Riboneogenesis

PathBank:SMP0002406

The six-reaction Saccharomyces cerevisiae route makes ribose 5-phosphate from fructose 6-phosphate and triose phosphates without producing NADPH. Transketolase and Fba1 supply sedoheptulose 1,7-bisphosphate; Shb17 hydrolysis provides the thermodynamic drive; transketolase, Rpe1 and Rki1 complete pentose formation. Evidence includes BY4743-derived mutants and FY4/FY5 controls, not a claim of identical flux in every yeast strain. Protein enables edges identify functional gene products while retaining homodimer evidence; no isolated-monomer sufficiency or Tkl1–Tkl2 heteromer is asserted. Tkl2 reaction/cofactor annotations are inferred by similarity. The graph selects riboneogenic flux through otherwise reversible reactions using exact directed Rhea equations and charge forms. These formal chemical representations do not equate the native cyclic ribose phosphate or the crystallographic beta-furanose SBP ligand with open-chain ChEBI structures. NADPH production, transaldolase bypass, octulose metabolism and Calvin-cycle carbon fixation are outside this route.

Pathway type
ribose phosphate biosynthesis
Organism scope

Read the source YAML

Pathway network

33 nodes · 50 asserted directed edges

Arrows show recorded subject → object relationships, not necessarily metabolic flow. Select a node for details or an arrow for evidence. Scroll, zoom or find a node to explore.

Pathway network: Riboneogenesis 33 nodes · 50 asserted directed edges. Every arrow links to its evidence table row; nodes link to their component details. Isolated declared components are retained. CHEBI:57634 — consumes → RHEA:27628; Coefficient 1 in the selected riboneogenic direction; Rhea's formal charge and sugar representation are retained.; Evidence: RHEA:27626consumes CHEBI:59776 — consumes → RHEA:27628; Coefficient 1 in the selected riboneogenic direction; Rhea's formal charge and sugar representation are retained.; Evidence: RHEA:27626consumes RHEA:27628 — produces → CHEBI:16897; Coefficient 1 in the selected riboneogenic direction; Rhea's formal charge and sugar representation are retained.; Evidence: RHEA:27626produces RHEA:27628 — produces → CHEBI:57737; Coefficient 1 in the selected riboneogenic direction; Rhea's formal charge and sugar representation are retained.; Evidence: RHEA:27626produces CHEBI:16897 — consumes → RHEA:30168; Coefficient 1 in the selected riboneogenic direction; Rhea's formal charge and sugar representation are retained.; Evidence: RHEA:30167consumes CHEBI:57642 — consumes → RHEA:30168; Coefficient 1 in the selected riboneogenic direction; Rhea's formal charge and sugar representation are retained.; Evidence: RHEA:30167consumes RHEA:30168 — produces → CHEBI:58335; Coefficient 1 in the selected riboneogenic direction; Rhea's formal charge and sugar representation are retained.; Evidence: RHEA:30167produces CHEBI:58335 — consumes → RHEA:17462; Coefficient 1 in the selected riboneogenic direction; Rhea's formal charge and sugar representation are retained.; Evidence: RHEA:17461consumes CHEBI:15377 — consumes → RHEA:17462; Coefficient 1 in the selected riboneogenic direction; Rhea's formal charge and sugar representation are retained.; Evidence: RHEA:17461consumes RHEA:17462 — produces → CHEBI:57483; Coefficient 1 in the selected riboneogenic direction; Rhea's formal charge and sugar representation are retained.; Evidence: RHEA:17461produces RHEA:17462 — produces → CHEBI:43474; Coefficient 1 in the selected riboneogenic direction; Rhea's formal charge and sugar representation are retained.; Evidence: RHEA:17461produces CHEBI:57483 — consumes → RHEA:10509; Coefficient 1 in the selected riboneogenic direction; Rhea's formal charge and sugar representation are retained.; Evidence: RHEA:10508consumes CHEBI:59776 — consumes → RHEA:10509; Coefficient 1 in the selected riboneogenic direction; Rhea's formal charge and sugar representation are retained.; Evidence: RHEA:10508consumes RHEA:10509 — produces → CHEBI:58273; Coefficient 1 in the selected riboneogenic direction; Rhea's formal charge and sugar representation are retained.; Evidence: RHEA:10508produces RHEA:10509 — produces → CHEBI:57737; Coefficient 1 in the selected riboneogenic direction; Rhea's formal charge and sugar representation are retained.; Evidence: RHEA:10508produces CHEBI:57737 — consumes → RHEA:13679; Coefficient 1 in the selected riboneogenic direction; Rhea's formal charge and sugar representation are retained.; Evidence: RHEA:13677consumes RHEA:13679 — produces → CHEBI:58121; Coefficient 1 in the selected riboneogenic direction; Rhea's formal charge and sugar representation are retained.; Evidence: RHEA:13677produces CHEBI:58121 — consumes → RHEA:14659; Coefficient 1 in the selected riboneogenic direction; Rhea's formal charge and sugar representation are retained.; Evidence: RHEA:14657consumes RHEA:14659 — produces → CHEBI:58273; Coefficient 1 in the selected riboneogenic direction; Rhea's formal charge and sugar representation are retained.; Evidence: RHEA:14657produces UniProtKB:P23254 — enables → RHEA:27628; Tkl1 functional contribution in its homodimeric enzyme context; this gene-product edge does not assert independent monomer activity. The primary route identifies Tkl1 as the main transketolase activity.; Evidence: PMID:21663798, UniProtKB:P23254, PathBank:SMP0002406enables UniProtKB:P23254 — enables → RHEA:10509; Tkl1 functional contribution in its homodimeric enzyme context; this gene-product edge does not assert independent monomer activity. The primary route identifies Tkl1 as the main transketolase activity.; Evidence: PMID:21663798, UniProtKB:P23254, UniProtKB:P23254enables UniProtKB:P33315 — enables → RHEA:27628; Tkl2 functional contribution in its homodimeric enzyme context; this gene-product edge does not assert independent monomer activity. Its specific reaction and assembly annotation is inferred by similarity, not separately purified Tkl2 evidence.; Evidence: PMID:21663798, UniProtKB:P33315, PathBank:SMP0002406enables UniProtKB:P33315 — enables → RHEA:10509; Tkl2 functional contribution in its homodimeric enzyme context; this gene-product edge does not assert independent monomer activity. Its specific reaction and assembly annotation is inferred by similarity, not separately purified Tkl2 evidence.; Evidence: PMID:21663798, UniProtKB:P33315, UniProtKB:P33315enables UniProtKB:P14540 — enables → RHEA:30168; Fba1 enables aldol condensation of erythrose 4-phosphate with DHAP. Reduced FBA1 expression slows SBP labeling; UniProt annotates a homodimer without an inline evidence code. No isolated-monomer sufficiency is claimed.; Evidence: PMID:21663798, PMID:21663798, UniProtKB:P14540enables UniProtKB:P36136 — enables → RHEA:17462; Shb17 hydrolysis is the committed step. The gene-product edge retains the homodimer context; the SBP-bound H13A structure contains two subunits. The possible Mg2+ density is not a demonstrated requirement and creates no cofactor edge.; Evidence: UniProtKB:P36136, PMID:21663798, PMID:21663798enables UniProtKB:P46969 — enables → RHEA:13679; Rpe1 supports xylulose-5-phosphate conversion to ribulose-5-phosphate in this route. Gene-deletion enzyme assays provide direct functional support; the current UniProt catalytic and metal annotations separately retain similarity evidence.; Evidence: UniProtKB:P46969, PMID:8929392, PMID:21663798enables UniProtKB:Q12189 — enables → RHEA:14659; Rki1 completes ribose-5-phosphate formation. Gene-dosage rescue supports the functional product; no oligomer stoichiometry is inferred from a missing SUBUNIT comment.; Evidence: UniProtKB:Q12189, PMID:8929392, PMID:21663798enables RHEA:27628 — part_of → PathBank:SMP0002406; Manual correspondence of the native reaction, primary route and exact Rhea chemistry. PathBank supplies no Rhea cross-reference; protonation/tautomer distinctions are not exact-identity mappings. The native step is reversible; the graph selects the riboneogenic flux.; Evidence: PathBank:SMP0002406, RHEA:27626, PMID:21663798part of RHEA:30168 — part_of → PathBank:SMP0002406; Manual correspondence of the native reaction, primary route and exact Rhea chemistry. PathBank supplies no Rhea cross-reference; protonation/tautomer distinctions are not exact-identity mappings. The native step is reversible; the graph selects the riboneogenic flux.; Evidence: PathBank:SMP0002406, RHEA:30167, PMID:21663798part of RHEA:17462 — part_of → PathBank:SMP0002406; Manual correspondence of the native reaction, primary route and exact Rhea chemistry. PathBank supplies no Rhea cross-reference; protonation/tautomer distinctions are not exact-identity mappings. Native hydrolysis is left-to-right.; Evidence: PathBank:SMP0002406, RHEA:17461, PMID:21663798part of RHEA:10509 — part_of → PathBank:SMP0002406; Manual correspondence of the native reaction, primary route and exact Rhea chemistry. PathBank supplies no Rhea cross-reference; protonation/tautomer distinctions are not exact-identity mappings. The native step is reversible; the graph selects the riboneogenic flux.; Evidence: PathBank:SMP0002406, RHEA:10508, PMID:21663798part of RHEA:13679 — part_of → PathBank:SMP0002406; Manual correspondence of the native reaction, primary route and exact Rhea chemistry. PathBank supplies no Rhea cross-reference; protonation/tautomer distinctions are not exact-identity mappings. The native step is reversible; the graph selects the riboneogenic flux.; Evidence: PathBank:SMP0002406, RHEA:13677, PMID:21663798part of RHEA:14659 — part_of → PathBank:SMP0002406; Manual correspondence of the native reaction, primary route and exact Rhea chemistry. PathBank supplies no Rhea cross-reference; protonation/tautomer distinctions are not exact-identity mappings. The native step is reversible; the graph selects the riboneogenic flux.; Evidence: PathBank:SMP0002406, RHEA:14657, PMID:21663798part of UniProtKB:P23254 — has_cofactor → CHEBI:18420; Reviewed protein cofactor annotation in its functional enzyme context. Binds 1 Mg(2+) ion per subunit (PubMed:18186462). Can also utilize other divalent metal cations, such as Ca(2+), Mn(2+) and Co(2+) (PubMed:18186462). These metals are alternatives, not simultaneous requirements.; Evidence: UniProtKB:P23254has cofactor UniProtKB:P23254 — has_cofactor → CHEBI:29108; Reviewed protein cofactor annotation in its functional enzyme context. Binds 1 Mg(2+) ion per subunit (PubMed:18186462). Can also utilize other divalent metal cations, such as Ca(2+), Mn(2+) and Co(2+) (PubMed:18186462). These metals are alternatives, not simultaneous requirements.; Evidence: UniProtKB:P23254has cofactor UniProtKB:P23254 — has_cofactor → CHEBI:29035; Reviewed protein cofactor annotation in its functional enzyme context. Binds 1 Mg(2+) ion per subunit (PubMed:18186462). Can also utilize other divalent metal cations, such as Ca(2+), Mn(2+) and Co(2+) (PubMed:18186462). These metals are alternatives, not simultaneous requirements.; Evidence: UniProtKB:P23254has cofactor UniProtKB:P23254 — has_cofactor → CHEBI:48828; Reviewed protein cofactor annotation in its functional enzyme context. Binds 1 Mg(2+) ion per subunit (PubMed:18186462). Can also utilize other divalent metal cations, such as Ca(2+), Mn(2+) and Co(2+) (PubMed:18186462). These metals are alternatives, not simultaneous requirements.; Evidence: UniProtKB:P23254has cofactor UniProtKB:P23254 — has_cofactor → CHEBI:58937; Reviewed protein cofactor annotation in its functional enzyme context. Binds 1 thiamine pyrophosphate per subunit.; Evidence: UniProtKB:P23254has cofactor UniProtKB:P33315 — has_cofactor → CHEBI:18420; Reviewed protein cofactor annotation in its functional enzyme context. Binds 1 Mg(2+) ion per subunit. Can also utilize other divalent metal cations, such as Ca(2+), Mn(2+) and Co(2+). The annotation is by similarity; it is not a direct yeast cofactor assay. These metals are alternatives, not simultaneous requirements.; Evidence: UniProtKB:P33315has cofactor UniProtKB:P33315 — has_cofactor → CHEBI:29108; Reviewed protein cofactor annotation in its functional enzyme context. Binds 1 Mg(2+) ion per subunit. Can also utilize other divalent metal cations, such as Ca(2+), Mn(2+) and Co(2+). The annotation is by similarity; it is not a direct yeast cofactor assay. These metals are alternatives, not simultaneous requirements.; Evidence: UniProtKB:P33315has cofactor UniProtKB:P33315 — has_cofactor → CHEBI:29035; Reviewed protein cofactor annotation in its functional enzyme context. Binds 1 Mg(2+) ion per subunit. Can also utilize other divalent metal cations, such as Ca(2+), Mn(2+) and Co(2+). The annotation is by similarity; it is not a direct yeast cofactor assay. These metals are alternatives, not simultaneous requirements.; Evidence: UniProtKB:P33315has cofactor UniProtKB:P33315 — has_cofactor → CHEBI:48828; Reviewed protein cofactor annotation in its functional enzyme context. Binds 1 Mg(2+) ion per subunit. Can also utilize other divalent metal cations, such as Ca(2+), Mn(2+) and Co(2+). The annotation is by similarity; it is not a direct yeast cofactor assay. These metals are alternatives, not simultaneous requirements.; Evidence: UniProtKB:P33315has cofactor UniProtKB:P33315 — has_cofactor → CHEBI:58937; Reviewed protein cofactor annotation in its functional enzyme context. Binds 1 thiamine pyrophosphate per subunit. The annotation is by similarity; it is not a direct yeast cofactor assay.; Evidence: UniProtKB:P33315has cofactor UniProtKB:P14540 — has_cofactor → CHEBI:29105; Reviewed protein cofactor annotation in its functional enzyme context. Binds 2 Zn(2+) ions per subunit. One is catalytic and the other provides a structural contribution. The annotation is by similarity; it is not a direct yeast cofactor assay.; Evidence: UniProtKB:P14540has cofactor UniProtKB:P46969 — has_cofactor → CHEBI:48828; Reviewed protein cofactor annotation in its functional enzyme context. Binds 1 divalent metal cation per subunit. Active with Co(2+), Fe(2+), Mn(2+) and Zn(2+). The annotation is by similarity; it is not a direct yeast cofactor assay. These metals are alternatives, not simultaneous requirements.; Evidence: UniProtKB:P46969has cofactor UniProtKB:P46969 — has_cofactor → CHEBI:29033; Reviewed protein cofactor annotation in its functional enzyme context. Binds 1 divalent metal cation per subunit. Active with Co(2+), Fe(2+), Mn(2+) and Zn(2+). The annotation is by similarity; it is not a direct yeast cofactor assay. These metals are alternatives, not simultaneous requirements.; Evidence: UniProtKB:P46969has cofactor UniProtKB:P46969 — has_cofactor → CHEBI:29035; Reviewed protein cofactor annotation in its functional enzyme context. Binds 1 divalent metal cation per subunit. Active with Co(2+), Fe(2+), Mn(2+) and Zn(2+). The annotation is by similarity; it is not a direct yeast cofactor assay. These metals are alternatives, not simultaneous requirements.; Evidence: UniProtKB:P46969has cofactor UniProtKB:P46969 — has_cofactor → CHEBI:29105; Reviewed protein cofactor annotation in its functional enzyme context. Binds 1 divalent metal cation per subunit. Active with Co(2+), Fe(2+), Mn(2+) and Zn(2+). The annotation is by similarity; it is not a direct yeast cofactor assay. These metals are alternatives, not simultaneous requirements.; Evidence: UniProtKB:P46969has cofactor UniProtKB:P36136 — located_in → GO:0005737; Reported protein localization, not a claim that every riboneogenic reaction occurs in both compartments or that localization is exclusive.; Evidence: UniProtKB:P36136located in UniProtKB:P36136 — located_in → GO:0005634; Reported protein localization, not a claim that every riboneogenic reaction occurs in both compartments or that localization is exclusive.; Evidence: UniProtKB:P36136located in beta-D-fructofuranose 6-phosphate(2-); CHEBI:57634; Declared type: small_molecule small molecule beta-D-fructofuranose 6-phosphate(2-) D-glyceraldehyde 3-phosphate(2-); CHEBI:59776; Declared type: small_molecule small molecule D-glyceraldehyde 3-phosphate(2-) D-erythrose 4-phosphate(2-); CHEBI:16897; Declared type: small_molecule small molecule D-erythrose 4-phosphate(2-) D-xylulose 5-phosphate(2-); CHEBI:57737; Declared type: small_molecule small molecule D-xylulose 5-phosphate(2-) glycerone phosphate(2-); CHEBI:57642; Declared type: small_molecule small molecule glycerone phosphate(2-) sedoheptulose 1,7-bisphosphate(4-); CHEBI:58335; Declared type: small_molecule small molecule sedoheptulose 1,7-bisphosphate(4-) water; CHEBI:15377; Declared type: small_molecule small molecule water sedoheptulose 7-phosphate(2-); CHEBI:57483; Declared type: small_molecule small molecule sedoheptulose 7-phosphate(2-) hydrogenphosphate; CHEBI:43474; Declared type: small_molecule small molecule hydrogenphosphate aldehydo-D-ribose 5-phosphate(2-); CHEBI:58273; Declared type: small_molecule small molecule aldehydo-D-ribose 5-phosphate(2-) D-ribulose 5-phosphate(2-); CHEBI:58121; Declared type: small_molecule small molecule D-ribulose 5-phosphate(2-) thiamine(1+) diphosphate(3-); CHEBI:58937; Declared type: cofactor cofactor thiamine(1+) diphosphate(3-) magnesium(2+); CHEBI:18420; Declared type: cofactor cofactor magnesium(2+) calcium(2+); CHEBI:29108; Declared type: cofactor cofactor calcium(2+) manganese(2+); CHEBI:29035; Declared type: cofactor cofactor manganese(2+) cobalt(2+); CHEBI:48828; Declared type: cofactor cofactor cobalt(2+) iron(2+); CHEBI:29033; Declared type: cofactor cofactor iron(2+) zinc(2+); CHEBI:29105; Declared type: cofactor cofactor zinc(2+) Transketolase 1; UniProtKB:P23254; Declared type: protein protein Transketolase 1 Transketolase 2; UniProtKB:P33315; Declared type: protein protein Transketolase 2 Fructose-bisphosphate aldolase; UniProtKB:P14540; Declared type: protein protein Fructose-bisphosphate aldolase Sedoheptulose 1,7-bisphosphatase; UniProtKB:P36136; Declared type: protein protein Sedoheptulose 1,7-bisphosphatase Ribulose-phosphate 3-epimerase; UniProtKB:P46969; Declared type: protein protein Ribulose-phosphate 3-epimerase Ribose-5-phosphate isomerase; UniProtKB:Q12189; Declared type: protein protein Ribose-5-phosphate isomerase cytoplasm; GO:0005737; Declared type: cellular_component cellular component cytoplasm nucleus; GO:0005634; Declared type: cellular_component cellular component nucleus beta-D-fructose 6-phosphate + D-glyceraldehyde 3-phosphate => D-erythrose 4-phosphate + D-xylulose 5-phosphate; RHEA:27628; Declared type: molecular_activity; Source reaction direction: right_to_left molecular activity beta-D-fructose 6-phosphate + D-glyceraldehyde 3-phosphate => D-erythrose 4-phosphate + D-xylulose 5-phosphate D-erythrose 4-phosphate + dihydroxyacetone phosphate => D-sedoheptulose 1,7-bisphosphate; RHEA:30168; Declared type: molecular_activity; Source reaction direction: left_to_right molecular activity D-erythrose 4-phosphate + dihydroxyacetone phosphate => D-sedoheptulose 1,7-bisphosphate D-sedoheptulose 1,7-bisphosphate + H2O => D-sedoheptulose 7-phosphate + phosphate; RHEA:17462; Declared type: molecular_activity; Source reaction direction: left_to_right molecular activity D-sedoheptulose 1,7-bisphosphate + H2O => D-sedoheptulose 7-phosphate + phosphate D-sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate => aldehydo-D-ribose 5-phosphate + D-xylulose 5-phosphate; RHEA:10509; Declared type: molecular_activity; Source reaction direction: left_to_right molecular activity D-sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate => aldehydo-D- ribose 5-phosphate + D-xylulose 5-phosphate D-xylulose 5-phosphate => D-ribulose 5-phosphate; RHEA:13679; Declared type: molecular_activity; Source reaction direction: right_to_left molecular activity D-xylulose 5-phosphate => D-ribulose 5-phosphate D-ribulose 5-phosphate => aldehydo-D-ribose 5-phosphate; RHEA:14659; Declared type: molecular_activity; Source reaction direction: right_to_left molecular activity D-ribulose 5-phosphate => aldehydo-D-ribose 5-phosphate Riboneogenesis; PathBank:SMP0002406; Declared type: pathway pathway Riboneogenesis

Components and activities

Declared biological components and source reaction directions
NodeKind or roleSource direction
Saccharomyces cerevisiae
NCBITaxon:4932		taxon
beta-D-fructofuranose 6-phosphate(2-)
CHEBI:57634		small molecule
D-glyceraldehyde 3-phosphate(2-)
CHEBI:59776		small molecule
D-erythrose 4-phosphate(2-)
CHEBI:16897		small molecule
D-xylulose 5-phosphate(2-)
CHEBI:57737		small molecule
glycerone phosphate(2-)
CHEBI:57642		small molecule
sedoheptulose 1,7-bisphosphate(4-)
CHEBI:58335		small molecule
water
CHEBI:15377		small molecule
sedoheptulose 7-phosphate(2-)
CHEBI:57483		small molecule
hydrogenphosphate
CHEBI:43474		small molecule
aldehydo-D-ribose 5-phosphate(2-)
CHEBI:58273		small molecule
D-ribulose 5-phosphate(2-)
CHEBI:58121		small molecule
thiamine(1+) diphosphate(3-)
CHEBI:58937		cofactor
magnesium(2+)
CHEBI:18420		cofactor
calcium(2+)
CHEBI:29108		cofactor
manganese(2+)
CHEBI:29035		cofactor
cobalt(2+)
CHEBI:48828		cofactor
iron(2+)
CHEBI:29033		cofactor
zinc(2+)
CHEBI:29105		cofactor
Transketolase 1
UniProtKB:P23254		protein
Transketolase 2
UniProtKB:P33315		protein
Fructose-bisphosphate aldolase
UniProtKB:P14540		protein
Sedoheptulose 1,7-bisphosphatase
UniProtKB:P36136		protein
Ribulose-phosphate 3-epimerase
UniProtKB:P46969		protein
Ribose-5-phosphate isomerase
UniProtKB:Q12189		protein
cytoplasm
GO:0005737		cellular component
nucleus
GO:0005634		cellular component
beta-D-fructose 6-phosphate + D-glyceraldehyde 3-phosphate => D-erythrose 4-phosphate + D-xylulose 5-phosphate
RHEA:27628		molecular activityright to left
D-erythrose 4-phosphate + dihydroxyacetone phosphate => D-sedoheptulose 1,7-bisphosphate
RHEA:30168		molecular activityleft to right
D-sedoheptulose 1,7-bisphosphate + H2O => D-sedoheptulose 7-phosphate + phosphate
RHEA:17462		molecular activityleft to right
D-sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate => aldehydo-D-ribose 5-phosphate + D-xylulose 5-phosphate
RHEA:10509		molecular activityleft to right
D-xylulose 5-phosphate => D-ribulose 5-phosphate
RHEA:13679		molecular activityright to left
D-ribulose 5-phosphate => aldehydo-D-ribose 5-phosphate
RHEA:14659		molecular activityright to left

Mechanistic edges

Mechanistic edges and their cited evidence
SubjectPredicate and descriptionObjectEvidence
beta-D-fructofuranose 6-phosphate(2-)
CHEBI:57634		consumes

Coefficient 1 in the selected riboneogenic direction; Rhea's formal charge and sugar representation are retained.

beta-D-fructose 6-phosphate + D-glyceraldehyde 3-phosphate => D-erythrose 4-phosphate + D-xylulose 5-phosphate
RHEA:27628
  • RHEA:27626

    Source assertion: RHEA:27628 substrates contain CHEBI:57634 with coefficient 1.

    Source locationhttp://rdf.rhea-db.org/27628 rh:substrates; http://rdf.rhea-db.org/27626_R rh:contains1 http://rdf.rhea-db.org/Participant_27626_compound_5371; rh:compound/rh:accession
D-glyceraldehyde 3-phosphate(2-)
CHEBI:59776		consumes

Coefficient 1 in the selected riboneogenic direction; Rhea's formal charge and sugar representation are retained.

beta-D-fructose 6-phosphate + D-glyceraldehyde 3-phosphate => D-erythrose 4-phosphate + D-xylulose 5-phosphate
RHEA:27628
  • RHEA:27626

    Source assertion: RHEA:27628 substrates contain CHEBI:59776 with coefficient 1.

    Source locationhttp://rdf.rhea-db.org/27628 rh:substrates; http://rdf.rhea-db.org/27626_R rh:contains1 http://rdf.rhea-db.org/Participant_27626_compound_6062; rh:compound/rh:accession
beta-D-fructose 6-phosphate + D-glyceraldehyde 3-phosphate => D-erythrose 4-phosphate + D-xylulose 5-phosphate
RHEA:27628		produces

Coefficient 1 in the selected riboneogenic direction; Rhea's formal charge and sugar representation are retained.

D-erythrose 4-phosphate(2-)
CHEBI:16897
  • RHEA:27626

    Source assertion: RHEA:27628 products contain CHEBI:16897 with coefficient 1.

    Source locationhttp://rdf.rhea-db.org/27628 rh:products; http://rdf.rhea-db.org/27626_L rh:contains1 http://rdf.rhea-db.org/Participant_27626_compound_5282; rh:compound/rh:accession
beta-D-fructose 6-phosphate + D-glyceraldehyde 3-phosphate => D-erythrose 4-phosphate + D-xylulose 5-phosphate
RHEA:27628		produces

Coefficient 1 in the selected riboneogenic direction; Rhea's formal charge and sugar representation are retained.

D-xylulose 5-phosphate(2-)
CHEBI:57737
  • RHEA:27626

    Source assertion: RHEA:27628 products contain CHEBI:57737 with coefficient 1.

    Source locationhttp://rdf.rhea-db.org/27628 rh:products; http://rdf.rhea-db.org/27626_L rh:contains1 http://rdf.rhea-db.org/Participant_27626_compound_1624; rh:compound/rh:accession
D-erythrose 4-phosphate(2-)
CHEBI:16897		consumes

Coefficient 1 in the selected riboneogenic direction; Rhea's formal charge and sugar representation are retained.

D-erythrose 4-phosphate + dihydroxyacetone phosphate => D-sedoheptulose 1,7-bisphosphate
RHEA:30168
  • RHEA:30167

    Source assertion: RHEA:30168 substrates contain CHEBI:16897 with coefficient 1.

    Source locationhttp://rdf.rhea-db.org/30168 rh:substrates; http://rdf.rhea-db.org/30167_L rh:contains1 http://rdf.rhea-db.org/Participant_30167_compound_5282; rh:compound/rh:accession
glycerone phosphate(2-)
CHEBI:57642		consumes

Coefficient 1 in the selected riboneogenic direction; Rhea's formal charge and sugar representation are retained.

D-erythrose 4-phosphate + dihydroxyacetone phosphate => D-sedoheptulose 1,7-bisphosphate
RHEA:30168
  • RHEA:30167

    Source assertion: RHEA:30168 substrates contain CHEBI:57642 with coefficient 1.

    Source locationhttp://rdf.rhea-db.org/30168 rh:substrates; http://rdf.rhea-db.org/30167_L rh:contains1 http://rdf.rhea-db.org/Participant_30167_compound_4255; rh:compound/rh:accession
D-erythrose 4-phosphate + dihydroxyacetone phosphate => D-sedoheptulose 1,7-bisphosphate
RHEA:30168		produces

Coefficient 1 in the selected riboneogenic direction; Rhea's formal charge and sugar representation are retained.

sedoheptulose 1,7-bisphosphate(4-)
CHEBI:58335
  • RHEA:30167

    Source assertion: RHEA:30168 products contain CHEBI:58335 with coefficient 1.

    Source locationhttp://rdf.rhea-db.org/30168 rh:products; http://rdf.rhea-db.org/30167_R rh:contains1 http://rdf.rhea-db.org/Participant_30167_compound_2479; rh:compound/rh:accession
sedoheptulose 1,7-bisphosphate(4-)
CHEBI:58335		consumes

Coefficient 1 in the selected riboneogenic direction; Rhea's formal charge and sugar representation are retained.

D-sedoheptulose 1,7-bisphosphate + H2O => D-sedoheptulose 7-phosphate + phosphate
RHEA:17462
  • RHEA:17461

    Source assertion: RHEA:17462 substrates contain CHEBI:58335 with coefficient 1.

    Source locationhttp://rdf.rhea-db.org/17462 rh:substrates; http://rdf.rhea-db.org/17461_L rh:contains1 http://rdf.rhea-db.org/Participant_17461_compound_2479; rh:compound/rh:accession
water
CHEBI:15377		consumes

Coefficient 1 in the selected riboneogenic direction; Rhea's formal charge and sugar representation are retained.

D-sedoheptulose 1,7-bisphosphate + H2O => D-sedoheptulose 7-phosphate + phosphate
RHEA:17462
  • RHEA:17461

    Source assertion: RHEA:17462 substrates contain CHEBI:15377 with coefficient 1.

    Source locationhttp://rdf.rhea-db.org/17462 rh:substrates; http://rdf.rhea-db.org/17461_L rh:contains1 http://rdf.rhea-db.org/Participant_17461_compound_1283; rh:compound/rh:accession
D-sedoheptulose 1,7-bisphosphate + H2O => D-sedoheptulose 7-phosphate + phosphate
RHEA:17462		produces

Coefficient 1 in the selected riboneogenic direction; Rhea's formal charge and sugar representation are retained.

sedoheptulose 7-phosphate(2-)
CHEBI:57483
  • RHEA:17461

    Source assertion: RHEA:17462 products contain CHEBI:57483 with coefficient 1.

    Source locationhttp://rdf.rhea-db.org/17462 rh:products; http://rdf.rhea-db.org/17461_R rh:contains1 http://rdf.rhea-db.org/Participant_17461_compound_3830; rh:compound/rh:accession
D-sedoheptulose 1,7-bisphosphate + H2O => D-sedoheptulose 7-phosphate + phosphate
RHEA:17462		produces

Coefficient 1 in the selected riboneogenic direction; Rhea's formal charge and sugar representation are retained.

hydrogenphosphate
CHEBI:43474
  • RHEA:17461

    Source assertion: RHEA:17462 products contain CHEBI:43474 with coefficient 1.

    Source locationhttp://rdf.rhea-db.org/17462 rh:products; http://rdf.rhea-db.org/17461_R rh:contains1 http://rdf.rhea-db.org/Participant_17461_compound_5518; rh:compound/rh:accession
sedoheptulose 7-phosphate(2-)
CHEBI:57483		consumes

Coefficient 1 in the selected riboneogenic direction; Rhea's formal charge and sugar representation are retained.

D-sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate => aldehydo-D-ribose 5-phosphate + D-xylulose 5-phosphate
RHEA:10509
  • RHEA:10508

    Source assertion: RHEA:10509 substrates contain CHEBI:57483 with coefficient 1.

    Source locationhttp://rdf.rhea-db.org/10509 rh:substrates; http://rdf.rhea-db.org/10508_L rh:contains1 http://rdf.rhea-db.org/Participant_10508_compound_3830; rh:compound/rh:accession
D-glyceraldehyde 3-phosphate(2-)
CHEBI:59776		consumes

Coefficient 1 in the selected riboneogenic direction; Rhea's formal charge and sugar representation are retained.

D-sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate => aldehydo-D-ribose 5-phosphate + D-xylulose 5-phosphate
RHEA:10509
  • RHEA:10508

    Source assertion: RHEA:10509 substrates contain CHEBI:59776 with coefficient 1.

    Source locationhttp://rdf.rhea-db.org/10509 rh:substrates; http://rdf.rhea-db.org/10508_L rh:contains1 http://rdf.rhea-db.org/Participant_10508_compound_6062; rh:compound/rh:accession
D-sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate => aldehydo-D-ribose 5-phosphate + D-xylulose 5-phosphate
RHEA:10509		produces

Coefficient 1 in the selected riboneogenic direction; Rhea's formal charge and sugar representation are retained.

aldehydo-D-ribose 5-phosphate(2-)
CHEBI:58273
  • RHEA:10508

    Source assertion: RHEA:10509 products contain CHEBI:58273 with coefficient 1.

    Source locationhttp://rdf.rhea-db.org/10509 rh:products; http://rdf.rhea-db.org/10508_R rh:contains1 http://rdf.rhea-db.org/Participant_10508_compound_6214; rh:compound/rh:accession
D-sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate => aldehydo-D-ribose 5-phosphate + D-xylulose 5-phosphate
RHEA:10509		produces

Coefficient 1 in the selected riboneogenic direction; Rhea's formal charge and sugar representation are retained.

D-xylulose 5-phosphate(2-)
CHEBI:57737
  • RHEA:10508

    Source assertion: RHEA:10509 products contain CHEBI:57737 with coefficient 1.

    Source locationhttp://rdf.rhea-db.org/10509 rh:products; http://rdf.rhea-db.org/10508_R rh:contains1 http://rdf.rhea-db.org/Participant_10508_compound_1624; rh:compound/rh:accession
D-xylulose 5-phosphate(2-)
CHEBI:57737		consumes

Coefficient 1 in the selected riboneogenic direction; Rhea's formal charge and sugar representation are retained.

D-xylulose 5-phosphate => D-ribulose 5-phosphate
RHEA:13679
  • RHEA:13677

    Source assertion: RHEA:13679 substrates contain CHEBI:57737 with coefficient 1.

    Source locationhttp://rdf.rhea-db.org/13679 rh:substrates; http://rdf.rhea-db.org/13677_R rh:contains1 http://rdf.rhea-db.org/Participant_13677_compound_1624; rh:compound/rh:accession
D-xylulose 5-phosphate => D-ribulose 5-phosphate
RHEA:13679		produces

Coefficient 1 in the selected riboneogenic direction; Rhea's formal charge and sugar representation are retained.

D-ribulose 5-phosphate(2-)
CHEBI:58121
  • RHEA:13677

    Source assertion: RHEA:13679 products contain CHEBI:58121 with coefficient 1.

    Source locationhttp://rdf.rhea-db.org/13679 rh:products; http://rdf.rhea-db.org/13677_L rh:contains1 http://rdf.rhea-db.org/Participant_13677_compound_1531; rh:compound/rh:accession
D-ribulose 5-phosphate(2-)
CHEBI:58121		consumes

Coefficient 1 in the selected riboneogenic direction; Rhea's formal charge and sugar representation are retained.

D-ribulose 5-phosphate => aldehydo-D-ribose 5-phosphate
RHEA:14659
  • RHEA:14657

    Source assertion: RHEA:14659 substrates contain CHEBI:58121 with coefficient 1.

    Source locationhttp://rdf.rhea-db.org/14659 rh:substrates; http://rdf.rhea-db.org/14657_R rh:contains1 http://rdf.rhea-db.org/Participant_14657_compound_1531; rh:compound/rh:accession
D-ribulose 5-phosphate => aldehydo-D-ribose 5-phosphate
RHEA:14659		produces

Coefficient 1 in the selected riboneogenic direction; Rhea's formal charge and sugar representation are retained.

aldehydo-D-ribose 5-phosphate(2-)
CHEBI:58273
  • RHEA:14657

    Source assertion: RHEA:14659 products contain CHEBI:58273 with coefficient 1.

    Source locationhttp://rdf.rhea-db.org/14659 rh:products; http://rdf.rhea-db.org/14657_L rh:contains1 http://rdf.rhea-db.org/Participant_14657_compound_6214; rh:compound/rh:accession
Transketolase 1
UniProtKB:P23254		enables

Tkl1 functional contribution in its homodimeric enzyme context; this gene-product edge does not assert independent monomer activity. The primary route identifies Tkl1 as the main transketolase activity.

beta-D-fructose 6-phosphate + D-glyceraldehyde 3-phosphate => D-erythrose 4-phosphate + D-xylulose 5-phosphate
RHEA:27628
  • PMID:21663798

    Source assertion: The pathway text assigns reactions 1 and 4 to transketolase TKL1/TKL2; Figure 6E places transketolase at both conversions.

    Source locationPMC3163394 main text following equations (1)-(5); Figure 6E and accompanying Results
  • UniProtKB:P23254

    Source assertion: SUBUNIT annotates a homodimer with experimental evidence ECO:0000269, including PMID:8176731.

    Source locationcomments[5].texts[0]; evidences
  • PathBank:SMP0002406

    Source assertion: Native Reactions/7089 is controlled by Catalysis/7068 through complex4403, whose TKL1/TKL2 protein references identify P23254/P33315. This supports source role assignment, not the asserted mixed-complex composition.

    Source locationPW002511.owl: Reactions/7089; Catalysis/7068; ProteinComplex/4403; ProteinReference/10736 and /10737
Transketolase 1
UniProtKB:P23254		enables

Tkl1 functional contribution in its homodimeric enzyme context; this gene-product edge does not assert independent monomer activity. The primary route identifies Tkl1 as the main transketolase activity.

D-sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate => aldehydo-D-ribose 5-phosphate + D-xylulose 5-phosphate
RHEA:10509
  • PMID:21663798

    Source assertion: The pathway text assigns reactions 1 and 4 to transketolase TKL1/TKL2; Figure 6E places transketolase at both conversions.

    Source locationPMC3163394 main text following equations (1)-(5); Figure 6E and accompanying Results
  • UniProtKB:P23254

    Source assertion: SUBUNIT annotates a homodimer with experimental evidence ECO:0000269, including PMID:8176731.

    Source locationcomments[5].texts[0]; evidences
  • UniProtKB:P23254

    Source assertion: CATALYTIC ACTIVITY assigns RHEA:10508 with ECO:0000269, including PMID:8521838.

    Source locationcomments[1].reaction; reactionCrossReferences; evidences
Transketolase 2
UniProtKB:P33315		enables

Tkl2 functional contribution in its homodimeric enzyme context; this gene-product edge does not assert independent monomer activity. Its specific reaction and assembly annotation is inferred by similarity, not separately purified Tkl2 evidence.

beta-D-fructose 6-phosphate + D-glyceraldehyde 3-phosphate => D-erythrose 4-phosphate + D-xylulose 5-phosphate
RHEA:27628
  • PMID:21663798

    Source assertion: The pathway text assigns reactions 1 and 4 to transketolase TKL1/TKL2; Figure 6E places transketolase at both conversions.

    Source locationPMC3163394 main text following equations (1)-(5); Figure 6E and accompanying Results
  • UniProtKB:P33315

    Source assertion: SUBUNIT annotates a homodimer by similarity to P23254 (ECO:0000250).

    Source locationcomments[5].texts[0]; evidences
  • PathBank:SMP0002406

    Source assertion: Native Reactions/7089 is controlled by Catalysis/7068 through complex4403, whose TKL1/TKL2 protein references identify P23254/P33315. This supports source role assignment, not the asserted mixed-complex composition.

    Source locationPW002511.owl: Reactions/7089; Catalysis/7068; ProteinComplex/4403; ProteinReference/10736 and /10737
Transketolase 2
UniProtKB:P33315		enables

Tkl2 functional contribution in its homodimeric enzyme context; this gene-product edge does not assert independent monomer activity. Its specific reaction and assembly annotation is inferred by similarity, not separately purified Tkl2 evidence.

D-sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate => aldehydo-D-ribose 5-phosphate + D-xylulose 5-phosphate
RHEA:10509
  • PMID:21663798

    Source assertion: The pathway text assigns reactions 1 and 4 to transketolase TKL1/TKL2; Figure 6E places transketolase at both conversions.

    Source locationPMC3163394 main text following equations (1)-(5); Figure 6E and accompanying Results
  • UniProtKB:P33315

    Source assertion: SUBUNIT annotates a homodimer by similarity to P23254 (ECO:0000250).

    Source locationcomments[5].texts[0]; evidences
  • UniProtKB:P33315

    Source assertion: CATALYTIC ACTIVITY assigns RHEA:10508 by similarity to P23254, ECO:0000250.

    Source locationcomments[1].reaction; reactionCrossReferences; evidences
Fructose-bisphosphate aldolase
UniProtKB:P14540		enables

Fba1 enables aldol condensation of erythrose 4-phosphate with DHAP. Reduced FBA1 expression slows SBP labeling; UniProt annotates a homodimer without an inline evidence code. No isolated-monomer sufficiency is claimed.

D-erythrose 4-phosphate + dihydroxyacetone phosphate => D-sedoheptulose 1,7-bisphosphate
RHEA:30168
  • PMID:21663798
    labeling of SBP and OBP was markedly slowed
    Source locationPMC3163394 Results, Sedoheptulose 1,7-bisphosphate is synthesized in vivo by fructose bisphosphate aldolase; Figure 4B
  • PMID:21663798

    Source assertion: FBA1-DAmP reduced aldolase expression; precursor labeling was unchanged while SBP labeling slowed. Equation (2) and Figure 6E identify DHAP plus erythrose 4-phosphate as the route substrates.

    Source locationPMC3163394 Results, aldolase isotope-labeling experiments; equation (2); Figures 4 and 6E
  • UniProtKB:P14540

    Source assertion: The reviewed FBA1/YKL060C gene product is fructose-bisphosphate aldolase; SUBUNIT states Homodimer. Its catalytic comment describes FBP cleavage, not the distinct SBP reaction.

    Source locationprimaryAccession; genes; proteinDescription; comments[1,4]
Sedoheptulose 1,7-bisphosphatase
UniProtKB:P36136		enables

Shb17 hydrolysis is the committed step. The gene-product edge retains the homodimer context; the SBP-bound H13A structure contains two subunits. The possible Mg2+ density is not a demonstrated requirement and creates no cofactor edge.

D-sedoheptulose 1,7-bisphosphate + H2O => D-sedoheptulose 7-phosphate + phosphate
RHEA:17462
  • UniProtKB:P36136

    Source assertion: CATALYTIC ACTIVITY assigns RHEA:17461 and SUBUNIT a homodimer, with ECO:0000269 citing PMID:21663798 and PMID:20427268.

    Source locationcomments[1].reaction; comments[3].texts[0]; evidences
  • PMID:21663798
    The structure revealed a protein dimer
    Source locationPMC3163394 Results, Structure of Shb17-SBP complex, first paragraph
  • PMID:21663798

    Source assertion: Purified Shb17 consumed SBP and produced S7P. Its H13A-SBP structure has possible Mg2+ density; the authors discuss optional phosphate coordination in a metal-independent enzyme, not an established Mg requirement.

    Source locationPMC3163394 Results, Shb17 is a selective sedoheptulose and octulose bisphosphatase; Structure of Shb17-SBP complex; Figure 3
Ribulose-phosphate 3-epimerase
UniProtKB:P46969		enables

Rpe1 supports xylulose-5-phosphate conversion to ribulose-5-phosphate in this route. Gene-deletion enzyme assays provide direct functional support; the current UniProt catalytic and metal annotations separately retain similarity evidence.

D-xylulose 5-phosphate => D-ribulose 5-phosphate
RHEA:13679
  • UniProtKB:P46969

    Source assertion: CATALYTIC ACTIVITY assigns RHEA:13677 with ECO:0000250 to human Q96AT9; this is database similarity evidence.

    Source locationcomments[1].reaction; reactionCrossReferences; evidences
  • PMID:8929392
    Deletion mutants of RPE1 show no enzyme activity
    Source locationEurope PMC core result[id="8929392"].abstractText
  • PMID:21663798

    Source assertion: Figure 6E and the following text assign conversion of xylulose 5-phosphate to ribulose 5-phosphate to Rpe1.

    Source locationPMC3163394 Figure 6E and Results, Shb17 oscillates with ribosomal transcripts in the yeast metabolic cycle
Ribose-5-phosphate isomerase
UniProtKB:Q12189		enables

Rki1 completes ribose-5-phosphate formation. Gene-dosage rescue supports the functional product; no oligomer stoichiometry is inferred from a missing SUBUNIT comment.

D-ribulose 5-phosphate => aldehydo-D-ribose 5-phosphate
RHEA:14659
  • UniProtKB:Q12189

    Source assertion: The RKI1 catalytic comment assigns RHEA:14657 with ECO:0000305 citing PMID:8929392, a curator-inference annotation.

    Source locationgenes; comments[0].reaction; reactionCrossReferences; evidences
  • PMID:8929392
    restored viability and specific D-ribose-5-phosphate ketol-isomerase activity
    Source locationEurope PMC core result[id="8929392"].abstractText
  • PMID:21663798

    Source assertion: Figure 6E and the following text assign conversion of ribulose 5-phosphate to ribose 5-phosphate to Rki1.

    Source locationPMC3163394 Figure 6E and Results, Shb17 oscillates with ribosomal transcripts in the yeast metabolic cycle
beta-D-fructose 6-phosphate + D-glyceraldehyde 3-phosphate => D-erythrose 4-phosphate + D-xylulose 5-phosphate
RHEA:27628		part_of

Manual correspondence of the native reaction, primary route and exact Rhea chemistry. PathBank supplies no Rhea cross-reference; protonation/tautomer distinctions are not exact-identity mappings. The native step is reversible; the graph selects the riboneogenic flux.

PathBank:SMP0002406
  • PathBank:SMP0002406

    Source assertion: The native pathway explicitly includes Reactions/7089; conversionDirection is REVERSIBLE.

    Source locationPW002511.owl: Pathway[@rdf:about="http://identifiers.org/smpdb/SMP0002406"]/pathwayComponent; Reactions/7089/conversionDirection; left; right
  • RHEA:27626

    Source assertion: RHEA:27626 lists RHEA:27628 as a directional reaction; its substrates and products define the selected orientation.

    Source locationhttp://rdf.rhea-db.org/27626 rh:directionalReaction http://rdf.rhea-db.org/27628; http://rdf.rhea-db.org/27628 rh:substrates; rh:products
  • PMID:21663798

    Source assertion: Equations (1)-(5) and Figure 6E define the aldolase/Shb17 route, with the final pentose conversion resolved into Rpe1 and Rki1 reactions.

    Source locationPMC3163394 equations (1)-(5); Figure 6E and accompanying Results
D-erythrose 4-phosphate + dihydroxyacetone phosphate => D-sedoheptulose 1,7-bisphosphate
RHEA:30168		part_of

Manual correspondence of the native reaction, primary route and exact Rhea chemistry. PathBank supplies no Rhea cross-reference; protonation/tautomer distinctions are not exact-identity mappings. The native step is reversible; the graph selects the riboneogenic flux.

PathBank:SMP0002406
  • PathBank:SMP0002406

    Source assertion: The native pathway explicitly includes Reactions/7090; conversionDirection is REVERSIBLE.

    Source locationPW002511.owl: Pathway[@rdf:about="http://identifiers.org/smpdb/SMP0002406"]/pathwayComponent; Reactions/7090/conversionDirection; left; right
  • RHEA:30167

    Source assertion: RHEA:30167 lists RHEA:30168 as a directional reaction; its substrates and products define the selected orientation.

    Source locationhttp://rdf.rhea-db.org/30167 rh:directionalReaction http://rdf.rhea-db.org/30168; http://rdf.rhea-db.org/30168 rh:substrates; rh:products
  • PMID:21663798

    Source assertion: Equations (1)-(5) and Figure 6E define the aldolase/Shb17 route, with the final pentose conversion resolved into Rpe1 and Rki1 reactions.

    Source locationPMC3163394 equations (1)-(5); Figure 6E and accompanying Results
D-sedoheptulose 1,7-bisphosphate + H2O => D-sedoheptulose 7-phosphate + phosphate
RHEA:17462		part_of

Manual correspondence of the native reaction, primary route and exact Rhea chemistry. PathBank supplies no Rhea cross-reference; protonation/tautomer distinctions are not exact-identity mappings. Native hydrolysis is left-to-right.

PathBank:SMP0002406
  • PathBank:SMP0002406

    Source assertion: The native pathway explicitly includes Reactions/7091; conversionDirection is LEFT_TO_RIGHT.

    Source locationPW002511.owl: Pathway[@rdf:about="http://identifiers.org/smpdb/SMP0002406"]/pathwayComponent; Reactions/7091/conversionDirection; left; right
  • RHEA:17461

    Source assertion: RHEA:17461 lists RHEA:17462 as a directional reaction; its substrates and products define the selected orientation.

    Source locationhttp://rdf.rhea-db.org/17461 rh:directionalReaction http://rdf.rhea-db.org/17462; http://rdf.rhea-db.org/17462 rh:substrates; rh:products
  • PMID:21663798

    Source assertion: Equations (1)-(5) and Figure 6E define the aldolase/Shb17 route, with the final pentose conversion resolved into Rpe1 and Rki1 reactions.

    Source locationPMC3163394 equations (1)-(5); Figure 6E and accompanying Results
D-sedoheptulose 7-phosphate + D-glyceraldehyde 3-phosphate => aldehydo-D-ribose 5-phosphate + D-xylulose 5-phosphate
RHEA:10509		part_of

Manual correspondence of the native reaction, primary route and exact Rhea chemistry. PathBank supplies no Rhea cross-reference; protonation/tautomer distinctions are not exact-identity mappings. The native step is reversible; the graph selects the riboneogenic flux.

PathBank:SMP0002406
  • PathBank:SMP0002406

    Source assertion: The native pathway explicitly includes Reactions/7092; conversionDirection is REVERSIBLE.

    Source locationPW002511.owl: Pathway[@rdf:about="http://identifiers.org/smpdb/SMP0002406"]/pathwayComponent; Reactions/7092/conversionDirection; left; right
  • RHEA:10508

    Source assertion: RHEA:10508 lists RHEA:10509 as a directional reaction; its substrates and products define the selected orientation.

    Source locationhttp://rdf.rhea-db.org/10508 rh:directionalReaction http://rdf.rhea-db.org/10509; http://rdf.rhea-db.org/10509 rh:substrates; rh:products
  • PMID:21663798

    Source assertion: Equations (1)-(5) and Figure 6E define the aldolase/Shb17 route, with the final pentose conversion resolved into Rpe1 and Rki1 reactions.

    Source locationPMC3163394 equations (1)-(5); Figure 6E and accompanying Results
D-xylulose 5-phosphate => D-ribulose 5-phosphate
RHEA:13679		part_of

Manual correspondence of the native reaction, primary route and exact Rhea chemistry. PathBank supplies no Rhea cross-reference; protonation/tautomer distinctions are not exact-identity mappings. The native step is reversible; the graph selects the riboneogenic flux.

PathBank:SMP0002406
  • PathBank:SMP0002406

    Source assertion: The native pathway explicitly includes Reactions/7094; conversionDirection is REVERSIBLE.

    Source locationPW002511.owl: Pathway[@rdf:about="http://identifiers.org/smpdb/SMP0002406"]/pathwayComponent; Reactions/7094/conversionDirection; left; right
  • RHEA:13677

    Source assertion: RHEA:13677 lists RHEA:13679 as a directional reaction; its substrates and products define the selected orientation.

    Source locationhttp://rdf.rhea-db.org/13677 rh:directionalReaction http://rdf.rhea-db.org/13679; http://rdf.rhea-db.org/13679 rh:substrates; rh:products
  • PMID:21663798

    Source assertion: Equations (1)-(5) and Figure 6E define the aldolase/Shb17 route, with the final pentose conversion resolved into Rpe1 and Rki1 reactions.

    Source locationPMC3163394 equations (1)-(5); Figure 6E and accompanying Results
D-ribulose 5-phosphate => aldehydo-D-ribose 5-phosphate
RHEA:14659		part_of

Manual correspondence of the native reaction, primary route and exact Rhea chemistry. PathBank supplies no Rhea cross-reference; protonation/tautomer distinctions are not exact-identity mappings. The native step is reversible; the graph selects the riboneogenic flux.

PathBank:SMP0002406
  • PathBank:SMP0002406

    Source assertion: The native pathway explicitly includes Reactions/7093; conversionDirection is REVERSIBLE.

    Source locationPW002511.owl: Pathway[@rdf:about="http://identifiers.org/smpdb/SMP0002406"]/pathwayComponent; Reactions/7093/conversionDirection; left; right
  • RHEA:14657

    Source assertion: RHEA:14657 lists RHEA:14659 as a directional reaction; its substrates and products define the selected orientation.

    Source locationhttp://rdf.rhea-db.org/14657 rh:directionalReaction http://rdf.rhea-db.org/14659; http://rdf.rhea-db.org/14659 rh:substrates; rh:products
  • PMID:21663798

    Source assertion: Equations (1)-(5) and Figure 6E define the aldolase/Shb17 route, with the final pentose conversion resolved into Rpe1 and Rki1 reactions.

    Source locationPMC3163394 equations (1)-(5); Figure 6E and accompanying Results
Transketolase 1
UniProtKB:P23254		has_cofactor

Reviewed protein cofactor annotation in its functional enzyme context. Binds 1 Mg(2+) ion per subunit (PubMed:18186462). Can also utilize other divalent metal cations, such as Ca(2+), Mn(2+) and Co(2+) (PubMed:18186462). These metals are alternatives, not simultaneous requirements.

magnesium(2+)
CHEBI:18420
  • UniProtKB:P23254

    Source assertion: COFACTOR identifies CHEBI:18420 (Mg(2+)) with evidence ECO:0000269.

    Source locationcomments[2].cofactors[0]; cofactorCrossReference; evidences; comments[2].note
Transketolase 1
UniProtKB:P23254		has_cofactor

Reviewed protein cofactor annotation in its functional enzyme context. Binds 1 Mg(2+) ion per subunit (PubMed:18186462). Can also utilize other divalent metal cations, such as Ca(2+), Mn(2+) and Co(2+) (PubMed:18186462). These metals are alternatives, not simultaneous requirements.

calcium(2+)
CHEBI:29108
  • UniProtKB:P23254

    Source assertion: COFACTOR identifies CHEBI:29108 (Ca(2+)) with evidence ECO:0000269.

    Source locationcomments[2].cofactors[1]; cofactorCrossReference; evidences; comments[2].note
Transketolase 1
UniProtKB:P23254		has_cofactor

Reviewed protein cofactor annotation in its functional enzyme context. Binds 1 Mg(2+) ion per subunit (PubMed:18186462). Can also utilize other divalent metal cations, such as Ca(2+), Mn(2+) and Co(2+) (PubMed:18186462). These metals are alternatives, not simultaneous requirements.

manganese(2+)
CHEBI:29035
  • UniProtKB:P23254

    Source assertion: COFACTOR identifies CHEBI:29035 (Mn(2+)) with evidence ECO:0000269.

    Source locationcomments[2].cofactors[2]; cofactorCrossReference; evidences; comments[2].note
Transketolase 1
UniProtKB:P23254		has_cofactor

Reviewed protein cofactor annotation in its functional enzyme context. Binds 1 Mg(2+) ion per subunit (PubMed:18186462). Can also utilize other divalent metal cations, such as Ca(2+), Mn(2+) and Co(2+) (PubMed:18186462). These metals are alternatives, not simultaneous requirements.

cobalt(2+)
CHEBI:48828
  • UniProtKB:P23254

    Source assertion: COFACTOR identifies CHEBI:48828 (Co(2+)) with evidence ECO:0000269.

    Source locationcomments[2].cofactors[3]; cofactorCrossReference; evidences; comments[2].note
Transketolase 1
UniProtKB:P23254		has_cofactor

Reviewed protein cofactor annotation in its functional enzyme context. Binds 1 thiamine pyrophosphate per subunit.

thiamine(1+) diphosphate(3-)
CHEBI:58937
  • UniProtKB:P23254

    Source assertion: COFACTOR identifies CHEBI:58937 (thiamine diphosphate) with evidence ECO:0000269.

    Source locationcomments[3].cofactors[0]; cofactorCrossReference; evidences; comments[3].note
Transketolase 2
UniProtKB:P33315		has_cofactor

Reviewed protein cofactor annotation in its functional enzyme context. Binds 1 Mg(2+) ion per subunit. Can also utilize other divalent metal cations, such as Ca(2+), Mn(2+) and Co(2+). The annotation is by similarity; it is not a direct yeast cofactor assay. These metals are alternatives, not simultaneous requirements.

magnesium(2+)
CHEBI:18420
  • UniProtKB:P33315

    Source assertion: COFACTOR identifies CHEBI:18420 (Mg(2+)) with evidence ECO:0000250.

    Source locationcomments[2].cofactors[0]; cofactorCrossReference; evidences; comments[2].note
Transketolase 2
UniProtKB:P33315		has_cofactor

Reviewed protein cofactor annotation in its functional enzyme context. Binds 1 Mg(2+) ion per subunit. Can also utilize other divalent metal cations, such as Ca(2+), Mn(2+) and Co(2+). The annotation is by similarity; it is not a direct yeast cofactor assay. These metals are alternatives, not simultaneous requirements.

calcium(2+)
CHEBI:29108
  • UniProtKB:P33315

    Source assertion: COFACTOR identifies CHEBI:29108 (Ca(2+)) with evidence ECO:0000250.

    Source locationcomments[2].cofactors[1]; cofactorCrossReference; evidences; comments[2].note
Transketolase 2
UniProtKB:P33315		has_cofactor

Reviewed protein cofactor annotation in its functional enzyme context. Binds 1 Mg(2+) ion per subunit. Can also utilize other divalent metal cations, such as Ca(2+), Mn(2+) and Co(2+). The annotation is by similarity; it is not a direct yeast cofactor assay. These metals are alternatives, not simultaneous requirements.

manganese(2+)
CHEBI:29035
  • UniProtKB:P33315

    Source assertion: COFACTOR identifies CHEBI:29035 (Mn(2+)) with evidence ECO:0000250.

    Source locationcomments[2].cofactors[2]; cofactorCrossReference; evidences; comments[2].note
Transketolase 2
UniProtKB:P33315		has_cofactor

Reviewed protein cofactor annotation in its functional enzyme context. Binds 1 Mg(2+) ion per subunit. Can also utilize other divalent metal cations, such as Ca(2+), Mn(2+) and Co(2+). The annotation is by similarity; it is not a direct yeast cofactor assay. These metals are alternatives, not simultaneous requirements.

cobalt(2+)
CHEBI:48828
  • UniProtKB:P33315

    Source assertion: COFACTOR identifies CHEBI:48828 (Co(2+)) with evidence ECO:0000250.

    Source locationcomments[2].cofactors[3]; cofactorCrossReference; evidences; comments[2].note
Transketolase 2
UniProtKB:P33315		has_cofactor

Reviewed protein cofactor annotation in its functional enzyme context. Binds 1 thiamine pyrophosphate per subunit. The annotation is by similarity; it is not a direct yeast cofactor assay.

thiamine(1+) diphosphate(3-)
CHEBI:58937
  • UniProtKB:P33315

    Source assertion: COFACTOR identifies CHEBI:58937 (thiamine diphosphate) with evidence ECO:0000250.

    Source locationcomments[3].cofactors[0]; cofactorCrossReference; evidences; comments[3].note
Fructose-bisphosphate aldolase
UniProtKB:P14540		has_cofactor

Reviewed protein cofactor annotation in its functional enzyme context. Binds 2 Zn(2+) ions per subunit. One is catalytic and the other provides a structural contribution. The annotation is by similarity; it is not a direct yeast cofactor assay.

zinc(2+)
CHEBI:29105
  • UniProtKB:P14540

    Source assertion: COFACTOR identifies CHEBI:29105 (Zn(2+)) with evidence ECO:0000250.

    Source locationcomments[2].cofactors[0]; cofactorCrossReference; evidences; comments[2].note
Ribulose-phosphate 3-epimerase
UniProtKB:P46969		has_cofactor

Reviewed protein cofactor annotation in its functional enzyme context. Binds 1 divalent metal cation per subunit. Active with Co(2+), Fe(2+), Mn(2+) and Zn(2+). The annotation is by similarity; it is not a direct yeast cofactor assay. These metals are alternatives, not simultaneous requirements.

cobalt(2+)
CHEBI:48828
  • UniProtKB:P46969

    Source assertion: COFACTOR identifies CHEBI:48828 (Co(2+)) with evidence ECO:0000250.

    Source locationcomments[2].cofactors[0]; cofactorCrossReference; evidences; comments[2].note
Ribulose-phosphate 3-epimerase
UniProtKB:P46969		has_cofactor

Reviewed protein cofactor annotation in its functional enzyme context. Binds 1 divalent metal cation per subunit. Active with Co(2+), Fe(2+), Mn(2+) and Zn(2+). The annotation is by similarity; it is not a direct yeast cofactor assay. These metals are alternatives, not simultaneous requirements.

iron(2+)
CHEBI:29033
  • UniProtKB:P46969

    Source assertion: COFACTOR identifies CHEBI:29033 (Fe(2+)) with evidence ECO:0000250.

    Source locationcomments[2].cofactors[1]; cofactorCrossReference; evidences; comments[2].note
Ribulose-phosphate 3-epimerase
UniProtKB:P46969		has_cofactor

Reviewed protein cofactor annotation in its functional enzyme context. Binds 1 divalent metal cation per subunit. Active with Co(2+), Fe(2+), Mn(2+) and Zn(2+). The annotation is by similarity; it is not a direct yeast cofactor assay. These metals are alternatives, not simultaneous requirements.

manganese(2+)
CHEBI:29035
  • UniProtKB:P46969

    Source assertion: COFACTOR identifies CHEBI:29035 (Mn(2+)) with evidence ECO:0000250.

    Source locationcomments[2].cofactors[2]; cofactorCrossReference; evidences; comments[2].note
Ribulose-phosphate 3-epimerase
UniProtKB:P46969		has_cofactor

Reviewed protein cofactor annotation in its functional enzyme context. Binds 1 divalent metal cation per subunit. Active with Co(2+), Fe(2+), Mn(2+) and Zn(2+). The annotation is by similarity; it is not a direct yeast cofactor assay. These metals are alternatives, not simultaneous requirements.

zinc(2+)
CHEBI:29105
  • UniProtKB:P46969

    Source assertion: COFACTOR identifies CHEBI:29105 (Zn(2+)) with evidence ECO:0000250.

    Source locationcomments[2].cofactors[3]; cofactorCrossReference; evidences; comments[2].note
Sedoheptulose 1,7-bisphosphatase
UniProtKB:P36136		located_in

Reported protein localization, not a claim that every riboneogenic reaction occurs in both compartments or that localization is exclusive.

cytoplasm
GO:0005737
  • UniProtKB:P36136

    Source assertion: SUBCELLULAR LOCATION lists Cytoplasm with experimental annotation ECO:0000269 citing PMID:14562095.

    Source locationcomments[4].subcellularLocations[location.value="Cytoplasm"].location; evidences
Sedoheptulose 1,7-bisphosphatase
UniProtKB:P36136		located_in

Reported protein localization, not a claim that every riboneogenic reaction occurs in both compartments or that localization is exclusive.

nucleus
GO:0005634
  • UniProtKB:P36136

    Source assertion: SUBCELLULAR LOCATION lists Nucleus with experimental annotation ECO:0000269 citing PMID:14562095.

    Source locationcomments[4].subcellularLocations[location.value="Nucleus"].location; evidences

References

Curation history