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. The C4 and CAM carbon-concentrating shuttles are siblings rather than parts: each includes the Calvin-Benson-Bassham module by reference in its own right, C4 operating between two cell types and CAM separating the two carboxylations in time (MODULE:c4_carbon_shuttle, MODULE:cam_carbon_shuttle).
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.
All recommended fields populated.
✓ present
5 leaf node(s) with no concrete protein grounding:
✓ every declared conforms_to bundle matches its template motif.
0 gene-function check(s) reflected in core functions · 0 conflict(s) · 4 evidence or coverage gap(s) (6 comparison(s))
Retained noncore functions are reported separately; they do not require promotion to core functions. Support from representative genes does not establish conservation across the whole family. Missing reviews or identifiers leave a claim unverified.
| Annoton | Participant | Function | Assessment |
|---|---|---|---|
| ccm_carbonic_anhydrase | ANY_WITH_FUNCTION Gene |
carbonate dehydratase activity GO:0004089 |
Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews. |
| por_reduction | ANY_WITH_FUNCTION Gene |
protochlorophyllide reductase activity GO:0016630 |
Participant Unchecked
No direct UniProt participant to compare. Abstract selectors and complex-wide activities cannot be inferred from donor or subunit gene reviews. |
| npq_psbs_xanthophyll | PsbS and xanthophyll-cycle enzymes (VDE/ZEP) Family |
heat dissipation of excess PSII excitation No function ID |
No Function Id
The family function has no GO identifier for comparison; prose is not matched. |
| state_transition_kinase | state-transition kinase (STN7/Stt7) and TAP38/PPH1 phosphatase Family |
redox-controlled LHCII phosphorylation balancing PSII/PSI No function ID |
No Function Id
The family function has no GO identifier for comparison; prose is not matched. |
| cef_pgr5_ndh | PGR5/PGRL1 and NDH(-1) complex Family |
cyclic electron transfer generating extra proton-motive force No function ID |
No Function Id
The family function has no GO identifier for comparison; prose is not matched. |
| mg_chelatase | magnesium chelatase (CHLH/CHLD/CHLI) Family |
magnesium chelatase activity No function ID |
No Function Id
The family function has no GO identifier for comparison; prose is not matched. |
1 complete review(s) · 1 with deep research · 0 missing review · 0 reviewed but lacking deep research
| Gene | Review | Complete | Deep research |
|---|---|---|---|
| LCI5 Q94ET8 | ✓ | ✓ | ✓ |
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.
Included by reference to MODULE:thylakoid_light_reactions, which models light harvesting, water oxidation at photosystem II, the cytochrome b6f complex, the mobile carriers, photosystem I, ferredoxin-NADP+ reductase and the ATP synthase. Extracted from this module so each stays small enough to read; the decomposition is unchanged.
Realized by module
thylakoid_light_reactions
Included by reference to MODULE:calvin_benson_bassham_cycle, which models Rubisco carboxylation, the reduction and regeneration phases, Rubisco activase and the CP12 redox scaffold. Extracted from this module both to keep each small and because the cycle is not specific to oxygenic photosynthesis: anoxygenic phototrophs and chemoautotrophs run the same cycle.
Realized by module
calvin_benson_bassham_cycle
Mechanisms that dissipate excess excitation, redistribute antennae, and tune the ATP:NADPH ratio under fluctuating light.
Rapid, reversible thermal dissipation protecting PSII under high light.
Rebalances excitation between the photosystems via antenna migration.
Raises ATP:NADPH and contributes to photoprotection.
Active inorganic-carbon uptake and CO2 concentration around Rubisco to suppress the oxygenase reaction; prominent in cyanobacteria and algae.
Bacterial microcompartment concentrating CO2 around Rubisco.
Eukaryotic algal biophysical CCM organized around the pyrenoid.
Supplies the chlorophyll cofactors required by antennae and reaction centers.