D-galactarate degradation I

MetaCyc:GALACTARDEG-PWY

The four-event bacterial pathway dehydrates meso-galactarate, cleaves the resulting 5-dehydro-4-deoxy-D-glucarate to pyruvate and (2R)-tartronate semialdehyde, reduces the latter with an NAD(P)H donor to D-glycerate, and phosphorylates D-glycerate to 2-phosphoglycerate. The historical pathway name retains D-galactarate although galactarate is meso. The GarD entry distinguishes this route from D-glucarate degradation; three downstream steps are shared. Native MetaCyc 27.0 stereochemistry and cofactor classes are preserved rather than equated with broader Rhea reactions. E. coli K-12 evidence, engineered enzyme assays, regulatory expression effects and database annotations retain their separate scopes.

Pathway type
carbohydrate degradation
Organism scope

Read the source YAML

Pathway network

49 nodes · 60 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: D-galactarate degradation I 49 nodes · 60 asserted directed edges. Every arrow links to its evidence table row; nodes link to their component details. Isolated declared components are retained. MetaCyc:GALACTARDEG-PWY — has_part → RHEA:16006; One native core event; mapped Rhea endpoints preserve the complete native chemistry and selected direction.; Evidence: MetaCyc:GALACTARDEG-PWY, MetaCyc:GALACTARDEHYDRA-RXNhas part MetaCyc:GALACTARDEG-PWY — has_part → MetaCyc:KDGALDOL-RXN; One native core event; the native reaction identifier preserves the exact intermediate stereochemistry and its source direction.; Evidence: MetaCyc:GALACTARDEG-PWYhas part MetaCyc:GALACTARDEG-PWY — has_part → MetaCyc:TSA-REDUCT-RXN; One native core event; the native reaction identifier preserves the exact intermediate stereochemistry and its source direction.; Evidence: MetaCyc:GALACTARDEG-PWYhas part MetaCyc:GALACTARDEG-PWY — has_part → RHEA:27378; One native core event; mapped Rhea endpoints preserve the complete native chemistry and selected direction.; Evidence: MetaCyc:GALACTARDEG-PWY, MetaCyc:GKI-RXNhas part CHEBI:16537 — consumes → RHEA:16006; The complete formal reaction includes this species with coefficient one.; Evidence: RHEA:16006consumes RHEA:16006 — produces → CHEBI:42819; The complete formal reaction includes this species with coefficient one.; Evidence: RHEA:16006produces RHEA:16006 — produces → CHEBI:15377; The complete formal reaction includes this species with coefficient one.; Evidence: RHEA:16006produces CHEBI:16659 — consumes → RHEA:27378; The complete formal reaction includes this species with coefficient one.; Evidence: RHEA:27378consumes CHEBI:30616 — consumes → RHEA:27378; The complete formal reaction includes this species with coefficient one.; Evidence: RHEA:27378consumes RHEA:27378 — produces → CHEBI:58289; The complete formal reaction includes this species with coefficient one.; Evidence: RHEA:27378produces RHEA:27378 — produces → CHEBI:456216; The complete formal reaction includes this species with coefficient one.; Evidence: RHEA:27378produces RHEA:27378 — produces → CHEBI:15378; The complete formal reaction includes this species with coefficient one.; Evidence: RHEA:27378produces CHEBI:42819 — consumes → MetaCyc:KDGALDOL-RXN; Preserves native chemical identity and physiological traversal. Native (2R) stereochemistry is a database assertion; it is not replaced by stereounspecified CHEBI:57978.; Evidence: MetaCyc:KDGALDOL-RXN, MetaCyc:GALACTARDEG-PWY, MetaCyc:5-KETO-4-DEOXY-D-GLUCARATEconsumes MetaCyc:KDGALDOL-RXN — produces → MetaCyc:CPD-26279; Preserves native chemical identity and physiological traversal. Native (2R) stereochemistry is a database assertion; it is not replaced by stereounspecified CHEBI:57978.; Evidence: MetaCyc:KDGALDOL-RXN, MetaCyc:GALACTARDEG-PWY, MetaCyc:CPD-26279produces MetaCyc:KDGALDOL-RXN — produces → CHEBI:15361; Preserves native chemical identity and physiological traversal. Native (2R) stereochemistry is a database assertion; it is not replaced by stereounspecified CHEBI:57978.; Evidence: MetaCyc:KDGALDOL-RXN, MetaCyc:GALACTARDEG-PWY, MetaCyc:PYRUVATEproduces MetaCyc:CPD-26279 — consumes → MetaCyc:TSA-REDUCT-RXN; Preserves native chemical identity and physiological traversal. Native (2R) stereochemistry is a database assertion; it is not replaced by stereounspecified CHEBI:57978.; Evidence: MetaCyc:TSA-REDUCT-RXN, MetaCyc:CPD-26279consumes MetaCyc:NADH-P-OR-NOP — consumes → MetaCyc:TSA-REDUCT-RXN; Preserves native chemical identity and physiological traversal. The NAD(P) class retains alternative redox donors and does not assert a fixed donor mixture.; Evidence: MetaCyc:TSA-REDUCT-RXN, MetaCyc:NADH-P-OR-NOPconsumes CHEBI:15378 — consumes → MetaCyc:TSA-REDUCT-RXN; Preserves native chemical identity and physiological traversal. Native (2R) stereochemistry is a database assertion; it is not replaced by stereounspecified CHEBI:57978.; Evidence: MetaCyc:TSA-REDUCT-RXN, MetaCyc:PROTONconsumes MetaCyc:TSA-REDUCT-RXN — produces → CHEBI:16659; Preserves native chemical identity and physiological traversal. Native (2R) stereochemistry is a database assertion; it is not replaced by stereounspecified CHEBI:57978.; Evidence: MetaCyc:TSA-REDUCT-RXN, MetaCyc:GLYCERATEproduces MetaCyc:TSA-REDUCT-RXN — produces → MetaCyc:NAD-P-OR-NOP; Preserves native chemical identity and physiological traversal. The NAD(P) class retains alternative redox donors and does not assert a fixed donor mixture.; Evidence: MetaCyc:TSA-REDUCT-RXN, MetaCyc:NAD-P-OR-NOPproduces RHEA:16006 — provides_input_for → MetaCyc:KDGALDOL-RXN; The native ordering and layout establish direct transfer of the shared intermediate in the selected pathway.; Evidence: MetaCyc:GALACTARDEG-PWYprovides input for MetaCyc:KDGALDOL-RXN — provides_input_for → MetaCyc:TSA-REDUCT-RXN; The native ordering and layout establish direct transfer of the shared intermediate in the selected pathway.; Evidence: MetaCyc:GALACTARDEG-PWYprovides input for MetaCyc:TSA-REDUCT-RXN — provides_input_for → RHEA:27378; The native ordering and layout establish direct transfer of the shared intermediate in the selected pathway.; Evidence: MetaCyc:GALACTARDEG-PWYprovides input for MetaCyc:CPLX0-8537 — has_part → UniProtKB:P39829; The identified native homomer contains 2 copies of this polypeptide. Assembly membership is separate from isolated-subunit catalysis.; Evidence: MetaCyc:CPLX0-8537, MetaCyc:GALACTARDEHYDRA-MONOMERhas part MetaCyc:CPLX0-7615 — has_part → UniProtKB:P23522; The identified native homomer contains 6 copies of this polypeptide. Assembly membership is separate from isolated-subunit catalysis.; Evidence: MetaCyc:CPLX0-7615, MetaCyc:KDGALDOL-MONOMERhas part MetaCyc:CPLX0-8537 — catalyzes → RHEA:16006; Curated native catalytic assignment; structured database statements retain their source status.; Evidence: MetaCyc:CPLX0-8537, MetaCyc:GALACTARDEHYDRA-RXNcatalyzes MetaCyc:CPLX0-7615 — catalyzes → MetaCyc:KDGALDOL-RXN; Curated native catalytic assignment; structured database statements retain their source status.; Evidence: MetaCyc:CPLX0-7615catalyzes UniProtKB:P0ABQ2 — catalyzes → MetaCyc:TSA-REDUCT-RXN; Curated native catalytic assignment; structured database statements retain their source status. UniProt separately annotates NADH and NADPH families with ECO:0000269 and HAMAP support; its stereounspecified Rhea substrate is not an exact replacement for native (2R)-tartronate semialdehyde.; Evidence: MetaCyc:TSA-REDUCT-MONOMER, MetaCyc:TSA-REDUCT-MONOMER, UniProtKB:P0ABQ2catalyzes UniProtKB:P23524 — catalyzes → RHEA:27378; Curated native catalytic assignment; structured database statements retain their source status. The current 2-phosphoglycerate product is retained; historical GKI/GKII naming and physiological isozyme roles must not be inferred from old names alone.; Evidence: MetaCyc:GKI-MONOMER, MetaCyc:GKI-MONOMER, MetaCyc:GKI-RXNcatalyzes MetaCyc:CPLX0-8537 — catalyzes → RHEA:16006; subject experimental construct: Recombinant, unlabeled E. coli GarD purified after TEV removal of its His6 tag; the structural preparation retains three residues after tag cleavage. Activity-sample scar and phosphorylation occupancy were not separately measured. Unlabeled activity material is distinct from SeMet/phospho-Asp168 crystal preparations.; Evidence PMID:31811683: the 6xHis-tag was removed with TEV protease (PDF printed p.719, Methods 4.1); Evidence PMID:31811683: Methods distinguish unlabeled activity preparation from SeMet structural material; the structure retains three residues after tag cleavage. (PDF Methods 4.1, 4.3, 4.4 and 4.5; Results 2.1); The recombinant preparation showed galactarate-dehydrating activity with added FeSO4 under reducing, semi-anaerobic assay conditions: 30°C, pH7, 30 mM substrate, 90 mM β-mercaptoethanol and 0 or 0.5 mM FeSO4. Semicarbazone detection supports product formation but does not independently establish stereochemical selectivity.; Evidence: PMID:31811683catalyzes UniProtKB:P39829 — has_cofactor → CHEBI:29033; The reviewed Fe2+ annotation is linked to the recombinant activity study. This does not establish iron-binding stoichiometry, a definite binding site, native cellular occupancy or catalytic substitution by the calcium observed in crystals.; Evidence: UniProtKB:P39829has cofactor UniProtKB:P23522 — has_cofactor → CHEBI:18420; Reviewed GarL annotation reports one Mg2+ per subunit and lower efficiency with Co2+, Fe2+ or Mn2+. These are alternatives under the cited biochemical conditions, not a simultaneous four-metal requirement or a claim of physiological occupancy.; Evidence: UniProtKB:P23522has cofactor UniProtKB:P23522 — has_cofactor → CHEBI:48828; Reviewed GarL annotation reports one Mg2+ per subunit and lower efficiency with Co2+, Fe2+ or Mn2+. These are alternatives under the cited biochemical conditions, not a simultaneous four-metal requirement or a claim of physiological occupancy.; Evidence: UniProtKB:P23522has cofactor UniProtKB:P23522 — has_cofactor → CHEBI:29033; Reviewed GarL annotation reports one Mg2+ per subunit and lower efficiency with Co2+, Fe2+ or Mn2+. These are alternatives under the cited biochemical conditions, not a simultaneous four-metal requirement or a claim of physiological occupancy.; Evidence: UniProtKB:P23522has cofactor UniProtKB:P23522 — has_cofactor → CHEBI:29035; Reviewed GarL annotation reports one Mg2+ per subunit and lower efficiency with Co2+, Fe2+ or Mn2+. These are alternatives under the cited biochemical conditions, not a simultaneous four-metal requirement or a claim of physiological occupancy.; Evidence: UniProtKB:P23522has cofactor UniProtKB:P23524 — catalyzes → RHEA:27378; subject experimental construct: Plasmid-expressed E. coli GarK in ΔgpmA ΔgpmM ΔgarK ΔglxK cells; cloning primers encode an N-terminal His6 sequence. The paper does not report tag cleavage. The printed donor spelling Mg1665 is retained as a source discrepancy.; Evidence PMID:25823014: Results, Figure 2 and Table 1 identify the four-deletion background; Cloning provides the procedure and His6-bearing Ec garK forward primer, with donor spelling K12 Mg1665. (Results & Discussion; Figure 2; Table 1; Materials and Methods / Cloning; Ec garK primer table); In a ΔgpmA ΔgpmM ΔgarK ΔglxK strain, plasmid GarK enabled growth on glycerol plus glycerate but not pyruvate plus glycerate. This engineered metabolic selection supports a 2-phosphoglycerate product; it does not establish native GarK assembly, metal occupancy or complete galactarate flux.; Evidence: PMID:25823014catalyzes UniProtKB:P37047 — activates → Entrez:947641; subject experimental construct: MC4100 reporter/loss-rescue context: active wild-type or pRM1-complemented SdaR/CdaR is inferred from loss in JA176 (paper-numbered P297S) and JA177 (Tn5 near the stop). The paper uses a 391-residue reference, unlike current P37047 (385 residues); numbering is not remapped.; Evidence PMID:10762278: JA176 and JA177 lose induced expression and utilization; pRM1 carrying MC4100 sdaR restores utilization. The mutants are inference controls, not the active regulator endpoint. (Isolation and mapping of pleiotropic mutants; Identification and cloning of the putative regulator); CdaR/SdaR positively controls the garD transcriptional unit in the MC4100 reporter/loss-rescue system. For garL, garR and garK this is shared-operon expression inference from the garP promoter, not independently mapped downstream promoters or direct protein activation. Direct ligand binding was not tested.; Evidence: PMID:10762278activates UniProtKB:P37047 — activates → Entrez:947630; subject experimental construct: MC4100 reporter/loss-rescue context: active wild-type or pRM1-complemented SdaR/CdaR is inferred from loss in JA176 (paper-numbered P297S) and JA177 (Tn5 near the stop). The paper uses a 391-residue reference, unlike current P37047 (385 residues); numbering is not remapped.; Evidence PMID:10762278: JA176 and JA177 lose induced expression and utilization; pRM1 carrying MC4100 sdaR restores utilization. The mutants are inference controls, not the active regulator endpoint. (Isolation and mapping of pleiotropic mutants; Identification and cloning of the putative regulator); CdaR/SdaR positively controls the garPLRK transcriptional unit in the MC4100 reporter/loss-rescue system. For garL, garR and garK this is shared-operon expression inference from the garP promoter, not independently mapped downstream promoters or direct protein activation. Direct ligand binding was not tested.; Evidence: PMID:10762278activates UniProtKB:P37047 — activates → Entrez:947631; subject experimental construct: MC4100 reporter/loss-rescue context: active wild-type or pRM1-complemented SdaR/CdaR is inferred from loss in JA176 (paper-numbered P297S) and JA177 (Tn5 near the stop). The paper uses a 391-residue reference, unlike current P37047 (385 residues); numbering is not remapped.; Evidence PMID:10762278: JA176 and JA177 lose induced expression and utilization; pRM1 carrying MC4100 sdaR restores utilization. The mutants are inference controls, not the active regulator endpoint. (Isolation and mapping of pleiotropic mutants; Identification and cloning of the putative regulator); CdaR/SdaR positively controls the garPLRK transcriptional unit in the MC4100 reporter/loss-rescue system. For garL, garR and garK this is shared-operon expression inference from the garP promoter, not independently mapped downstream promoters or direct protein activation. Direct ligand binding was not tested.; Evidence: PMID:10762278activates UniProtKB:P37047 — activates → Entrez:947632; subject experimental construct: MC4100 reporter/loss-rescue context: active wild-type or pRM1-complemented SdaR/CdaR is inferred from loss in JA176 (paper-numbered P297S) and JA177 (Tn5 near the stop). The paper uses a 391-residue reference, unlike current P37047 (385 residues); numbering is not remapped.; Evidence PMID:10762278: JA176 and JA177 lose induced expression and utilization; pRM1 carrying MC4100 sdaR restores utilization. The mutants are inference controls, not the active regulator endpoint. (Isolation and mapping of pleiotropic mutants; Identification and cloning of the putative regulator); CdaR/SdaR positively controls the garPLRK transcriptional unit in the MC4100 reporter/loss-rescue system. For garL, garR and garK this is shared-operon expression inference from the garP promoter, not independently mapped downstream promoters or direct protein activation. Direct ligand binding was not tested.; Evidence: PMID:10762278activates UniProtKB:P37047 — activates → Entrez:947642; subject experimental construct: MC4100 reporter/loss-rescue context: active wild-type or pRM1-complemented SdaR/CdaR is inferred from loss in JA176 (paper-numbered P297S) and JA177 (Tn5 near the stop). The paper uses a 391-residue reference, unlike current P37047 (385 residues); numbering is not remapped.; Evidence PMID:10762278: JA176 and JA177 lose induced expression and utilization; pRM1 carrying MC4100 sdaR restores utilization. The mutants are inference controls, not the active regulator endpoint. (Isolation and mapping of pleiotropic mutants; Identification and cloning of the putative regulator); CdaR/SdaR positively controls the garPLRK transcriptional unit in the MC4100 reporter/loss-rescue system. For garL, garR and garK this is shared-operon expression inference from the garP promoter, not independently mapped downstream promoters or direct protein activation. Direct ligand binding was not tested.; Evidence: PMID:10762278activates UniProtKB:P37047 — activates → Entrez:944860; subject experimental construct: MC4100 reporter/loss-rescue context: active wild-type or pRM1-complemented SdaR/CdaR is inferred from loss in JA176 (paper-numbered P297S) and JA177 (Tn5 near the stop). The paper uses a 391-residue reference, unlike current P37047 (385 residues); numbering is not remapped.; Evidence PMID:10762278: JA176 and JA177 lose induced expression and utilization; pRM1 carrying MC4100 sdaR restores utilization. The mutants are inference controls, not the active regulator endpoint. (Isolation and mapping of pleiotropic mutants; Identification and cloning of the putative regulator); Positive autoregulation is supported by the MC4100 sdaR-lacZ reporter and loss of induction without functional SdaR; the proposed ligand-activated molecular mechanism was not directly measured.; Evidence: PMID:10762278activates CHEBI:16537 — activates → Entrez:947641; Expression-level induction in the tested MC4100 culture/reporter system. The chemical CURIE normalizes the named acid to its defined ionic species; this is not direct ligand binding to CdaR or direct activation of an enzyme. GarK represents the shared garPLRK transcriptional unit.; Evidence: PMID:10762278activates CHEBI:16537 — activates → Entrez:947632; Expression-level induction in the tested MC4100 culture/reporter system. The chemical CURIE normalizes the named acid to its defined ionic species; this is not direct ligand binding to CdaR or direct activation of an enzyme. GarK represents the shared garPLRK transcriptional unit.; Evidence: PMID:10762278activates CHEBI:16537 — activates → Entrez:944860; Expression-level induction in the tested MC4100 culture/reporter system. The chemical CURIE normalizes the named acid to its defined ionic species; this is not direct ligand binding to CdaR or direct activation of an enzyme. GarK represents the shared garPLRK transcriptional unit.; Evidence: PMID:10762278activates CHEBI:16537 — activates → Entrez:947642; Expression-level induction in the tested MC4100 culture/reporter system. The chemical CURIE normalizes the named acid to its defined ionic species; this is not direct ligand binding to CdaR or direct activation of an enzyme. GarK represents the shared garPLRK transcriptional unit.; Evidence: PMID:10762278activates CHEBI:30612 — activates → Entrez:947641; Expression-level induction in the tested MC4100 culture/reporter system. The chemical CURIE normalizes the named acid to its defined ionic species; this is not direct ligand binding to CdaR or direct activation of an enzyme. GarK represents the shared garPLRK transcriptional unit.; Evidence: PMID:10762278activates CHEBI:30612 — activates → Entrez:947632; Expression-level induction in the tested MC4100 culture/reporter system. The chemical CURIE normalizes the named acid to its defined ionic species; this is not direct ligand binding to CdaR or direct activation of an enzyme. GarK represents the shared garPLRK transcriptional unit.; Evidence: PMID:10762278activates CHEBI:30612 — activates → Entrez:944860; Expression-level induction in the tested MC4100 culture/reporter system. The chemical CURIE normalizes the named acid to its defined ionic species; this is not direct ligand binding to CdaR or direct activation of an enzyme. GarK represents the shared garPLRK transcriptional unit.; Evidence: PMID:10762278activates CHEBI:30612 — activates → Entrez:947642; Expression-level induction in the tested MC4100 culture/reporter system. The chemical CURIE normalizes the named acid to its defined ionic species; this is not direct ligand binding to CdaR or direct activation of an enzyme. GarK represents the shared garPLRK transcriptional unit.; Evidence: PMID:10762278activates CHEBI:16659 — activates → Entrez:947641; Expression-level induction in the tested MC4100 culture/reporter system. The chemical CURIE normalizes the named acid to its defined ionic species; this is not direct ligand binding to CdaR or direct activation of an enzyme. GarK represents the shared garPLRK transcriptional unit.; Evidence: PMID:10762278activates CHEBI:16659 — activates → Entrez:947632; Expression-level induction in the tested MC4100 culture/reporter system. The chemical CURIE normalizes the named acid to its defined ionic species; this is not direct ligand binding to CdaR or direct activation of an enzyme. GarK represents the shared garPLRK transcriptional unit.; Evidence: PMID:10762278activates CHEBI:16659 — activates → Entrez:944860; Expression-level induction in the tested MC4100 culture/reporter system. The chemical CURIE normalizes the named acid to its defined ionic species; this is not direct ligand binding to CdaR or direct activation of an enzyme. GarK represents the shared garPLRK transcriptional unit.; Evidence: PMID:10762278activates CHEBI:16659 — activates → Entrez:947642; Expression-level induction in the tested MC4100 culture/reporter system. The chemical CURIE normalizes the named acid to its defined ionic species; this is not direct ligand binding to CdaR or direct activation of an enzyme. GarK represents the shared garPLRK transcriptional unit.; Evidence: PMID:10762278activates UniProtKB:P0AA80 — enables → MetaCyc:GALACTARDEG-PWY; Reviewed annotation proposes GarP-dependent galactarate availability. Uptake is probable (ECO:0000305), not directly measured transport or established proton coupling. This context is separate from the four core biochemical events.; Evidence: UniProtKB:P0AA80enables UniProtKB:P0AA80 — enables → MetaCyc:GALACTARDEG-PWY; subject experimental construct: BW25113 garP plasmid complementation in the corresponding Keio deletion strain: pCW-lic/tac, 100 µM IPTG, 25°C, 48 h, peptone plus galactarate, acidification endpoint. The reference protein denotes gene-product identity; exact insert sequence, tags and equivalence to MG1655 were not independently established.; Evidence PMID:39875389: Methods describe Keio strains, pCW-lic gene cloning and induced fermentation assays; these are engineered complementation experiments, not native-expression or purified-protein assays. (Par43; Par45; Par47; Fig3 caption); The garP deletion attenuated galactarate fermentation, and native-gene plasmid rescue restored the signal in BW25113 derivatives. This pH endpoint supports pathway participation; it does not measure exact chemistry, transport coupling, reductant specificity or assembly. The figure names BL21 as the positive comparator.; Evidence: PMID:39875389enables UniProtKB:P23522 — enables → MetaCyc:GALACTARDEG-PWY; subject experimental construct: BW25113 garL plasmid complementation in the corresponding Keio deletion strain: pCW-lic/tac, 100 µM IPTG, 25°C, 48 h, peptone plus galactarate, acidification endpoint. The reference protein denotes gene-product identity; exact insert sequence, tags and equivalence to MG1655 were not independently established.; Evidence PMID:39875389: Methods describe Keio strains, pCW-lic gene cloning and induced fermentation assays; these are engineered complementation experiments, not native-expression or purified-protein assays. (Par43; Par45; Par47; Fig3 caption); The garL deletion markedly diminished galactarate fermentation, and native-gene plasmid rescue restored the signal in BW25113 derivatives. This pH endpoint supports pathway participation; it does not measure exact chemistry, transport coupling, reductant specificity or assembly. The figure names BL21 as the positive comparator.; Evidence: PMID:39875389enables UniProtKB:P0ABQ2 — enables → MetaCyc:GALACTARDEG-PWY; subject experimental construct: BW25113 garR plasmid complementation in the corresponding Keio deletion strain: pCW-lic/tac, 100 µM IPTG, 25°C, 48 h, peptone plus galactarate, acidification endpoint. The reference protein denotes gene-product identity; exact insert sequence, tags and equivalence to MG1655 were not independently established.; Evidence PMID:39875389: Methods describe Keio strains, pCW-lic gene cloning and induced fermentation assays; these are engineered complementation experiments, not native-expression or purified-protein assays. (Par43; Par45; Par47; Fig3 caption); The garR deletion attenuated galactarate fermentation, and native-gene plasmid rescue restored the signal in BW25113 derivatives. This pH endpoint supports pathway participation; it does not measure exact chemistry, transport coupling, reductant specificity or assembly. The figure names BL21 as the positive comparator.; Evidence: PMID:39875389enables NCBITaxon:511145 — enables → MetaCyc:GALACTARDEG-PWY; The native pathway species annotation identifies the MG1655 reference context. This is a curated database assertion; it does not relabel MC4100 experiments as MG1655.; Evidence: MetaCyc:GALACTARDEG-PWYenables NCBITaxon:83333 — enables → MetaCyc:GALACTARDEG-PWY; MC4100 and its named derivatives provide bounded E. coli K-12 growth and enzyme-expression evidence. This does not establish all strains or all Bacteria as experimentally characterized.; Evidence: PMID:10762278enables galactarate(2-); CHEBI:16537; Declared type: small_molecule small molecule galactarate(2-) 5-dehydro-4-deoxy-D-glucarate(2-); CHEBI:42819; Declared type: small_molecule small molecule 5-dehydro-4-deoxy-D- glucarate(2-) water; CHEBI:15377; Declared type: small_molecule small molecule water pyruvate; CHEBI:15361; Declared type: small_molecule small molecule pyruvate hydron; CHEBI:15378; Declared type: small_molecule small molecule hydron D-glycerate; CHEBI:16659; Declared type: small_molecule small molecule D-glycerate ATP(4-); CHEBI:30616; Declared type: small_molecule small molecule ATP(4-) 2-phosphonato-D-glycerate(3-); CHEBI:58289; Declared type: small_molecule small molecule 2-phosphonato-D- glycerate(3-) ADP(3-); CHEBI:456216; Declared type: small_molecule small molecule ADP(3-) (2R)-tartronate semialdehyde; MetaCyc:CPD-26279; Declared type: small_molecule small molecule (2R)-tartronate semialdehyde D-glucarate(2-); CHEBI:30612; Declared type: small_molecule small molecule D-glucarate(2-) NAD(P)+; MetaCyc:NAD-P-OR-NOP; Declared type: chemical_entity chemical entity NAD(P)+ NAD(P)H; MetaCyc:NADH-P-OR-NOP; Declared type: chemical_entity chemical entity NAD(P)H iron(2+); CHEBI:29033; Declared type: cofactor cofactor iron(2+) magnesium(2+); CHEBI:18420; Declared type: cofactor cofactor magnesium(2+) cobalt(2+); CHEBI:48828; Declared type: cofactor cofactor cobalt(2+) manganese(2+); CHEBI:29035; Declared type: cofactor cofactor manganese(2+) Galactarate dehydratase (L-threo-forming); UniProtKB:P39829; Declared type: protein protein Galactarate dehydratase (L-threo-forming) 5-keto-4-deoxy-D-glucarate aldolase; UniProtKB:P23522; Declared type: protein protein 5-keto-4-deoxy-D-glucarate aldolase 2-hydroxy-3-oxopropionate reductase; UniProtKB:P0ABQ2; Declared type: protein protein 2-hydroxy-3-oxopropionate reductase Glycerate 2-kinase; UniProtKB:P23524; Declared type: protein protein Glycerate 2-kinase Carbohydrate diacid regulator; UniProtKB:P37047; Declared type: protein protein Carbohydrate diacid regulator Probable galactarate/D-glucarate transporter GarP; UniProtKB:P0AA80; Declared type: protein protein Probable galactarate/D-glucarate transporter GarP galactarate dehydratase; MetaCyc:CPLX0-8537; Declared type: complex complex galactarate dehydratase α-dehydro-β-deoxy-D-glucarate aldolase; MetaCyc:CPLX0-7615; Declared type: complex complex α-dehydro-β-deoxy-D- glucarate aldolase garD; Entrez:947641; Declared type: gene gene garD garL; Entrez:947630; Declared type: gene gene garL garR; Entrez:947631; Declared type: gene gene garR garK; Entrez:947632; Declared type: gene gene garK cdaR; Entrez:944860; Declared type: gene gene cdaR garP; Entrez:947642; Declared type: gene gene garP galactarate => 5-dehydro-4-deoxy-D-glucarate + H2O; RHEA:16006; Declared type: molecular_activity; Source reaction direction: left_to_right molecular activity galactarate => 5-dehydro-4-deoxy-D- glucarate + H2O 5-dehydro-4-deoxy-D-glucarate ⇌ (2R)-tartronate semialdehyde + pyruvate; MetaCyc:KDGALDOL-RXN; Declared type: molecular_activity; Source reaction direction: reversible molecular activity 5-dehydro-4-deoxy-D- glucarate ⇌ (2R)-tartronate semialdehyde + pyruvate D-glycerate + NAD(P)+ ⇐ (2R)-tartronate semialdehyde + NAD(P)H + H+; MetaCyc:TSA-REDUCT-RXN; Declared type: molecular_activity; Source reaction direction: right_to_left molecular activity D-glycerate + NAD(P)+ ⇐ (2R)-tartronate semialdehyde + NAD(P)H + H+ (R)-glycerate + ATP => (2R)-2-phosphoglycerate + ADP + H(+); RHEA:27378; Declared type: molecular_activity; Source reaction direction: left_to_right molecular activity (R)-glycerate + ATP => (2R)-2-phosphoglycerate + ADP + H(+) Escherichia coli K-12; NCBITaxon:83333; Declared type: taxon taxon Escherichia coli K-12 Escherichia coli str. K-12 substr. MG1655; NCBITaxon:511145; Declared type: taxon taxon Escherichia coli str. K-12 substr. MG1655 D-galactarate degradation I; MetaCyc:GALACTARDEG-PWY; Declared type: pathway pathway D-galactarate degradation I galactarate dehydratase; MetaCyc:CPLX0-8537; Declared type: complex; experimental construct: Recombinant, unlabeled E. coli GarD purified after TEV removal of its His6 tag; the structural preparation retains three residues after tag cleavage. Activity-sample scar and phosphorylation occupancy were not separately measured. Unlabeled activity material is distinct from SeMet/phospho-Asp168 crystal preparations.; Evidence PMID:31811683: the 6xHis-tag was removed with TEV protease (PDF printed p.719, Methods 4.1); Evidence PMID:31811683: Methods distinguish unlabeled activity preparation from SeMet structural material; the structure retains three residues after tag cleavage. (PDF Methods 4.1, 4.3, 4.4 and 4.5; Results 2.1) experimental construct galactarate dehydratase [experimental construct: Recombinant, unlabeled E. coli GarD purified after TEV removal of its His6 tag; the structural…] Glycerate 2-kinase; UniProtKB:P23524; Declared type: protein; experimental construct: Plasmid-expressed E. coli GarK in ΔgpmA ΔgpmM ΔgarK ΔglxK cells; cloning primers encode an N-terminal His6 sequence. The paper does not report tag cleavage. The printed donor spelling Mg1665 is retained as a source discrepancy.; Evidence PMID:25823014: Results, Figure 2 and Table 1 identify the four-deletion background; Cloning provides the procedure and His6-bearing Ec garK forward primer, with donor spelling K12 Mg1665. (Results & Discussion; Figure 2; Table 1; Materials and Methods / Cloning; Ec garK primer table) experimental construct Glycerate 2-kinase [experimental construct: Plasmid-expressed E. coli GarK in ΔgpmA ΔgpmM ΔgarK ΔglxK cells; cloning primers encode an…] Carbohydrate diacid regulator; UniProtKB:P37047; Declared type: protein; experimental construct: MC4100 reporter/loss-rescue context: active wild-type or pRM1-complemented SdaR/CdaR is inferred from loss in JA176 (paper-numbered P297S) and JA177 (Tn5 near the stop). The paper uses a 391-residue reference, unlike current P37047 (385 residues); numbering is not remapped.; Evidence PMID:10762278: JA176 and JA177 lose induced expression and utilization; pRM1 carrying MC4100 sdaR restores utilization. The mutants are inference controls, not the active regulator endpoint. (Isolation and mapping of pleiotropic mutants; Identification and cloning of the putative regulator) experimental construct Carbohydrate diacid regulator [experimental construct: MC4100 reporter/loss-rescue context: active wild-type or pRM1-complemented SdaR/CdaR is inferred…] Carbohydrate diacid regulator; UniProtKB:P37047; Declared type: protein; experimental construct: MC4100 reporter/loss-rescue context: active wild-type or pRM1-complemented SdaR/CdaR is inferred from loss in JA176 (paper-numbered P297S) and JA177 (Tn5 near the stop). The paper uses a 391-residue reference, unlike current P37047 (385 residues); numbering is not remapped.; Evidence PMID:10762278: JA176 and JA177 lose induced expression and utilization; pRM1 carrying MC4100 sdaR restores utilization. The mutants are inference controls, not the active regulator endpoint. (Isolation and mapping of pleiotropic mutants; Identification and cloning of the putative regulator) experimental construct Carbohydrate diacid regulator [experimental construct: MC4100 reporter/loss-rescue context: active wild-type or pRM1-complemented SdaR/CdaR is inferred…] Carbohydrate diacid regulator; UniProtKB:P37047; Declared type: protein; experimental construct: MC4100 reporter/loss-rescue context: active wild-type or pRM1-complemented SdaR/CdaR is inferred from loss in JA176 (paper-numbered P297S) and JA177 (Tn5 near the stop). The paper uses a 391-residue reference, unlike current P37047 (385 residues); numbering is not remapped.; Evidence PMID:10762278: JA176 and JA177 lose induced expression and utilization; pRM1 carrying MC4100 sdaR restores utilization. The mutants are inference controls, not the active regulator endpoint. (Isolation and mapping of pleiotropic mutants; Identification and cloning of the putative regulator) experimental construct Carbohydrate diacid regulator [experimental construct: MC4100 reporter/loss-rescue context: active wild-type or pRM1-complemented SdaR/CdaR is inferred…] Carbohydrate diacid regulator; UniProtKB:P37047; Declared type: protein; experimental construct: MC4100 reporter/loss-rescue context: active wild-type or pRM1-complemented SdaR/CdaR is inferred from loss in JA176 (paper-numbered P297S) and JA177 (Tn5 near the stop). The paper uses a 391-residue reference, unlike current P37047 (385 residues); numbering is not remapped.; Evidence PMID:10762278: JA176 and JA177 lose induced expression and utilization; pRM1 carrying MC4100 sdaR restores utilization. The mutants are inference controls, not the active regulator endpoint. (Isolation and mapping of pleiotropic mutants; Identification and cloning of the putative regulator) experimental construct Carbohydrate diacid regulator [experimental construct: MC4100 reporter/loss-rescue context: active wild-type or pRM1-complemented SdaR/CdaR is inferred…] Carbohydrate diacid regulator; UniProtKB:P37047; Declared type: protein; experimental construct: MC4100 reporter/loss-rescue context: active wild-type or pRM1-complemented SdaR/CdaR is inferred from loss in JA176 (paper-numbered P297S) and JA177 (Tn5 near the stop). The paper uses a 391-residue reference, unlike current P37047 (385 residues); numbering is not remapped.; Evidence PMID:10762278: JA176 and JA177 lose induced expression and utilization; pRM1 carrying MC4100 sdaR restores utilization. The mutants are inference controls, not the active regulator endpoint. (Isolation and mapping of pleiotropic mutants; Identification and cloning of the putative regulator) experimental construct Carbohydrate diacid regulator [experimental construct: MC4100 reporter/loss-rescue context: active wild-type or pRM1-complemented SdaR/CdaR is inferred…] Carbohydrate diacid regulator; UniProtKB:P37047; Declared type: protein; experimental construct: MC4100 reporter/loss-rescue context: active wild-type or pRM1-complemented SdaR/CdaR is inferred from loss in JA176 (paper-numbered P297S) and JA177 (Tn5 near the stop). The paper uses a 391-residue reference, unlike current P37047 (385 residues); numbering is not remapped.; Evidence PMID:10762278: JA176 and JA177 lose induced expression and utilization; pRM1 carrying MC4100 sdaR restores utilization. The mutants are inference controls, not the active regulator endpoint. (Isolation and mapping of pleiotropic mutants; Identification and cloning of the putative regulator) experimental construct Carbohydrate diacid regulator [experimental construct: MC4100 reporter/loss-rescue context: active wild-type or pRM1-complemented SdaR/CdaR is inferred…] Probable galactarate/D-glucarate transporter GarP; UniProtKB:P0AA80; Declared type: protein; experimental construct: BW25113 garP plasmid complementation in the corresponding Keio deletion strain: pCW-lic/tac, 100 µM IPTG, 25°C, 48 h, peptone plus galactarate, acidification endpoint. The reference protein denotes gene-product identity; exact insert sequence, tags and equivalence to MG1655 were not independently established.; Evidence PMID:39875389: Methods describe Keio strains, pCW-lic gene cloning and induced fermentation assays; these are engineered complementation experiments, not native-expression or purified-protein assays. (Par43; Par45; Par47; Fig3 caption) experimental construct Probable galactarate/D-glucarate transporter GarP [experimental construct: BW25113 garP plasmid complementation in the corresponding Keio deletion strain: pCW-lic/tac, 100 µM…] 5-keto-4-deoxy-D-glucarate aldolase; UniProtKB:P23522; Declared type: protein; experimental construct: BW25113 garL plasmid complementation in the corresponding Keio deletion strain: pCW-lic/tac, 100 µM IPTG, 25°C, 48 h, peptone plus galactarate, acidification endpoint. The reference protein denotes gene-product identity; exact insert sequence, tags and equivalence to MG1655 were not independently established.; Evidence PMID:39875389: Methods describe Keio strains, pCW-lic gene cloning and induced fermentation assays; these are engineered complementation experiments, not native-expression or purified-protein assays. (Par43; Par45; Par47; Fig3 caption) experimental construct 5-keto-4-deoxy-D-glucarate aldolase [experimental construct: BW25113 garL plasmid complementation in the corresponding Keio deletion strain: pCW- lic/tac, 100 µM…] 2-hydroxy-3-oxopropionate reductase; UniProtKB:P0ABQ2; Declared type: protein; experimental construct: BW25113 garR plasmid complementation in the corresponding Keio deletion strain: pCW-lic/tac, 100 µM IPTG, 25°C, 48 h, peptone plus galactarate, acidification endpoint. The reference protein denotes gene-product identity; exact insert sequence, tags and equivalence to MG1655 were not independently established.; Evidence PMID:39875389: Methods describe Keio strains, pCW-lic gene cloning and induced fermentation assays; these are engineered complementation experiments, not native-expression or purified-protein assays. (Par43; Par45; Par47; Fig3 caption) experimental construct 2-hydroxy-3-oxopropionate reductase [experimental construct: BW25113 garR plasmid complementation in the corresponding Keio deletion strain: pCW- lic/tac, 100 µM…]

Components and activities

Declared biological components and source reaction directions
NodeKind or roleSource direction
Escherichia coli K-12
NCBITaxon:83333		taxon
Escherichia coli str. K-12 substr. MG1655
NCBITaxon:511145		taxon
galactarate(2-)
CHEBI:16537		small molecule
5-dehydro-4-deoxy-D-glucarate(2-)
CHEBI:42819		small molecule
water
CHEBI:15377		small molecule
pyruvate
CHEBI:15361		small molecule
hydron
CHEBI:15378		small molecule
D-glycerate
CHEBI:16659		small molecule
ATP(4-)
CHEBI:30616		small molecule
2-phosphonato-D-glycerate(3-)
CHEBI:58289		small molecule
ADP(3-)
CHEBI:456216		small molecule
(2R)-tartronate semialdehyde
MetaCyc:CPD-26279		small molecule
D-glucarate(2-)
CHEBI:30612		small molecule
NAD(P)+
MetaCyc:NAD-P-OR-NOP		chemical entity
NAD(P)H
MetaCyc:NADH-P-OR-NOP		chemical entity
iron(2+)
CHEBI:29033		cofactor
magnesium(2+)
CHEBI:18420		cofactor
cobalt(2+)
CHEBI:48828		cofactor
manganese(2+)
CHEBI:29035		cofactor
Galactarate dehydratase (L-threo-forming)
UniProtKB:P39829		protein
5-keto-4-deoxy-D-glucarate aldolase
UniProtKB:P23522		protein
2-hydroxy-3-oxopropionate reductase
UniProtKB:P0ABQ2		protein
Glycerate 2-kinase
UniProtKB:P23524		protein
Carbohydrate diacid regulator
UniProtKB:P37047		protein
Probable galactarate/D-glucarate transporter GarP
UniProtKB:P0AA80		protein
galactarate dehydratase
MetaCyc:CPLX0-8537		complex
α-dehydro-β-deoxy-D-glucarate aldolase
MetaCyc:CPLX0-7615		complex
garD
Entrez:947641		gene
garL
Entrez:947630		gene
garR
Entrez:947631		gene
garK
Entrez:947632		gene
cdaR
Entrez:944860		gene
garP
Entrez:947642		gene
galactarate => 5-dehydro-4-deoxy-D-glucarate + H2O
RHEA:16006		molecular activityleft to right
5-dehydro-4-deoxy-D-glucarate ⇌ (2R)-tartronate semialdehyde + pyruvate
MetaCyc:KDGALDOL-RXN		molecular activityreversible
D-glycerate + NAD(P)+ ⇐ (2R)-tartronate semialdehyde + NAD(P)H + H+
MetaCyc:TSA-REDUCT-RXN		molecular activityright to left
(R)-glycerate + ATP => (2R)-2-phosphoglycerate + ADP + H(+)
RHEA:27378		molecular activityleft to right

Mechanistic edges

Mechanistic edges and their cited evidence
SubjectPredicate and descriptionObjectEvidence
MetaCyc:GALACTARDEG-PWYhas_part

One native core event; mapped Rhea endpoints preserve the complete native chemistry and selected direction.

galactarate => 5-dehydro-4-deoxy-D-glucarate + H2O
RHEA:16006
  • MetaCyc:GALACTARDEG-PWY

    Source assertion: The explicit reaction-list contains GALACTARDEHYDRA-RXN.

    Source location/ptools-xml/Pathway/reaction-list/Reaction[@frameid="GALACTARDEHYDRA-RXN"]
  • MetaCyc:GALACTARDEHYDRA-RXN

    Source assertion: The native reaction directly cross-references RHEA:16006.

    Source location/ptools-xml/Reaction/dblink[dblink-db="RHEA"]
MetaCyc:GALACTARDEG-PWYhas_part

One native core event; the native reaction identifier preserves the exact intermediate stereochemistry and its source direction.

5-dehydro-4-deoxy-D-glucarate ⇌ (2R)-tartronate semialdehyde + pyruvate
MetaCyc:KDGALDOL-RXN
  • MetaCyc:GALACTARDEG-PWY

    Source assertion: The explicit reaction-list contains KDGALDOL-RXN.

    Source location/ptools-xml/Pathway/reaction-list/Reaction[@frameid="KDGALDOL-RXN"]
MetaCyc:GALACTARDEG-PWYhas_part

One native core event; the native reaction identifier preserves the exact intermediate stereochemistry and its source direction.

D-glycerate + NAD(P)+ ⇐ (2R)-tartronate semialdehyde + NAD(P)H + H+
MetaCyc:TSA-REDUCT-RXN
  • MetaCyc:GALACTARDEG-PWY

    Source assertion: The explicit reaction-list contains TSA-REDUCT-RXN.

    Source location/ptools-xml/Pathway/reaction-list/Reaction[@frameid="TSA-REDUCT-RXN"]
MetaCyc:GALACTARDEG-PWYhas_part

One native core event; mapped Rhea endpoints preserve the complete native chemistry and selected direction.

(R)-glycerate + ATP => (2R)-2-phosphoglycerate + ADP + H(+)
RHEA:27378
  • MetaCyc:GALACTARDEG-PWY

    Source assertion: The explicit reaction-list contains GKI-RXN.

    Source location/ptools-xml/Pathway/reaction-list/Reaction[@frameid="GKI-RXN"]
  • MetaCyc:GKI-RXN

    Source assertion: The native reaction directly cross-references RHEA:27378.

    Source location/ptools-xml/Reaction/dblink[dblink-db="RHEA"]
galactarate(2-)
CHEBI:16537		consumes

The complete formal reaction includes this species with coefficient one.

galactarate => 5-dehydro-4-deoxy-D-glucarate + H2O
RHEA:16006
  • RHEA:16006

    Source assertion: RHEA:16006 places CHEBI:16537 on its substrates side with coefficient 1.

    Source locationAggregate rdf:Description by rdf:about: http://rdf.rhea-db.org/16006 / rh:substrates -> 16005_L / rh:contains1 -> participant / rh:compound -> compound / rh:accession="CHEBI:16537"
galactarate => 5-dehydro-4-deoxy-D-glucarate + H2O
RHEA:16006		produces

The complete formal reaction includes this species with coefficient one.

5-dehydro-4-deoxy-D-glucarate(2-)
CHEBI:42819
  • RHEA:16006

    Source assertion: RHEA:16006 places CHEBI:42819 on its products side with coefficient 1.

    Source locationAggregate rdf:Description by rdf:about: http://rdf.rhea-db.org/16006 / rh:products -> 16005_R / rh:contains1 -> participant / rh:compound -> compound / rh:accession="CHEBI:42819"
galactarate => 5-dehydro-4-deoxy-D-glucarate + H2O
RHEA:16006		produces

The complete formal reaction includes this species with coefficient one.

water
CHEBI:15377
  • RHEA:16006

    Source assertion: RHEA:16006 places CHEBI:15377 on its products side with coefficient 1.

    Source locationAggregate rdf:Description by rdf:about: http://rdf.rhea-db.org/16006 / rh:products -> 16005_R / rh:contains1 -> participant / rh:compound -> compound / rh:accession="CHEBI:15377"
D-glycerate
CHEBI:16659		consumes

The complete formal reaction includes this species with coefficient one.

(R)-glycerate + ATP => (2R)-2-phosphoglycerate + ADP + H(+)
RHEA:27378
  • RHEA:27378

    Source assertion: RHEA:27378 places CHEBI:16659 on its substrates side with coefficient 1.

    Source locationAggregate rdf:Description by rdf:about: http://rdf.rhea-db.org/27378 / rh:substrates -> 27377_L / rh:contains1 -> participant / rh:compound -> compound / rh:accession="CHEBI:16659"
ATP(4-)
CHEBI:30616		consumes

The complete formal reaction includes this species with coefficient one.

(R)-glycerate + ATP => (2R)-2-phosphoglycerate + ADP + H(+)
RHEA:27378
  • RHEA:27378

    Source assertion: RHEA:27378 places CHEBI:30616 on its substrates side with coefficient 1.

    Source locationAggregate rdf:Description by rdf:about: http://rdf.rhea-db.org/27378 / rh:substrates -> 27377_L / rh:contains1 -> participant / rh:compound -> compound / rh:accession="CHEBI:30616"
(R)-glycerate + ATP => (2R)-2-phosphoglycerate + ADP + H(+)
RHEA:27378		produces

The complete formal reaction includes this species with coefficient one.

2-phosphonato-D-glycerate(3-)
CHEBI:58289
  • RHEA:27378

    Source assertion: RHEA:27378 places CHEBI:58289 on its products side with coefficient 1.

    Source locationAggregate rdf:Description by rdf:about: http://rdf.rhea-db.org/27378 / rh:products -> 27377_R / rh:contains1 -> participant / rh:compound -> compound / rh:accession="CHEBI:58289"
(R)-glycerate + ATP => (2R)-2-phosphoglycerate + ADP + H(+)
RHEA:27378		produces

The complete formal reaction includes this species with coefficient one.

ADP(3-)
CHEBI:456216
  • RHEA:27378

    Source assertion: RHEA:27378 places CHEBI:456216 on its products side with coefficient 1.

    Source locationAggregate rdf:Description by rdf:about: http://rdf.rhea-db.org/27378 / rh:products -> 27377_R / rh:contains1 -> participant / rh:compound -> compound / rh:accession="CHEBI:456216"
(R)-glycerate + ATP => (2R)-2-phosphoglycerate + ADP + H(+)
RHEA:27378		produces

The complete formal reaction includes this species with coefficient one.

hydron
CHEBI:15378
  • RHEA:27378

    Source assertion: RHEA:27378 places CHEBI:15378 on its products side with coefficient 1.

    Source locationAggregate rdf:Description by rdf:about: http://rdf.rhea-db.org/27378 / rh:products -> 27377_R / rh:contains1 -> participant / rh:compound -> compound / rh:accession="CHEBI:15378"
5-dehydro-4-deoxy-D-glucarate(2-)
CHEBI:42819		consumes

Preserves native chemical identity and physiological traversal. Native (2R) stereochemistry is a database assertion; it is not replaced by stereounspecified CHEBI:57978.

5-dehydro-4-deoxy-D-glucarate ⇌ (2R)-tartronate semialdehyde + pyruvate
MetaCyc:KDGALDOL-RXN
  • MetaCyc:KDGALDOL-RXN

    Source assertion: The native left side contains 5-KETO-4-DEOXY-D-GLUCARATE; the native reaction direction is REVERSIBLE.

    Source location/ptools-xml/Reaction/left/Compound[@frameid="5-KETO-4-DEOXY-D-GLUCARATE"]; reaction-direction
  • MetaCyc:GALACTARDEG-PWY

    Source assertion: The aldolase layout selects left-to-right cleavage in this pathway, independently of the reversible reaction definition.

    Source location/ptools-xml/Pathway/reaction-layout[Reaction/@frameid="KDGALDOL-RXN"]/direction
  • MetaCyc:5-KETO-4-DEOXY-D-GLUCARATE

    Source assertion: The native chemical directly cross-references CHEBI:42819 and supplies its complete InChI.

    Source location/ptools-xml/Compound/dblink[dblink-db="CHEBI"]; inchi
5-dehydro-4-deoxy-D-glucarate ⇌ (2R)-tartronate semialdehyde + pyruvate
MetaCyc:KDGALDOL-RXN		produces

Preserves native chemical identity and physiological traversal. Native (2R) stereochemistry is a database assertion; it is not replaced by stereounspecified CHEBI:57978.

(2R)-tartronate semialdehyde
MetaCyc:CPD-26279
  • MetaCyc:KDGALDOL-RXN

    Source assertion: The native right side contains CPD-26279; the native reaction direction is REVERSIBLE.

    Source location/ptools-xml/Reaction/right/Compound[@frameid="CPD-26279"]; reaction-direction
  • MetaCyc:GALACTARDEG-PWY

    Source assertion: The aldolase layout selects left-to-right cleavage in this pathway, independently of the reversible reaction definition.

    Source location/ptools-xml/Pathway/reaction-layout[Reaction/@frameid="KDGALDOL-RXN"]/direction
  • MetaCyc:CPD-26279

    Source assertion: The native common-name and full InChI specify (2R)-tartronate semialdehyde; the stereocentre is retained.

    Source location/ptools-xml/Compound/common-name; inchi; cml
5-dehydro-4-deoxy-D-glucarate ⇌ (2R)-tartronate semialdehyde + pyruvate
MetaCyc:KDGALDOL-RXN		produces

Preserves native chemical identity and physiological traversal. Native (2R) stereochemistry is a database assertion; it is not replaced by stereounspecified CHEBI:57978.

pyruvate
CHEBI:15361
  • MetaCyc:KDGALDOL-RXN

    Source assertion: The native right side contains PYRUVATE; the native reaction direction is REVERSIBLE.

    Source location/ptools-xml/Reaction/right/Compound[@frameid="PYRUVATE"]; reaction-direction
  • MetaCyc:GALACTARDEG-PWY

    Source assertion: The aldolase layout selects left-to-right cleavage in this pathway, independently of the reversible reaction definition.

    Source location/ptools-xml/Pathway/reaction-layout[Reaction/@frameid="KDGALDOL-RXN"]/direction
  • MetaCyc:PYRUVATE

    Source assertion: The native chemical directly cross-references CHEBI:15361 and supplies its complete InChI.

    Source location/ptools-xml/Compound/dblink[dblink-db="CHEBI"]; inchi
(2R)-tartronate semialdehyde
MetaCyc:CPD-26279		consumes

Preserves native chemical identity and physiological traversal. Native (2R) stereochemistry is a database assertion; it is not replaced by stereounspecified CHEBI:57978.

D-glycerate + NAD(P)+ ⇐ (2R)-tartronate semialdehyde + NAD(P)H + H+
MetaCyc:TSA-REDUCT-RXN
  • MetaCyc:TSA-REDUCT-RXN

    Source assertion: The native right side contains CPD-26279; the native reaction direction is RIGHT-TO-LEFT.

    Source location/ptools-xml/Reaction/right/Compound[@frameid="CPD-26279"]; reaction-direction
  • MetaCyc:CPD-26279

    Source assertion: The native common-name and full InChI specify (2R)-tartronate semialdehyde; the stereocentre is retained.

    Source location/ptools-xml/Compound/common-name; inchi; cml
NAD(P)H
MetaCyc:NADH-P-OR-NOP		consumes

Preserves native chemical identity and physiological traversal. The NAD(P) class retains alternative redox donors and does not assert a fixed donor mixture.

D-glycerate + NAD(P)+ ⇐ (2R)-tartronate semialdehyde + NAD(P)H + H+
MetaCyc:TSA-REDUCT-RXN
  • MetaCyc:TSA-REDUCT-RXN

    Source assertion: The native right side contains NADH-P-OR-NOP; the native reaction direction is RIGHT-TO-LEFT.

    Source location/ptools-xml/Reaction/right/Compound[@frameid="NADH-P-OR-NOP"]; reaction-direction
  • MetaCyc:NADH-P-OR-NOP

    Source assertion: This is an explicit Compound class with instances NADH and NADPH; it denotes alternatives, not simultaneous substrates.

    Source location/ptools-xml/Compound/@class; common-name; instance/Compound
hydron
CHEBI:15378		consumes

Preserves native chemical identity and physiological traversal. Native (2R) stereochemistry is a database assertion; it is not replaced by stereounspecified CHEBI:57978.

D-glycerate + NAD(P)+ ⇐ (2R)-tartronate semialdehyde + NAD(P)H + H+
MetaCyc:TSA-REDUCT-RXN
  • MetaCyc:TSA-REDUCT-RXN

    Source assertion: The native right side contains PROTON; the native reaction direction is RIGHT-TO-LEFT.

    Source location/ptools-xml/Reaction/right/Compound[@frameid="PROTON"]; reaction-direction
  • MetaCyc:PROTON

    Source assertion: The native chemical directly cross-references CHEBI:15378 and supplies its complete InChI.

    Source location/ptools-xml/Compound/dblink[dblink-db="CHEBI"]; inchi
D-glycerate + NAD(P)+ ⇐ (2R)-tartronate semialdehyde + NAD(P)H + H+
MetaCyc:TSA-REDUCT-RXN		produces

Preserves native chemical identity and physiological traversal. Native (2R) stereochemistry is a database assertion; it is not replaced by stereounspecified CHEBI:57978.

D-glycerate
CHEBI:16659
  • MetaCyc:TSA-REDUCT-RXN

    Source assertion: The native left side contains GLYCERATE; the native reaction direction is RIGHT-TO-LEFT.

    Source location/ptools-xml/Reaction/left/Compound[@frameid="GLYCERATE"]; reaction-direction
  • MetaCyc:GLYCERATE

    Source assertion: The native chemical directly cross-references CHEBI:16659 and supplies its complete InChI.

    Source location/ptools-xml/Compound/dblink[dblink-db="CHEBI"]; inchi
D-glycerate + NAD(P)+ ⇐ (2R)-tartronate semialdehyde + NAD(P)H + H+
MetaCyc:TSA-REDUCT-RXN		produces

Preserves native chemical identity and physiological traversal. The NAD(P) class retains alternative redox donors and does not assert a fixed donor mixture.

NAD(P)+
MetaCyc:NAD-P-OR-NOP
  • MetaCyc:TSA-REDUCT-RXN

    Source assertion: The native left side contains NAD-P-OR-NOP; the native reaction direction is RIGHT-TO-LEFT.

    Source location/ptools-xml/Reaction/left/Compound[@frameid="NAD-P-OR-NOP"]; reaction-direction
  • MetaCyc:NAD-P-OR-NOP

    Source assertion: This is an explicit Compound class with instances NAD and NADP; it denotes alternatives, not simultaneous substrates.

    Source location/ptools-xml/Compound/@class; common-name; instance/Compound
galactarate => 5-dehydro-4-deoxy-D-glucarate + H2O
RHEA:16006		provides_input_for

The native ordering and layout establish direct transfer of the shared intermediate in the selected pathway.

5-dehydro-4-deoxy-D-glucarate ⇌ (2R)-tartronate semialdehyde + pyruvate
MetaCyc:KDGALDOL-RXN
  • MetaCyc:GALACTARDEG-PWY

    Source assertion: KDGALDOL-RXN names GALACTARDEHYDRA-RXN as its predecessor; the adjacent layouts share the pathway intermediate.

    Source location/ptools-xml/Pathway/reaction-ordering; reaction-layout
5-dehydro-4-deoxy-D-glucarate ⇌ (2R)-tartronate semialdehyde + pyruvate
MetaCyc:KDGALDOL-RXN		provides_input_for

The native ordering and layout establish direct transfer of the shared intermediate in the selected pathway.

D-glycerate + NAD(P)+ ⇐ (2R)-tartronate semialdehyde + NAD(P)H + H+
MetaCyc:TSA-REDUCT-RXN
  • MetaCyc:GALACTARDEG-PWY

    Source assertion: TSA-REDUCT-RXN names KDGALDOL-RXN as its predecessor; the adjacent layouts share the pathway intermediate.

    Source location/ptools-xml/Pathway/reaction-ordering; reaction-layout
D-glycerate + NAD(P)+ ⇐ (2R)-tartronate semialdehyde + NAD(P)H + H+
MetaCyc:TSA-REDUCT-RXN		provides_input_for

The native ordering and layout establish direct transfer of the shared intermediate in the selected pathway.

(R)-glycerate + ATP => (2R)-2-phosphoglycerate + ADP + H(+)
RHEA:27378
  • MetaCyc:GALACTARDEG-PWY

    Source assertion: GKI-RXN names TSA-REDUCT-RXN as its predecessor; the adjacent layouts share the pathway intermediate.

    Source location/ptools-xml/Pathway/reaction-ordering; reaction-layout
galactarate dehydratase
MetaCyc:CPLX0-8537		has_part

The identified native homomer contains 2 copies of this polypeptide. Assembly membership is separate from isolated-subunit catalysis.

Galactarate dehydratase (L-threo-forming)
UniProtKB:P39829
  • MetaCyc:CPLX0-8537

    Source assertion: The component list gives GALACTARDEHYDRA-MONOMER at coefficient 2.

    Source location/ptools-xml/Protein/component[Protein/@frameid="GALACTARDEHYDRA-MONOMER"]
  • MetaCyc:GALACTARDEHYDRA-MONOMER

    Source assertion: The native polypeptide directly cross-references UniProt P39829.

    Source location/ptools-xml/Protein/dblink[dblink-db="UNIPROT"]
α-dehydro-β-deoxy-D-glucarate aldolase
MetaCyc:CPLX0-7615		has_part

The identified native homomer contains 6 copies of this polypeptide. Assembly membership is separate from isolated-subunit catalysis.

5-keto-4-deoxy-D-glucarate aldolase
UniProtKB:P23522
  • MetaCyc:CPLX0-7615

    Source assertion: The component list gives KDGALDOL-MONOMER at coefficient 6.

    Source location/ptools-xml/Protein/component[Protein/@frameid="KDGALDOL-MONOMER"]
  • MetaCyc:KDGALDOL-MONOMER

    Source assertion: The native polypeptide directly cross-references UniProt P23522.

    Source location/ptools-xml/Protein/dblink[dblink-db="UNIPROT"]
galactarate dehydratase
MetaCyc:CPLX0-8537		catalyzes

Curated native catalytic assignment; structured database statements retain their source status.

galactarate => 5-dehydro-4-deoxy-D-glucarate + H2O
RHEA:16006
  • MetaCyc:CPLX0-8537

    Source assertion: The native catalyst has a catalyzes activity with an enzyme backlink and the corresponding pathway reaction.

    Source location/ptools-xml/Protein/catalyzes/Enzymatic-Reaction/enzyme; reaction
  • MetaCyc:GALACTARDEHYDRA-RXN

    Source assertion: The native reaction directly cross-references RHEA:16006.

    Source location/ptools-xml/Reaction/dblink[dblink-db="RHEA"]
α-dehydro-β-deoxy-D-glucarate aldolase
MetaCyc:CPLX0-7615		catalyzes

Curated native catalytic assignment; structured database statements retain their source status.

5-dehydro-4-deoxy-D-glucarate ⇌ (2R)-tartronate semialdehyde + pyruvate
MetaCyc:KDGALDOL-RXN
  • MetaCyc:CPLX0-7615

    Source assertion: The native catalyst has a catalyzes activity with an enzyme backlink and the corresponding pathway reaction.

    Source location/ptools-xml/Protein/catalyzes/Enzymatic-Reaction/enzyme; reaction
2-hydroxy-3-oxopropionate reductase
UniProtKB:P0ABQ2		catalyzes

Curated native catalytic assignment; structured database statements retain their source status. UniProt separately annotates NADH and NADPH families with ECO:0000269 and HAMAP support; its stereounspecified Rhea substrate is not an exact replacement for native (2R)-tartronate semialdehyde.

D-glycerate + NAD(P)+ ⇐ (2R)-tartronate semialdehyde + NAD(P)H + H+
MetaCyc:TSA-REDUCT-RXN
  • MetaCyc:TSA-REDUCT-MONOMER

    Source assertion: The native catalyst has a catalyzes activity with an enzyme backlink and the corresponding pathway reaction.

    Source location/ptools-xml/Protein/catalyzes/Enzymatic-Reaction/enzyme; reaction
  • MetaCyc:TSA-REDUCT-MONOMER

    Source assertion: The native protein has a direct UNIPROT cross-reference to P0ABQ2.

    Source location/ptools-xml/Protein/dblink[dblink-db="UNIPROT"]
  • UniProtKB:P0ABQ2

    Source assertion: The catalytic-activity annotations include NADH and NADPH reaction families; evidences cite PMID9772162 and HAMAP MF_02032.

    Source locationcomments[commentType=CATALYTIC ACTIVITY].reaction; evidences
Glycerate 2-kinase
UniProtKB:P23524		catalyzes

Curated native catalytic assignment; structured database statements retain their source status. The current 2-phosphoglycerate product is retained; historical GKI/GKII naming and physiological isozyme roles must not be inferred from old names alone.

(R)-glycerate + ATP => (2R)-2-phosphoglycerate + ADP + H(+)
RHEA:27378
  • MetaCyc:GKI-MONOMER

    Source assertion: The native catalyst has a catalyzes activity with an enzyme backlink and the corresponding pathway reaction.

    Source location/ptools-xml/Protein/catalyzes/Enzymatic-Reaction/enzyme; reaction
  • MetaCyc:GKI-MONOMER

    Source assertion: The native protein has a direct UNIPROT cross-reference to P23524.

    Source location/ptools-xml/Protein/dblink[dblink-db="UNIPROT"]
  • MetaCyc:GKI-RXN

    Source assertion: The native reaction directly cross-references RHEA:27378.

    Source location/ptools-xml/Reaction/dblink[dblink-db="RHEA"]
galactarate dehydratase
MetaCyc:CPLX0-8537

experimental construct: Recombinant, unlabeled E. coli GarD purified after TEV removal of its His6 tag; the structural preparation retains three residues after tag cleavage. Activity-sample scar and phosphorylation occupancy were not separately measured. Unlabeled activity material is distinct from SeMet/phospho-Asp168 crystal preparations.

Qualification evidence
  • PMID:31811683
    the 6xHis-tag was removed with TEV protease
    Source locationPDF printed p.719, Methods 4.1
  • PMID:31811683

    Source assertion: Methods distinguish unlabeled activity preparation from SeMet structural material; the structure retains three residues after tag cleavage.

    Source locationPDF Methods 4.1, 4.3, 4.4 and 4.5; Results 2.1
catalyzes

The recombinant preparation showed galactarate-dehydrating activity with added FeSO4 under reducing, semi-anaerobic assay conditions: 30°C, pH7, 30 mM substrate, 90 mM β-mercaptoethanol and 0 or 0.5 mM FeSO4. Semicarbazone detection supports product formation but does not independently establish stereochemical selectivity.

galactarate => 5-dehydro-4-deoxy-D-glucarate + H2O
RHEA:16006
  • PMID:31811683
    upon iron addition the enzyme produced 4 μmol/min of 5-keto-4-D-dehydroxyglucarate
    Source locationPDF printed p.716, Results 2.5; Figure 5; Methods 4.5
Galactarate dehydratase (L-threo-forming)
UniProtKB:P39829		has_cofactor

The reviewed Fe2+ annotation is linked to the recombinant activity study. This does not establish iron-binding stoichiometry, a definite binding site, native cellular occupancy or catalytic substitution by the calcium observed in crystals.

iron(2+)
CHEBI:29033
  • UniProtKB:P39829

    Source assertion: The COFACTOR comment specifies Fe(2+) / CHEBI:29033 with ECO:0000269 and PMID31811683.

    Source locationcomments[commentType=COFACTOR].cofactors; evidences
5-keto-4-deoxy-D-glucarate aldolase
UniProtKB:P23522		has_cofactor

Reviewed GarL annotation reports one Mg2+ per subunit and lower efficiency with Co2+, Fe2+ or Mn2+. These are alternatives under the cited biochemical conditions, not a simultaneous four-metal requirement or a claim of physiological occupancy.

magnesium(2+)
CHEBI:18420
  • UniProtKB:P23522

    Source assertion: The COFACTOR comment includes Mg(2+), citing ECO:0000269 / Ref.5; its note distinguishes magnesium from less-efficient alternatives.

    Source locationcomments[commentType=COFACTOR].cofactors; note; references[referenceNumber=5]
5-keto-4-deoxy-D-glucarate aldolase
UniProtKB:P23522		has_cofactor

Reviewed GarL annotation reports one Mg2+ per subunit and lower efficiency with Co2+, Fe2+ or Mn2+. These are alternatives under the cited biochemical conditions, not a simultaneous four-metal requirement or a claim of physiological occupancy.

cobalt(2+)
CHEBI:48828
  • UniProtKB:P23522

    Source assertion: The COFACTOR comment includes Co(2+), citing ECO:0000269 / Ref.5; its note distinguishes magnesium from less-efficient alternatives.

    Source locationcomments[commentType=COFACTOR].cofactors; note; references[referenceNumber=5]
5-keto-4-deoxy-D-glucarate aldolase
UniProtKB:P23522		has_cofactor

Reviewed GarL annotation reports one Mg2+ per subunit and lower efficiency with Co2+, Fe2+ or Mn2+. These are alternatives under the cited biochemical conditions, not a simultaneous four-metal requirement or a claim of physiological occupancy.

iron(2+)
CHEBI:29033
  • UniProtKB:P23522

    Source assertion: The COFACTOR comment includes Fe(2+), citing ECO:0000269 / Ref.5; its note distinguishes magnesium from less-efficient alternatives.

    Source locationcomments[commentType=COFACTOR].cofactors; note; references[referenceNumber=5]
5-keto-4-deoxy-D-glucarate aldolase
UniProtKB:P23522		has_cofactor

Reviewed GarL annotation reports one Mg2+ per subunit and lower efficiency with Co2+, Fe2+ or Mn2+. These are alternatives under the cited biochemical conditions, not a simultaneous four-metal requirement or a claim of physiological occupancy.

manganese(2+)
CHEBI:29035
  • UniProtKB:P23522

    Source assertion: The COFACTOR comment includes Mn(2+), citing ECO:0000269 / Ref.5; its note distinguishes magnesium from less-efficient alternatives.

    Source locationcomments[commentType=COFACTOR].cofactors; note; references[referenceNumber=5]
Glycerate 2-kinase
UniProtKB:P23524

experimental construct: Plasmid-expressed E. coli GarK in ΔgpmA ΔgpmM ΔgarK ΔglxK cells; cloning primers encode an N-terminal His6 sequence. The paper does not report tag cleavage. The printed donor spelling Mg1665 is retained as a source discrepancy.

Qualification evidence
  • PMID:25823014

    Source assertion: Results, Figure 2 and Table 1 identify the four-deletion background; Cloning provides the procedure and His6-bearing Ec garK forward primer, with donor spelling K12 Mg1665.

    Source locationResults & Discussion; Figure 2; Table 1; Materials and Methods / Cloning; Ec garK primer table
catalyzes

In a ΔgpmA ΔgpmM ΔgarK ΔglxK strain, plasmid GarK enabled growth on glycerol plus glycerate but not pyruvate plus glycerate. This engineered metabolic selection supports a 2-phosphoglycerate product; it does not establish native GarK assembly, metal occupancy or complete galactarate flux.

(R)-glycerate + ATP => (2R)-2-phosphoglycerate + ADP + H(+)
RHEA:27378
  • PMID:25823014

    Source assertion: GarK expression restores the lower-metabolism glycerate entry phenotype in the four-deletion background; Table 1 distinguishes glycerate plus glycerol from glycerate plus pyruvate.

    Source locationResults & Discussion; Figure 2; Table 1
Carbohydrate diacid regulator
UniProtKB:P37047

experimental construct: MC4100 reporter/loss-rescue context: active wild-type or pRM1-complemented SdaR/CdaR is inferred from loss in JA176 (paper-numbered P297S) and JA177 (Tn5 near the stop). The paper uses a 391-residue reference, unlike current P37047 (385 residues); numbering is not remapped.

Qualification evidence
  • PMID:10762278

    Source assertion: JA176 and JA177 lose induced expression and utilization; pRM1 carrying MC4100 sdaR restores utilization. The mutants are inference controls, not the active regulator endpoint.

    Source locationIsolation and mapping of pleiotropic mutants; Identification and cloning of the putative regulator
activates

CdaR/SdaR positively controls the garD transcriptional unit in the MC4100 reporter/loss-rescue system. For garL, garR and garK this is shared-operon expression inference from the garP promoter, not independently mapped downstream promoters or direct protein activation. Direct ligand binding was not tested.

garD
Entrez:947641
  • PMID:10762278

    Source assertion: Single-copy garD/garP promoter fusions respond to the sugar acids; loss-of-function sdaR mutations remove the induced phenotype and complementation restores utilization.

    Source locationExpression of the transcriptional units; Isolation and mapping of pleiotropic mutants; Identification and cloning of the putative regulator
Carbohydrate diacid regulator
UniProtKB:P37047

experimental construct: MC4100 reporter/loss-rescue context: active wild-type or pRM1-complemented SdaR/CdaR is inferred from loss in JA176 (paper-numbered P297S) and JA177 (Tn5 near the stop). The paper uses a 391-residue reference, unlike current P37047 (385 residues); numbering is not remapped.

Qualification evidence
  • PMID:10762278

    Source assertion: JA176 and JA177 lose induced expression and utilization; pRM1 carrying MC4100 sdaR restores utilization. The mutants are inference controls, not the active regulator endpoint.

    Source locationIsolation and mapping of pleiotropic mutants; Identification and cloning of the putative regulator
activates

CdaR/SdaR positively controls the garPLRK transcriptional unit in the MC4100 reporter/loss-rescue system. For garL, garR and garK this is shared-operon expression inference from the garP promoter, not independently mapped downstream promoters or direct protein activation. Direct ligand binding was not tested.

garL
Entrez:947630
  • PMID:10762278

    Source assertion: Single-copy garD/garP promoter fusions respond to the sugar acids; loss-of-function sdaR mutations remove the induced phenotype and complementation restores utilization.

    Source locationExpression of the transcriptional units; Isolation and mapping of pleiotropic mutants; Identification and cloning of the putative regulator
Carbohydrate diacid regulator
UniProtKB:P37047

experimental construct: MC4100 reporter/loss-rescue context: active wild-type or pRM1-complemented SdaR/CdaR is inferred from loss in JA176 (paper-numbered P297S) and JA177 (Tn5 near the stop). The paper uses a 391-residue reference, unlike current P37047 (385 residues); numbering is not remapped.

Qualification evidence
  • PMID:10762278

    Source assertion: JA176 and JA177 lose induced expression and utilization; pRM1 carrying MC4100 sdaR restores utilization. The mutants are inference controls, not the active regulator endpoint.

    Source locationIsolation and mapping of pleiotropic mutants; Identification and cloning of the putative regulator
activates

CdaR/SdaR positively controls the garPLRK transcriptional unit in the MC4100 reporter/loss-rescue system. For garL, garR and garK this is shared-operon expression inference from the garP promoter, not independently mapped downstream promoters or direct protein activation. Direct ligand binding was not tested.

garR
Entrez:947631
  • PMID:10762278

    Source assertion: Single-copy garD/garP promoter fusions respond to the sugar acids; loss-of-function sdaR mutations remove the induced phenotype and complementation restores utilization.

    Source locationExpression of the transcriptional units; Isolation and mapping of pleiotropic mutants; Identification and cloning of the putative regulator
Carbohydrate diacid regulator
UniProtKB:P37047

experimental construct: MC4100 reporter/loss-rescue context: active wild-type or pRM1-complemented SdaR/CdaR is inferred from loss in JA176 (paper-numbered P297S) and JA177 (Tn5 near the stop). The paper uses a 391-residue reference, unlike current P37047 (385 residues); numbering is not remapped.

Qualification evidence
  • PMID:10762278

    Source assertion: JA176 and JA177 lose induced expression and utilization; pRM1 carrying MC4100 sdaR restores utilization. The mutants are inference controls, not the active regulator endpoint.

    Source locationIsolation and mapping of pleiotropic mutants; Identification and cloning of the putative regulator
activates

CdaR/SdaR positively controls the garPLRK transcriptional unit in the MC4100 reporter/loss-rescue system. For garL, garR and garK this is shared-operon expression inference from the garP promoter, not independently mapped downstream promoters or direct protein activation. Direct ligand binding was not tested.

garK
Entrez:947632
  • PMID:10762278

    Source assertion: Single-copy garD/garP promoter fusions respond to the sugar acids; loss-of-function sdaR mutations remove the induced phenotype and complementation restores utilization.

    Source locationExpression of the transcriptional units; Isolation and mapping of pleiotropic mutants; Identification and cloning of the putative regulator
Carbohydrate diacid regulator
UniProtKB:P37047

experimental construct: MC4100 reporter/loss-rescue context: active wild-type or pRM1-complemented SdaR/CdaR is inferred from loss in JA176 (paper-numbered P297S) and JA177 (Tn5 near the stop). The paper uses a 391-residue reference, unlike current P37047 (385 residues); numbering is not remapped.

Qualification evidence
  • PMID:10762278

    Source assertion: JA176 and JA177 lose induced expression and utilization; pRM1 carrying MC4100 sdaR restores utilization. The mutants are inference controls, not the active regulator endpoint.

    Source locationIsolation and mapping of pleiotropic mutants; Identification and cloning of the putative regulator
activates

CdaR/SdaR positively controls the garPLRK transcriptional unit in the MC4100 reporter/loss-rescue system. For garL, garR and garK this is shared-operon expression inference from the garP promoter, not independently mapped downstream promoters or direct protein activation. Direct ligand binding was not tested.

garP
Entrez:947642
  • PMID:10762278

    Source assertion: Single-copy garD/garP promoter fusions respond to the sugar acids; loss-of-function sdaR mutations remove the induced phenotype and complementation restores utilization.

    Source locationExpression of the transcriptional units; Isolation and mapping of pleiotropic mutants; Identification and cloning of the putative regulator
Carbohydrate diacid regulator
UniProtKB:P37047

experimental construct: MC4100 reporter/loss-rescue context: active wild-type or pRM1-complemented SdaR/CdaR is inferred from loss in JA176 (paper-numbered P297S) and JA177 (Tn5 near the stop). The paper uses a 391-residue reference, unlike current P37047 (385 residues); numbering is not remapped.

Qualification evidence
  • PMID:10762278

    Source assertion: JA176 and JA177 lose induced expression and utilization; pRM1 carrying MC4100 sdaR restores utilization. The mutants are inference controls, not the active regulator endpoint.

    Source locationIsolation and mapping of pleiotropic mutants; Identification and cloning of the putative regulator
activates

Positive autoregulation is supported by the MC4100 sdaR-lacZ reporter and loss of induction without functional SdaR; the proposed ligand-activated molecular mechanism was not directly measured.

cdaR
Entrez:944860
  • PMID:10762278

    Source assertion: The sdaR promoter fusion is induced by galactarate, glucarate and glycerate; loss of functional sdaR abolishes activation.

    Source locationRegulation of sdaR expression
galactarate(2-)
CHEBI:16537		activates

Expression-level induction in the tested MC4100 culture/reporter system. The chemical CURIE normalizes the named acid to its defined ionic species; this is not direct ligand binding to CdaR or direct activation of an enzyme. GarK represents the shared garPLRK transcriptional unit.

garD
Entrez:947641
  • PMID:10762278

    Source assertion: Growth or exposure to galactarate, glucarate or glycerate induces the garD/garP transcriptional units and sdaR reporter relative to glycerol; glycerate gives the largest response.

    Source locationCoordinate regulation; Table 1; Expression of the transcriptional units; Figure 2; Regulation of sdaR expression
galactarate(2-)
CHEBI:16537		activates

Expression-level induction in the tested MC4100 culture/reporter system. The chemical CURIE normalizes the named acid to its defined ionic species; this is not direct ligand binding to CdaR or direct activation of an enzyme. GarK represents the shared garPLRK transcriptional unit.

garK
Entrez:947632
  • PMID:10762278

    Source assertion: Growth or exposure to galactarate, glucarate or glycerate induces the garD/garP transcriptional units and sdaR reporter relative to glycerol; glycerate gives the largest response.

    Source locationCoordinate regulation; Table 1; Expression of the transcriptional units; Figure 2; Regulation of sdaR expression
galactarate(2-)
CHEBI:16537		activates

Expression-level induction in the tested MC4100 culture/reporter system. The chemical CURIE normalizes the named acid to its defined ionic species; this is not direct ligand binding to CdaR or direct activation of an enzyme. GarK represents the shared garPLRK transcriptional unit.

cdaR
Entrez:944860
  • PMID:10762278

    Source assertion: Growth or exposure to galactarate, glucarate or glycerate induces the garD/garP transcriptional units and sdaR reporter relative to glycerol; glycerate gives the largest response.

    Source locationCoordinate regulation; Table 1; Expression of the transcriptional units; Figure 2; Regulation of sdaR expression
galactarate(2-)
CHEBI:16537		activates

Expression-level induction in the tested MC4100 culture/reporter system. The chemical CURIE normalizes the named acid to its defined ionic species; this is not direct ligand binding to CdaR or direct activation of an enzyme. GarK represents the shared garPLRK transcriptional unit.

garP
Entrez:947642
  • PMID:10762278

    Source assertion: Growth or exposure to galactarate, glucarate or glycerate induces the garD/garP transcriptional units and sdaR reporter relative to glycerol; glycerate gives the largest response.

    Source locationCoordinate regulation; Table 1; Expression of the transcriptional units; Figure 2; Regulation of sdaR expression
D-glucarate(2-)
CHEBI:30612		activates

Expression-level induction in the tested MC4100 culture/reporter system. The chemical CURIE normalizes the named acid to its defined ionic species; this is not direct ligand binding to CdaR or direct activation of an enzyme. GarK represents the shared garPLRK transcriptional unit.

garD
Entrez:947641
  • PMID:10762278

    Source assertion: Growth or exposure to galactarate, glucarate or glycerate induces the garD/garP transcriptional units and sdaR reporter relative to glycerol; glycerate gives the largest response.

    Source locationCoordinate regulation; Table 1; Expression of the transcriptional units; Figure 2; Regulation of sdaR expression
D-glucarate(2-)
CHEBI:30612		activates

Expression-level induction in the tested MC4100 culture/reporter system. The chemical CURIE normalizes the named acid to its defined ionic species; this is not direct ligand binding to CdaR or direct activation of an enzyme. GarK represents the shared garPLRK transcriptional unit.

garK
Entrez:947632
  • PMID:10762278

    Source assertion: Growth or exposure to galactarate, glucarate or glycerate induces the garD/garP transcriptional units and sdaR reporter relative to glycerol; glycerate gives the largest response.

    Source locationCoordinate regulation; Table 1; Expression of the transcriptional units; Figure 2; Regulation of sdaR expression
D-glucarate(2-)
CHEBI:30612		activates

Expression-level induction in the tested MC4100 culture/reporter system. The chemical CURIE normalizes the named acid to its defined ionic species; this is not direct ligand binding to CdaR or direct activation of an enzyme. GarK represents the shared garPLRK transcriptional unit.

cdaR
Entrez:944860
  • PMID:10762278

    Source assertion: Growth or exposure to galactarate, glucarate or glycerate induces the garD/garP transcriptional units and sdaR reporter relative to glycerol; glycerate gives the largest response.

    Source locationCoordinate regulation; Table 1; Expression of the transcriptional units; Figure 2; Regulation of sdaR expression
D-glucarate(2-)
CHEBI:30612		activates

Expression-level induction in the tested MC4100 culture/reporter system. The chemical CURIE normalizes the named acid to its defined ionic species; this is not direct ligand binding to CdaR or direct activation of an enzyme. GarK represents the shared garPLRK transcriptional unit.

garP
Entrez:947642
  • PMID:10762278

    Source assertion: Growth or exposure to galactarate, glucarate or glycerate induces the garD/garP transcriptional units and sdaR reporter relative to glycerol; glycerate gives the largest response.

    Source locationCoordinate regulation; Table 1; Expression of the transcriptional units; Figure 2; Regulation of sdaR expression
D-glycerate
CHEBI:16659		activates

Expression-level induction in the tested MC4100 culture/reporter system. The chemical CURIE normalizes the named acid to its defined ionic species; this is not direct ligand binding to CdaR or direct activation of an enzyme. GarK represents the shared garPLRK transcriptional unit.

garD
Entrez:947641
  • PMID:10762278

    Source assertion: Growth or exposure to galactarate, glucarate or glycerate induces the garD/garP transcriptional units and sdaR reporter relative to glycerol; glycerate gives the largest response.

    Source locationCoordinate regulation; Table 1; Expression of the transcriptional units; Figure 2; Regulation of sdaR expression
D-glycerate
CHEBI:16659		activates

Expression-level induction in the tested MC4100 culture/reporter system. The chemical CURIE normalizes the named acid to its defined ionic species; this is not direct ligand binding to CdaR or direct activation of an enzyme. GarK represents the shared garPLRK transcriptional unit.

garK
Entrez:947632
  • PMID:10762278

    Source assertion: Growth or exposure to galactarate, glucarate or glycerate induces the garD/garP transcriptional units and sdaR reporter relative to glycerol; glycerate gives the largest response.

    Source locationCoordinate regulation; Table 1; Expression of the transcriptional units; Figure 2; Regulation of sdaR expression
D-glycerate
CHEBI:16659		activates

Expression-level induction in the tested MC4100 culture/reporter system. The chemical CURIE normalizes the named acid to its defined ionic species; this is not direct ligand binding to CdaR or direct activation of an enzyme. GarK represents the shared garPLRK transcriptional unit.

cdaR
Entrez:944860
  • PMID:10762278

    Source assertion: Growth or exposure to galactarate, glucarate or glycerate induces the garD/garP transcriptional units and sdaR reporter relative to glycerol; glycerate gives the largest response.

    Source locationCoordinate regulation; Table 1; Expression of the transcriptional units; Figure 2; Regulation of sdaR expression
D-glycerate
CHEBI:16659		activates

Expression-level induction in the tested MC4100 culture/reporter system. The chemical CURIE normalizes the named acid to its defined ionic species; this is not direct ligand binding to CdaR or direct activation of an enzyme. GarK represents the shared garPLRK transcriptional unit.

garP
Entrez:947642
  • PMID:10762278

    Source assertion: Growth or exposure to galactarate, glucarate or glycerate induces the garD/garP transcriptional units and sdaR reporter relative to glycerol; glycerate gives the largest response.

    Source locationCoordinate regulation; Table 1; Expression of the transcriptional units; Figure 2; Regulation of sdaR expression
Probable galactarate/D-glucarate transporter GarP
UniProtKB:P0AA80		enables

Reviewed annotation proposes GarP-dependent galactarate availability. Uptake is probable (ECO:0000305), not directly measured transport or established proton coupling. This context is separate from the four core biochemical events.

MetaCyc:GALACTARDEG-PWY
  • UniProtKB:P0AA80

    Source assertion: The FUNCTION comment describes probable galactarate and/or D-glucarate uptake, citing ECO:0000305 with PMID10762278 and PMID9772162.

    Source locationcomments[commentType=FUNCTION].texts[0].value; evidences
Probable galactarate/D-glucarate transporter GarP
UniProtKB:P0AA80

experimental construct: BW25113 garP plasmid complementation in the corresponding Keio deletion strain: pCW-lic/tac, 100 µM IPTG, 25°C, 48 h, peptone plus galactarate, acidification endpoint. The reference protein denotes gene-product identity; exact insert sequence, tags and equivalence to MG1655 were not independently established.

Qualification evidence
  • PMID:39875389

    Source assertion: Methods describe Keio strains, pCW-lic gene cloning and induced fermentation assays; these are engineered complementation experiments, not native-expression or purified-protein assays.

    Source locationPar43; Par45; Par47; Fig3 caption
enables

The garP deletion attenuated galactarate fermentation, and native-gene plasmid rescue restored the signal in BW25113 derivatives. This pH endpoint supports pathway participation; it does not measure exact chemistry, transport coupling, reductant specificity or assembly. The figure names BL21 as the positive comparator.

MetaCyc:GALACTARDEG-PWY
  • PMID:39875389

    Source assertion: The garP deletion and native-gene rescue differ in the 48-hour galactarate fermentation endpoint; methods identify the Keio BW25113 deletion library and inducible complementation.

    Source locationPar15; Par18; Par43; Par45; Par47; Fig3B
5-keto-4-deoxy-D-glucarate aldolase
UniProtKB:P23522

experimental construct: BW25113 garL plasmid complementation in the corresponding Keio deletion strain: pCW-lic/tac, 100 µM IPTG, 25°C, 48 h, peptone plus galactarate, acidification endpoint. The reference protein denotes gene-product identity; exact insert sequence, tags and equivalence to MG1655 were not independently established.

Qualification evidence
  • PMID:39875389

    Source assertion: Methods describe Keio strains, pCW-lic gene cloning and induced fermentation assays; these are engineered complementation experiments, not native-expression or purified-protein assays.

    Source locationPar43; Par45; Par47; Fig3 caption
enables

The garL deletion markedly diminished galactarate fermentation, and native-gene plasmid rescue restored the signal in BW25113 derivatives. This pH endpoint supports pathway participation; it does not measure exact chemistry, transport coupling, reductant specificity or assembly. The figure names BL21 as the positive comparator.

MetaCyc:GALACTARDEG-PWY
  • PMID:39875389

    Source assertion: The garL deletion and native-gene rescue differ in the 48-hour galactarate fermentation endpoint; methods identify the Keio BW25113 deletion library and inducible complementation.

    Source locationPar15; Par18; Par43; Par45; Par47; Fig3C
2-hydroxy-3-oxopropionate reductase
UniProtKB:P0ABQ2

experimental construct: BW25113 garR plasmid complementation in the corresponding Keio deletion strain: pCW-lic/tac, 100 µM IPTG, 25°C, 48 h, peptone plus galactarate, acidification endpoint. The reference protein denotes gene-product identity; exact insert sequence, tags and equivalence to MG1655 were not independently established.

Qualification evidence
  • PMID:39875389

    Source assertion: Methods describe Keio strains, pCW-lic gene cloning and induced fermentation assays; these are engineered complementation experiments, not native-expression or purified-protein assays.

    Source locationPar43; Par45; Par47; Fig3 caption
enables

The garR deletion attenuated galactarate fermentation, and native-gene plasmid rescue restored the signal in BW25113 derivatives. This pH endpoint supports pathway participation; it does not measure exact chemistry, transport coupling, reductant specificity or assembly. The figure names BL21 as the positive comparator.

MetaCyc:GALACTARDEG-PWY
  • PMID:39875389

    Source assertion: The garR deletion and native-gene rescue differ in the 48-hour galactarate fermentation endpoint; methods identify the Keio BW25113 deletion library and inducible complementation.

    Source locationPar15; Par18; Par43; Par45; Par47; Fig3D
Escherichia coli str. K-12 substr. MG1655
NCBITaxon:511145		enables

The native pathway species annotation identifies the MG1655 reference context. This is a curated database assertion; it does not relabel MC4100 experiments as MG1655.

MetaCyc:GALACTARDEG-PWY
  • MetaCyc:GALACTARDEG-PWY

    Source assertion: The species object identifies E. coli K-12 MG1655 and NCBI Taxonomy 511145; the broader Bacteria taxonomic-range is a different slot.

    Source location/ptools-xml/Pathway/species/Organism; dblink[dblink-db="NCBI-TAXONOMY-DB"]
Escherichia coli K-12
NCBITaxon:83333		enables

MC4100 and its named derivatives provide bounded E. coli K-12 growth and enzyme-expression evidence. This does not establish all strains or all Bacteria as experimentally characterized.

MetaCyc:GALACTARDEG-PWY
  • PMID:10762278

    Source assertion: MC4100 grown aerobically on galactarate has measurable galactarate dehydratase, tartronate-semialdehyde reductase and glycerate-kinase activities; mutant/complementation tests address utilization.

    Source locationCoordinate regulation; Table 1; Identification and cloning of the putative regulator

References

Curation history