport chain term: id: GO:0009767 label: photosynthetic electron transport chain parts: - order: 1 role: light harvesting / antenna node: id: light_harvesting label: Light-harvesting antenna module_type: MOLECULAR_FUNCTION annotons: - id: antenna_chlorophyll_binding label: Antenna chlorophyll/carotenoid light capture participant: selector_type: FAMILY family: preferred_term: light-harvesting chlorophyll a/b binding (LHC) family description: >- Membrane antenna proteins (LHCII/LHCI in plants and algae; phycobilisomes substitute in most cyanobacteria). function: preferred_term: chlorophyll binding for excitation energy transfer term: id: GO:0016168 label: chlorophyll binding cofactors: - preferred_term: chlorophyll a - preferred_term: chlorophyll b - preferred_term: carotenoid locations: - preferred_term: thylakoid membrane term: id: GO:0034357 label: photosynthetic membrane role_description: >- Increases absorption cross-section and funnels excitation to the reaction centers; also a site of photoprotective quenching. - order: 2 role: water oxidation (photosystem II) node: id: photosystem_II label: Photosystem II (water:plastoquinone oxidoreductase) module_type: PROTEIN_COMPLEX concepts: - preferred_term: photosystem II term: id: GO:0009523 label: photosystem II annotons: - id: psii_water_oxidation label: Light-driven water oxidation / oxygen evolution participant: selector_type: PROTEIN_COMPLEX protein_complex: preferred_term: photosystem II complex term: id: GO:0009523 label: photosystem II active_units: - id: psii_d1 label: D1 reaction-center subunit (PsbA) role: binds P680 and the Mn4CaO5 cluster; high-turnover repair substrate participant: selector_type: FAMILY family: preferred_term: PsbA / D1 - id: psii_d2 label: D2 reaction-center subunit (PsbD) role: reaction-center partner of D1 participant: selector_type: FAMILY family: preferred_term: PsbD / D2 - id: psii_cp43_cp47 label: Core antennae CP43/CP47 (PsbC/PsbB) role: inner chlorophyll antennae feeding excitation to P680 participant: selector_type: FAMILY family: preferred_term: PsbB/PsbC core antenna - id: psii_oec label: Oxygen-evolving complex extrinsic proteins (PsbO/PsbP/PsbQ) role: stabilize the Mn4CaO5 water-oxidation cluster on the lumenal side participant: selector_type: FAMILY family: preferred_term: oxygen-evolving complex extrinsic proteins representative_members: - preferred_term: spinach PsbO (oxygen-evolving enhancer protein 1) term: id: UniProtKB:P12359 label: Oxygen-evolving enhancer protein 1, chloroplastic function: preferred_term: oxygen evolving activity term: id: GO:0010242 label: oxygen evolving activity substrates: - preferred_term: water - preferred_term: plastoquinone products: - preferred_term: dioxygen - preferred_term: plastoquinol - preferred_term: proton (lumen) locations: - preferred_term: thylakoid membrane term: id: GO:0042651 label: thylakoid membrane role_description: >- Uses light energy to oxidize water at the Mn4CaO5 cluster, reducing plastoquinone and releasing O2 and lumenal protons. evidence: - source_id: PMID:21499260 statement: PSII structure defining the reaction center, antennae, and Mn4CaO5 cluster. - order: 3 role: plastoquinol oxidation and proton translocation (cytochrome b6f) node: id: cytochrome_b6f label: Cytochrome b6f complex module_type: PROTEIN_COMPLEX concepts: - preferred_term: cytochrome b6f complex term: id: GO:0009512 label: cytochrome b6f complex annotons: - id: b6f_plastoquinol_plastocyanin_reductase label: Plastoquinol--plastocyanin reductase (Q-cycle) participant: selector_type: PROTEIN_COMPLEX protein_complex: preferred_term: cytochrome b6f complex term: id: GO:0009512 label: cytochrome b6f complex active_units: - id: b6f_cytf label: Cytochrome f (PetA) role: high-potential heme; reduces plastocyanin/cyt c6 participant: selector_type: FAMILY family: preferred_term: cytochrome f (PetA) representative_members: - preferred_term: Synechocystis cytochrome f (petA) term: id: UniProtKB:P26287 label: Cytochrome f - id: b6f_cytb6 label: Cytochrome b6 (PetB) role: low-potential hemes; Q-cycle electron bifurcation participant: selector_type: FAMILY family: preferred_term: cytochrome b6 (PetB) - id: b6f_rieske label: Rieske iron-sulfur protein (PetC) role: 2Fe-2S cluster; oxidizes plastoquinol participant: selector_type: FAMILY family: preferred_term: Rieske Fe-S protein (PetC) representative_members: - preferred_term: wheat Rieske Fe-S subunit (petC) term: id: UniProtKB:Q7X9A6 label: Cytochrome b6-f complex iron-sulfur subunit, chloroplastic function: preferred_term: plastoquinol--plastocyanin reductase activity term: id: GO:0009496 label: plastoquinol--plastocyanin reductase activity substrates: - preferred_term: plastoquinol - preferred_term: plastocyanin (oxidized) products: - preferred_term: plastoquinone - preferred_term: plastocyanin (reduced) - preferred_term: proton (lumen) locations: - preferred_term: thylakoid membrane term: id: GO:0009535 label: chloroplast thylakoid membrane role_description: >- Links PSII to PSI, oxidizing plastoquinol and reducing the mobile carrier while translocating protons via the Q-cycle; frequently rate-limiting for linear electron transport. - order: 4 role: inter-photosystem mobile electron carrier node: id: mobile_carrier_b6f_to_psi label: Mobile carrier from b6f to PSI module_type: MOLECULAR_FUNCTION description: >- Soluble lumenal carrier shuttling electrons from cytochrome b6f to photosystem I; the carrier used is lineage- and metal-availability-dependent. variant_sets: - id: lumenal_carrier_variants label: Plastocyanin vs cytochrome c6 axis: lineage / metal availability selection: EXACTLY_ONE variants: - id: plastocyanin_variant label: Plastocyanin (copper carrier) module_type: MOLECULAR_FUNCTION annotons: - id: plastocyanin_electron_transfer label: Plastocyanin electron transfer participant: selector_type: FAMILY family: preferred_term: plastocyanin function: preferred_term: electron transfer activity term: id: GO:0009055 label: electron transfer activity cofactors: - preferred_term: copper ion locations: - preferred_term: thylakoid lumen term: id: GO:0009543 label: chloroplast thylakoid lumen - id: cytochrome_c6_variant label: Cytochrome c6 (iron carrier) module_type: MOLECULAR_FUNCTION annotons: - id: cytc6_electron_transfer label: Cytochrome c6 electron transfer participant: selector_type: FAMILY family: preferred_term: cytochrome c6 function: preferred_term: electron transfer activity term: id: GO:0009055 label: electron transfer activity cofactors: - preferred_term: heme c locations: - preferred_term: thylakoid lumen term: id: GO:0031977 label: thylakoid lumen notes: >- Many cyanobacteria and algae switch between plastocyanin and cytochrome c6 depending on copper/iron availability. - order: 5 role: P700 photo-oxidation and ferredoxin reduction (photosystem I) node: id: photosystem_I label: Photosystem I (plastocyanin:ferredoxin oxidoreductase) module_type: PROTEIN_COMPLEX concepts: - preferred_term: photosystem I term: id: GO:0009522 label: photosystem I annotons: - id: psi_ferredoxin_reduction label: Light-driven ferredoxin reduction participant: selector_type: PROTEIN_COMPLEX protein_complex: preferred_term: photosystem I complex term: id: GO:0009522 label: photosystem I active_units: - id: psi_psaa_psab label: PsaA/PsaB reaction-center heterodimer role: bind P700 and early electron-transfer cofactors participant: selector_type: FAMILY family: preferred_term: PsaA/PsaB reaction-center - id: psi_psac label: PsaC terminal Fe-S clusters (FA/FB) role: terminal 4Fe-4S clusters that reduce ferredoxin participant: selector_type: FAMILY family: preferred_term: PsaC representative_members: - preferred_term: Chlamydomonas psaC term: id: UniProtKB:Q00914 label: Photosystem I iron-sulfur center function: preferred_term: light-driven plastocyanin:ferredoxin oxidoreduction description: >- Photo-oxidation of P700 drives electron transfer through Fe-S clusters to reduce ferredoxin; no single exact GO MF is asserted for the whole complex here. substrates: - preferred_term: plastocyanin (reduced) or cytochrome c6 - preferred_term: ferredoxin (oxidized) products: - preferred_term: ferredoxin (reduced) processes: - preferred_term: photosynthetic electron transport in photosystem I term: id: GO:0009773 label: photosynthetic electron transport in photosystem I locations: - preferred_term: thylakoid membrane term: id: GO:0009535 label: chloroplast thylakoid membrane evidence: - source_id: PMID:11418848 statement: PSI structure defining PsaA/PsaB and terminal Fe-S clusters. - order: 6 role: NADPH production node: id: fnr_step label: Ferredoxin-NADP+ reductase module_type: REACTION annotons: - id: fnr_activity label: Ferredoxin-NADP+ reductase participant: selector_type: ANY_WITH_FUNCTION required_function: preferred_term: ferredoxin-NADP+ reductase activity term: id: GO:0004324 label: ferredoxin-NADP+ reductase activity function: preferred_term: ferredoxin-NADP+ reductase activity term: id: GO:0004324 label: ferredoxin-NADP+ reductase activity substrates: - preferred_term: ferredoxin (reduced) - preferred_term: NADP+ products: - preferred_term: ferredoxin (oxidized) - preferred_term: NADPH - order: 7 role: ATP synthesis from the proton-motive force node: id: atp_synthase label: Thylakoid (chloroplast/cyanobacterial) ATP synthase module_type: PROTEIN_COMPLEX concepts: - preferred_term: proton-transporting ATP synthase complex term: id: GO:0045259 label: proton-transporting ATP synthase complex annotons: - id: photophosphorylation label: Proton-motive-force-driven ATP synthesis participant: selector_type: PROTEIN_COMPLEX protein_complex: preferred_term: thylakoid ATP synthase (CF1FO) term: id: GO:0045259 label: proton-transporting ATP synthase complex function: preferred_term: "proton-transporting ATP synthase activity, rotational mechanism" term: id: GO:0046933 label: "proton-transporting ATP synthase activity, rotational mechanism" substrates: - preferred_term: ADP - preferred_term: phosphate - preferred_term: proton (lumen) products: - preferred_term: ATP locations: - preferred_term: thylakoid membrane term: id: GO:0009535 label: chloroplast thylakoid membrane connections: - source: photosystem_II target: cytochrome_b6f connection_type: PROVIDES_INPUT_FOR description: PSII reduces plastoquinone to plastoquinol, the substrate oxidized by b6f. - source: cytochrome_b6f target: mobile_carrier_b6f_to_psi connection_type: PROVIDES_INPUT_FOR description: b6f reduces the mobile lumenal carrier (plastocyanin or cyt c6). - source: mobile_carrier_b6f_to_psi target: photosystem_I connection_type: PROVIDES_INPUT_FOR description: The reduced carrier re-reduces photo-oxidized P700 in PSI. - source: photosystem_I target: fnr_step connection_type: PROVIDES_INPUT_FOR description: PSI-reduced ferredoxin is the electron donor for FNR. - source: fnr_step target: atp_synthase connection_type: PRECEDES description: >- Linear electron flow and water oxidation build the proton-motive force used by the ATP synthase (coupling, not a metabolite hand-off). - order: 2 role: carbon fixation (Calvin-Benson-Bassham cycle) node: id: carbon_fixation label: Calvin-Benson-Bassham reductive pentose-phosphate cycle module_type: METABOLIC_PATHWAY concepts: - preferred_term: reductive pentose-phosphate cycle term: id: GO:0019253 label: reductive pentose-phosphate cycle - preferred_term: carbon fixation term: id: GO:0015977 label: carbon fixation parts: - order: 1 role: carboxylation node: id: rubisco_carboxylation label: Rubisco carboxylation of RuBP module_type: REACTION annotons: - id: rubisco_activity label: Ribulose-bisphosphate carboxylase participant: selector_type: ANY_WITH_FUNCTION required_function: preferred_term: ribulose-bisphosphate carboxylase activity term: id: GO:0016984 label: ribulose-bisphosphate carboxylase activity description: >- Form I Rubisco (L8S8, RbcL+RbcS) in plants, algae, and cyanobacteria; form II (L2) in some bacteria/dinoflagellates. function: preferred_term: ribulose-bisphosphate carboxylase activity term: id: GO:0016984 label: ribulose-bisphosphate carboxylase activity substrates: - preferred_term: ribulose 1,5-bisphosphate - preferred_term: CO2 products: - preferred_term: 3-phosphoglycerate locations: - preferred_term: chloroplast stroma / cyanobacterial cytoplasm term: id: GO:0009570 label: chloroplast stroma role_description: >- Fixes CO2 onto RuBP. The competing oxygenase reaction with O2 produces 2-phosphoglycolate (the substrate of photorespiration). evidence: - source_id: PMID:18294858 statement: Rubisco as the principal carboxylating enzyme with a competing oxygenase activity. - order: 2 role: reduction phase node: id: cbb_reduction_phase label: Reduction of 3-phosphoglycerate to triose phosphate module_type: METABOLIC_PATHWAY description: >- ATP- and NADPH-consuming reduction of 3-phosphoglycerate via 1,3-bisphosphoglycerate to glyceraldehyde 3-phosphate (phosphoglycerate kinase + chloroplastic NADP-GAPDH). annotons: - id: cbb_gapdh label: NADP-dependent glyceraldehyde-3-phosphate dehydrogenase participant: selector_type: FAMILY family: preferred_term: chloroplastic GAPDH (GapA/GapB) function: preferred_term: glyceraldehyde-3-phosphate dehydrogenase (NADP+) (phosphorylating) activity description: NADPH-consuming reduction step; no confident exact GO MF id asserted here. substrates: - preferred_term: 1,3-bisphosphoglycerate - preferred_term: NADPH products: - preferred_term: glyceraldehyde 3-phosphate - preferred_term: NADP+ - order: 3 role: regeneration phase node: id: cbb_regeneration_phase label: Regeneration of ribulose 1,5-bisphosphate module_type: METABOLIC_PATHWAY description: >- Rearrangement of triose phosphates through transketolase, aldolase, fructose-1,6-bisphosphatase, and sedoheptulose-1,7- bisphosphatase, ending in phosphoribulokinase regeneration of RuBP. annotons: - id: cbb_prk label: Phosphoribulokinase participant: selector_type: ANY_WITH_FUNCTION required_function: preferred_term: phosphoribulokinase activity term: id: GO:0008974 label: phosphoribulokinase activity function: preferred_term: phosphoribulokinase activity term: id: GO:0008974 label: phosphoribulokinase activity substrates: - preferred_term: ribulose 5-phosphate - preferred_term: ATP products: - preferred_term: ribulose 1,5-bisphosphate - preferred_term: ADP role_description: Regenerates the Rubisco substrate; a major redox-regulated control point. - id: cbb_sbpase_fbpase label: Bisphosphatase regeneration steps (FBPase, SBPase) participant: selector_type: FAMILY family: preferred_term: chloroplast FBPase / SBPase function: preferred_term: bisphosphatase regeneration steps description: >- Fructose-1,6-bisphosphatase and sedoheptulose-1,7- bisphosphatase; SBPase is a frequent yield-engineering target. - order: 4 role: Rubisco activation and inhibitor repair optional: true node: id: rubisco_activation label: Rubisco activase and inhibitor removal module_type: REGULATORY_STEP annotons: - id: rubisco_activase label: Rubisco activase participant: selector_type: FAMILY family: preferred_term: Rubisco activase (Rca) function: preferred_term: ATP-dependent removal of inhibitory sugar phosphates from Rubisco description: AAA+ chaperone-like remodeling of Rubisco active sites; thermolabile. role_description: Restores catalytically competent Rubisco; major thermal-tolerance target. - order: 5 role: redox gating of the CBB cycle optional: true node: id: cbb_redox_regulation label: CP12-mediated redox regulation module_type: REGULATORY_STEP annotons: - id: cp12_scaffold label: CP12 redox scaffold participant: selector_type: FAMILY family: preferred_term: CP12 representative_members: - preferred_term: Chlamydomonas CP12 term: id: UniProtKB:A6Q0K5 label: Calvin cycle protein CP12 function: preferred_term: redox-dependent scaffolding of the PRK-GAPDH-CP12 ternary complex description: >- In the dark/oxidizing conditions CP12 assembles an autoinhibitory PRK-GAPDH complex; reduction (thioredoxin/ NTRC) dissociates it to activate the cycle. targets: - preferred_term: phosphoribulokinase - preferred_term: glyceraldehyde-3-phosphate dehydrogenase role_description: Couples CBB-cycle activity to the light/redox state of the chloroplast. evidence: - source_id: PMID:33761918 statement: CP12 forms a PRK-GAPDH ternary complex regulating the CBB cycle. - source_id: PMID:37549282 statement: NTRC-dependent redox control of the PRK-CP12-GAPDH supracomplex. connections: - source: cp12_scaffold target: cbb_prk connection_type: NEGATIVELY_REGULATES description: CP12 inhibits PRK in the dark/oxidized state. - source: cp12_scaffold target: cbb_gapdh connection_type: NEGATIVELY_REGULATES description: CP12 inhibits GAPDH in the dark/oxidized state. - order: 3 role: photoprotection and ATP/NADPH balancing optional: true node: id: photoprotection_balancing label: Photoprotection and electron/energy balancing module_type: REGULATORY_STEP description: >- Mechanisms that dissipate excess excitation, redistribute antennae, and tune the ATP:NADPH ratio under fluctuating light. variant_sets: - id: balancing_mechanisms label: Photoprotection and balancing mechanisms axis: regulatory mechanism selection: ZERO_OR_MORE variants: - id: npq_variant label: Non-photochemical quenching (qE) module_type: REGULATORY_STEP annotons: - id: npq_psbs_xanthophyll label: PsbS- and xanthophyll-cycle-dependent quenching participant: selector_type: FAMILY family: preferred_term: PsbS and xanthophyll-cycle enzymes (VDE/ZEP) function: preferred_term: heat dissipation of excess PSII excitation role_description: Rapid, reversible thermal dissipation protecting PSII under high light. - id: state_transitions_variant label: State transitions module_type: REGULATORY_STEP annotons: - id: state_transition_kinase label: STN7/Stt7-dependent LHCII redistribution participant: selector_type: FAMILY family: preferred_term: state-transition kinase (STN7/Stt7) and TAP38/PPH1 phosphatase function: preferred_term: redox-controlled LHCII phosphorylation balancing PSII/PSI role_description: Rebalances excitation between the photosystems via antenna migration. - id: cyclic_electron_flow_variant label: Cyclic electron flow around PSI module_type: REGULATORY_STEP annotons: - id: cef_pgr5_ndh label: PGR5/PGRL1- and NDH-dependent cyclic electron flow participant: selector_type: FAMILY family: preferred_term: PGR5/PGRL1 and NDH(-1) complex function: preferred_term: cyclic electron transfer generating extra proton-motive force role_description: Raises ATP:NADPH and contributes to photoprotection. - order: 4 role: inorganic carbon-concentrating mechanism (CCM) optional: true node: id: carbon_concentrating_mechanism label: Carbon-concentrating mechanism module_type: REGULATORY_STEP description: >- Active inorganic-carbon uptake and CO2 concentration around Rubisco to suppress the oxygenase reaction; prominent in cyanobacteria and algae. annotons: - id: ccm_carbonic_anhydrase label: Carbonic anhydrase (CO2/HCO3- interconversion) participant: selector_type: ANY_WITH_FUNCTION required_function: preferred_term: carbonate dehydratase activity term: id: GO:0004089 label: carbonate dehydratase activity function: preferred_term: carbonate dehydratase activity term: id: GO:0004089 label: carbonate dehydratase activity substrates: - preferred_term: bicarbonate products: - preferred_term: CO2 - preferred_term: water variant_sets: - id: ccm_strategy label: CCM compartmentation strategy axis: lineage / compartment selection: EXACTLY_ONE variants: - id: carboxysome_ccm label: Cyanobacterial carboxysome CCM module_type: CELLULAR_COMPONENT annotons: - id: carboxysome_unit label: Carboxysome microcompartment with encapsulated Rubisco/CA participant: selector_type: FAMILY family: preferred_term: carboxysome shell and cargo (Ccm/Cso) role_description: Bacterial microcompartment concentrating CO2 around Rubisco. - id: pyrenoid_ccm label: Algal pyrenoid CCM module_type: CELLULAR_COMPONENT annotons: - id: pyrenoid_unit label: Pyrenoid and bicarbonate transporter network participant: selector_type: FAMILY family: preferred_term: pyrenoid CCM components (HLA3, LCIA, LCI1, LCIB, CAH3, CCM1/CIA5) representative_members: - preferred_term: Chlamydomonas LCI5 (low-CO2-inducible protein) term: id: UniProtKB:Q94ET8 label: Low-CO2-inducible protein 5 role_description: Eukaryotic algal biophysical CCM organized around the pyrenoid. - order: 5 role: chlorophyll supply (supporting context) optional: true node: id: pigment_biosynthesis label: Chlorophyll biosynthesis (supporting) module_type: METABOLIC_PATHWAY description: Supplies the chlorophyll cofactors required by antennae and reaction centers. annotons: - id: mg_chelatase label: Magnesium chelatase (committed step) participant: selector_type: FAMILY family: preferred_term: magnesium chelatase (CHLH/CHLD/CHLI) function: preferred_term: magnesium chelatase activity description: Inserts Mg2+ into protoporphyrin IX; committed step toward chlorophyll. No confident GO MF id asserted here. - id: por_reduction label: Protochlorophyllide reductase participant: selector_type: ANY_WITH_FUNCTION required_function: preferred_term: protochlorophyllide reductase activity term: id: GO:0016630 label: protochlorophyllide reductase activity function: preferred_term: protochlorophyllide reductase activity term: id: GO:0016630 label: protochlorophyllide reductase activity substrates: - preferred_term: protochlorophyllide products: - preferred_term: chlorophyllide connections: - source: light_reactions target: carbon_fixation connection_type: PROVIDES_INPUT_FOR description: >- The light reactions supply the ATP and NADPH consumed by the Calvin-Benson-Bassham cycle. - source: carbon_concentrating_mechanism target: rubisco_carboxylation connection_type: POSITIVELY_REGULATES description: The CCM raises CO2 around Rubisco, favoring carboxylation over oxygenation. notes: >- Concrete organism modules can specialize abstract participants with specific genes, complexes, compartments, and transporters (e.g. Synechocystis psbA/ psaA, Chlamydomonas pyrenoid CCM, Arabidopsis PsbS/RbcS) without the generic module naming every protein.