Reduced ferredoxin
KEGG:C00138 | consumes Stoichiometric coefficient 2; derived acid-base normalization of native KEGG R01196, with generic ferredoxin identity and unmeasured proton bookkeeping. | pyruvate:ferredoxin 2-oxidoreductase (CoA-acetylating)
KEGG:R01196 | - KEGG:R01196
Source assertion: Native R01196 defines reversible acetyl-CoA/CO2 reduction with two reduced-to-oxidized generic ferredoxins and two H+. The selected KEGG:C00138 substrates coefficient 2 uses an explicitly derived one-H+ normalization of its acid reference forms. Source locationOriginal flatfile ENTRY R01196; NAME; DEFINITION; EQUATION; MODULE M00374 - KEGG:C00024
Source assertion: The native batch gives acetyl-CoA C23H38N7O17P3S, CoA C21H36N7O16P3S and C00022 C3H4O3. Equal four-proton CoA shifts cancel; deprotonating product pyruvic acid releases one H+, reducing net input from two to one. This is derived bookkeeping. Source locationOriginal five-entry batch ENTRY C00024/C00010/C00022; FORMULA; DBLINKS ChEBI - KEGG:C00138
Source assertion: The native Compound name denotes a generic ferredoxin redox state without a formula or a specific carrier accession or Fe-S cluster stoichiometry. It is not equated to a particular Rhea Fe-S protein class. Source locationOriginal flatfile ENTRY; NAME; no FORMULA field
|
acetyl-CoA(4-)
CHEBI:57288 | consumes Stoichiometric coefficient 1; derived acid-base normalization of native KEGG R01196, with generic ferredoxin identity and unmeasured proton bookkeeping. | pyruvate:ferredoxin 2-oxidoreductase (CoA-acetylating)
KEGG:R01196 | - KEGG:R01196
Source assertion: Native R01196 defines reversible acetyl-CoA/CO2 reduction with two reduced-to-oxidized generic ferredoxins and two H+. The selected CHEBI:57288 substrates coefficient 1 uses an explicitly derived one-H+ normalization of its acid reference forms. Source locationOriginal flatfile ENTRY R01196; NAME; DEFINITION; EQUATION; MODULE M00374 - KEGG:C00024
Source assertion: The native batch gives acetyl-CoA C23H38N7O17P3S, CoA C21H36N7O16P3S and C00022 C3H4O3. Equal four-proton CoA shifts cancel; deprotonating product pyruvic acid releases one H+, reducing net input from two to one. This is derived bookkeeping. Source locationOriginal five-entry batch ENTRY C00024/C00010/C00022; FORMULA; DBLINKS ChEBI - CHEBI:15361
Source assertion: ChEBI defines pyruvate as the conjugate base of pyruvic acid. The selected CoA and acetyl-CoA tetraanions each lose four H relative to the KEGG acid formulas; this does not change their carbon skeletons. Source locationChEBI255 CHEBI:15361 IAO:0000115/formula; CHEBI:57287 and CHEBI:57288 definitions/formulas; acid forms CHEBI:32816/15346/15351
|
carbon dioxide
CHEBI:16526 | consumes Stoichiometric coefficient 1; derived acid-base normalization of native KEGG R01196, with generic ferredoxin identity and unmeasured proton bookkeeping. | pyruvate:ferredoxin 2-oxidoreductase (CoA-acetylating)
KEGG:R01196 | - KEGG:R01196
Source assertion: Native R01196 defines reversible acetyl-CoA/CO2 reduction with two reduced-to-oxidized generic ferredoxins and two H+. The selected CHEBI:16526 substrates coefficient 1 uses an explicitly derived one-H+ normalization of its acid reference forms. Source locationOriginal flatfile ENTRY R01196; NAME; DEFINITION; EQUATION; MODULE M00374 - KEGG:C00024
Source assertion: The native batch gives acetyl-CoA C23H38N7O17P3S, CoA C21H36N7O16P3S and C00022 C3H4O3. Equal four-proton CoA shifts cancel; deprotonating product pyruvic acid releases one H+, reducing net input from two to one. This is derived bookkeeping. Source locationOriginal five-entry batch ENTRY C00024/C00010/C00022; FORMULA; DBLINKS ChEBI
|
hydron
CHEBI:15378 | consumes Stoichiometric coefficient 1; derived acid-base normalization of native KEGG R01196, with generic ferredoxin identity and unmeasured proton bookkeeping. | pyruvate:ferredoxin 2-oxidoreductase (CoA-acetylating)
KEGG:R01196 | - KEGG:R01196
Source assertion: Native R01196 defines reversible acetyl-CoA/CO2 reduction with two reduced-to-oxidized generic ferredoxins and two H+. The selected CHEBI:15378 substrates coefficient 1 uses an explicitly derived one-H+ normalization of its acid reference forms. Source locationOriginal flatfile ENTRY R01196; NAME; DEFINITION; EQUATION; MODULE M00374 - KEGG:C00024
Source assertion: The native batch gives acetyl-CoA C23H38N7O17P3S, CoA C21H36N7O16P3S and C00022 C3H4O3. Equal four-proton CoA shifts cancel; deprotonating product pyruvic acid releases one H+, reducing net input from two to one. This is derived bookkeeping. Source locationOriginal five-entry batch ENTRY C00024/C00010/C00022; FORMULA; DBLINKS ChEBI - CHEBI:15361
Source assertion: ChEBI defines pyruvate as the conjugate base of pyruvic acid. The selected CoA and acetyl-CoA tetraanions each lose four H relative to the KEGG acid formulas; this does not change their carbon skeletons. Source locationChEBI255 CHEBI:15361 IAO:0000115/formula; CHEBI:57287 and CHEBI:57288 definitions/formulas; acid forms CHEBI:32816/15346/15351
|
pyruvate:ferredoxin 2-oxidoreductase (CoA-acetylating)
KEGG:R01196 | produces Stoichiometric coefficient 2; derived acid-base normalization of native KEGG R01196, with generic ferredoxin identity and unmeasured proton bookkeeping. | Oxidized ferredoxin
KEGG:C00139 | - KEGG:R01196
Source assertion: Native R01196 defines reversible acetyl-CoA/CO2 reduction with two reduced-to-oxidized generic ferredoxins and two H+. The selected KEGG:C00139 products coefficient 2 uses an explicitly derived one-H+ normalization of its acid reference forms. Source locationOriginal flatfile ENTRY R01196; NAME; DEFINITION; EQUATION; MODULE M00374 - KEGG:C00024
Source assertion: The native batch gives acetyl-CoA C23H38N7O17P3S, CoA C21H36N7O16P3S and C00022 C3H4O3. Equal four-proton CoA shifts cancel; deprotonating product pyruvic acid releases one H+, reducing net input from two to one. This is derived bookkeeping. Source locationOriginal five-entry batch ENTRY C00024/C00010/C00022; FORMULA; DBLINKS ChEBI - KEGG:C00139
Source assertion: The native Compound name denotes a generic ferredoxin redox state without a formula or a specific carrier accession or Fe-S cluster stoichiometry. It is not equated to a particular Rhea Fe-S protein class. Source locationOriginal flatfile ENTRY; NAME; no FORMULA field
|
pyruvate:ferredoxin 2-oxidoreductase (CoA-acetylating)
KEGG:R01196 | produces Stoichiometric coefficient 1; derived acid-base normalization of native KEGG R01196, with generic ferredoxin identity and unmeasured proton bookkeeping. | pyruvate
CHEBI:15361 | - KEGG:R01196
Source assertion: Native R01196 defines reversible acetyl-CoA/CO2 reduction with two reduced-to-oxidized generic ferredoxins and two H+. The selected CHEBI:15361 products coefficient 1 uses an explicitly derived one-H+ normalization of its acid reference forms. Source locationOriginal flatfile ENTRY R01196; NAME; DEFINITION; EQUATION; MODULE M00374 - KEGG:C00024
Source assertion: The native batch gives acetyl-CoA C23H38N7O17P3S, CoA C21H36N7O16P3S and C00022 C3H4O3. Equal four-proton CoA shifts cancel; deprotonating product pyruvic acid releases one H+, reducing net input from two to one. This is derived bookkeeping. Source locationOriginal five-entry batch ENTRY C00024/C00010/C00022; FORMULA; DBLINKS ChEBI - CHEBI:15361
Source assertion: ChEBI defines pyruvate as the conjugate base of pyruvic acid. The selected CoA and acetyl-CoA tetraanions each lose four H relative to the KEGG acid formulas; this does not change their carbon skeletons. Source locationChEBI255 CHEBI:15361 IAO:0000115/formula; CHEBI:57287 and CHEBI:57288 definitions/formulas; acid forms CHEBI:32816/15346/15351
|
pyruvate:ferredoxin 2-oxidoreductase (CoA-acetylating)
KEGG:R01196 | produces Stoichiometric coefficient 1; derived acid-base normalization of native KEGG R01196, with generic ferredoxin identity and unmeasured proton bookkeeping. | coenzyme A(4-)
CHEBI:57287 | - KEGG:R01196
Source assertion: Native R01196 defines reversible acetyl-CoA/CO2 reduction with two reduced-to-oxidized generic ferredoxins and two H+. The selected CHEBI:57287 products coefficient 1 uses an explicitly derived one-H+ normalization of its acid reference forms. Source locationOriginal flatfile ENTRY R01196; NAME; DEFINITION; EQUATION; MODULE M00374 - KEGG:C00024
Source assertion: The native batch gives acetyl-CoA C23H38N7O17P3S, CoA C21H36N7O16P3S and C00022 C3H4O3. Equal four-proton CoA shifts cancel; deprotonating product pyruvic acid releases one H+, reducing net input from two to one. This is derived bookkeeping. Source locationOriginal five-entry batch ENTRY C00024/C00010/C00022; FORMULA; DBLINKS ChEBI - CHEBI:15361
Source assertion: ChEBI defines pyruvate as the conjugate base of pyruvic acid. The selected CoA and acetyl-CoA tetraanions each lose four H relative to the KEGG acid formulas; this does not change their carbon skeletons. Source locationChEBI255 CHEBI:15361 IAO:0000115/formula; CHEBI:57287 and CHEBI:57288 definitions/formulas; acid forms CHEBI:32816/15346/15351
|
pyruvate
CHEBI:15361 | consumes Stoichiometric coefficient 1. | pyruvate + ATP + H2O => phosphoenolpyruvate + AMP + phosphate + 2 H(+)
RHEA:11365 | |
ATP(4-)
CHEBI:30616 | consumes Stoichiometric coefficient 1. | pyruvate + ATP + H2O => phosphoenolpyruvate + AMP + phosphate + 2 H(+)
RHEA:11365 | |
water
CHEBI:15377 | consumes Stoichiometric coefficient 1. | pyruvate + ATP + H2O => phosphoenolpyruvate + AMP + phosphate + 2 H(+)
RHEA:11365 | |
pyruvate + ATP + H2O => phosphoenolpyruvate + AMP + phosphate + 2 H(+)
RHEA:11365 | produces Stoichiometric coefficient 1. | phosphonatoenolpyruvate
CHEBI:58702 | |
pyruvate + ATP + H2O => phosphoenolpyruvate + AMP + phosphate + 2 H(+)
RHEA:11365 | produces Stoichiometric coefficient 1. | adenosine 5'-monophosphate(2-)
CHEBI:456215 | |
pyruvate + ATP + H2O => phosphoenolpyruvate + AMP + phosphate + 2 H(+)
RHEA:11365 | produces Stoichiometric coefficient 1. | hydrogenphosphate
CHEBI:43474 | |
pyruvate + ATP + H2O => phosphoenolpyruvate + AMP + phosphate + 2 H(+)
RHEA:11365 | produces Stoichiometric coefficient 2. | hydron
CHEBI:15378 | |
phosphonatoenolpyruvate
CHEBI:58702 | consumes Stoichiometric coefficient 1. | phosphoenolpyruvate + hydrogencarbonate => oxaloacetate + phosphate
RHEA:28372 | |
hydrogencarbonate
CHEBI:17544 | consumes Stoichiometric coefficient 1. | phosphoenolpyruvate + hydrogencarbonate => oxaloacetate + phosphate
RHEA:28372 | |
phosphoenolpyruvate + hydrogencarbonate => oxaloacetate + phosphate
RHEA:28372 | produces Stoichiometric coefficient 1. | oxaloacetate(2-)
CHEBI:16452 | |
phosphoenolpyruvate + hydrogencarbonate => oxaloacetate + phosphate
RHEA:28372 | produces Stoichiometric coefficient 1. | hydrogenphosphate
CHEBI:43474 | |
oxaloacetate(2-)
CHEBI:16452 | consumes Stoichiometric coefficient 1. | oxaloacetate + NADH + H(+) => (S)-malate + NAD(+)
RHEA:21434 | |
NADH(2-)
CHEBI:57945 | consumes Stoichiometric coefficient 1. | oxaloacetate + NADH + H(+) => (S)-malate + NAD(+)
RHEA:21434 | |
hydron
CHEBI:15378 | consumes Stoichiometric coefficient 1. | oxaloacetate + NADH + H(+) => (S)-malate + NAD(+)
RHEA:21434 | |
oxaloacetate + NADH + H(+) => (S)-malate + NAD(+)
RHEA:21434 | produces Stoichiometric coefficient 1. | (S)-malate(2-)
CHEBI:15589 | |
oxaloacetate + NADH + H(+) => (S)-malate + NAD(+)
RHEA:21434 | produces Stoichiometric coefficient 1. | NAD(1-)
CHEBI:57540 | |
(S)-malate(2-)
CHEBI:15589 | consumes Stoichiometric coefficient 1. | (S)-malate => fumarate + H2O
RHEA:12461 | |
(S)-malate => fumarate + H2O
RHEA:12461 | produces Stoichiometric coefficient 1. | fumarate(2-)
CHEBI:29806 | |
(S)-malate => fumarate + H2O
RHEA:12461 | produces Stoichiometric coefficient 1. | water
CHEBI:15377 | |
fumarate(2-)
CHEBI:29806 | consumes Stoichiometric coefficient 1. | fumarate + AH2 => succinate + A
RHEA:16359 | |
hydrogen donor
CHEBI:17499 | consumes Stoichiometric coefficient 1. | fumarate + AH2 => succinate + A
RHEA:16359 | |
fumarate + AH2 => succinate + A
RHEA:16359 | produces Stoichiometric coefficient 1. | succinate(2-)
CHEBI:30031 | |
fumarate + AH2 => succinate + A
RHEA:16359 | produces Stoichiometric coefficient 1. | hydrogen acceptor
CHEBI:13193 | |
succinate(2-)
CHEBI:30031 | consumes Stoichiometric coefficient 1. | succinate + ATP + CoA => succinyl-CoA + ADP + phosphate
RHEA:17662 | |
ATP(4-)
CHEBI:30616 | consumes Stoichiometric coefficient 1. | succinate + ATP + CoA => succinyl-CoA + ADP + phosphate
RHEA:17662 | |
coenzyme A(4-)
CHEBI:57287 | consumes Stoichiometric coefficient 1. | succinate + ATP + CoA => succinyl-CoA + ADP + phosphate
RHEA:17662 | |
succinate + ATP + CoA => succinyl-CoA + ADP + phosphate
RHEA:17662 | produces Stoichiometric coefficient 1. | succinyl-CoA(5-)
CHEBI:57292 | |
succinate + ATP + CoA => succinyl-CoA + ADP + phosphate
RHEA:17662 | produces Stoichiometric coefficient 1. | ADP(3-)
CHEBI:456216 | |
succinate + ATP + CoA => succinyl-CoA + ADP + phosphate
RHEA:17662 | produces Stoichiometric coefficient 1. | hydrogenphosphate
CHEBI:43474 | |
succinyl-CoA(5-)
CHEBI:57292 | consumes Stoichiometric coefficient 1. | succinyl-CoA + NADPH + H(+) => succinate semialdehyde + NADP(+) + CoA
RHEA:26452 | |
NADPH(4-)
CHEBI:57783 | consumes Stoichiometric coefficient 1. | succinyl-CoA + NADPH + H(+) => succinate semialdehyde + NADP(+) + CoA
RHEA:26452 | |
hydron
CHEBI:15378 | consumes Stoichiometric coefficient 1. | succinyl-CoA + NADPH + H(+) => succinate semialdehyde + NADP(+) + CoA
RHEA:26452 | |
succinyl-CoA + NADPH + H(+) => succinate semialdehyde + NADP(+) + CoA
RHEA:26452 | produces Stoichiometric coefficient 1. | 4-oxobutanoate
CHEBI:57706 | |
succinyl-CoA + NADPH + H(+) => succinate semialdehyde + NADP(+) + CoA
RHEA:26452 | produces Stoichiometric coefficient 1. | NADP(3-)
CHEBI:58349 | |
succinyl-CoA + NADPH + H(+) => succinate semialdehyde + NADP(+) + CoA
RHEA:26452 | produces Stoichiometric coefficient 1. | coenzyme A(4-)
CHEBI:57287 | |
4-oxobutanoate
CHEBI:57706 | consumes Stoichiometric coefficient 1. | succinate semialdehyde + NADPH + H(+) => 4-hydroxybutanoate + NADP(+)
RHEA:26383 | |
NADPH(4-)
CHEBI:57783 | consumes Stoichiometric coefficient 1. | succinate semialdehyde + NADPH + H(+) => 4-hydroxybutanoate + NADP(+)
RHEA:26383 | |
hydron
CHEBI:15378 | consumes Stoichiometric coefficient 1. | succinate semialdehyde + NADPH + H(+) => 4-hydroxybutanoate + NADP(+)
RHEA:26383 | |
succinate semialdehyde + NADPH + H(+) => 4-hydroxybutanoate + NADP(+)
RHEA:26383 | produces Stoichiometric coefficient 1. | 4-hydroxybutyrate
CHEBI:16724 | |
succinate semialdehyde + NADPH + H(+) => 4-hydroxybutanoate + NADP(+)
RHEA:26383 | produces Stoichiometric coefficient 1. | NADP(3-)
CHEBI:58349 | |
4-hydroxybutyrate
CHEBI:16724 | consumes Stoichiometric coefficient 1. | 4-hydroxybutanoate + ATP + CoA => 4-hydroxybutanoyl-CoA + AMP + diphosphate
RHEA:23129 | |
ATP(4-)
CHEBI:30616 | consumes Stoichiometric coefficient 1. | 4-hydroxybutanoate + ATP + CoA => 4-hydroxybutanoyl-CoA + AMP + diphosphate
RHEA:23129 | |
coenzyme A(4-)
CHEBI:57287 | consumes Stoichiometric coefficient 1. | 4-hydroxybutanoate + ATP + CoA => 4-hydroxybutanoyl-CoA + AMP + diphosphate
RHEA:23129 | |
4-hydroxybutanoate + ATP + CoA => 4-hydroxybutanoyl-CoA + AMP + diphosphate
RHEA:23129 | produces Stoichiometric coefficient 1. | 4-hydroxybutyryl-CoA(4-)
CHEBI:58574 | |
4-hydroxybutanoate + ATP + CoA => 4-hydroxybutanoyl-CoA + AMP + diphosphate
RHEA:23129 | produces Stoichiometric coefficient 1. | adenosine 5'-monophosphate(2-)
CHEBI:456215 | |
4-hydroxybutanoate + ATP + CoA => 4-hydroxybutanoyl-CoA + AMP + diphosphate
RHEA:23129 | produces Stoichiometric coefficient 1. | diphosphate(3-)
CHEBI:33019 | |
4-hydroxybutyryl-CoA(4-)
CHEBI:58574 | consumes Stoichiometric coefficient 1. | 4-hydroxybutanoyl-CoA => (2E)-butenoyl-CoA + H2O
RHEA:26531 | |
4-hydroxybutanoyl-CoA => (2E)-butenoyl-CoA + H2O
RHEA:26531 | produces Stoichiometric coefficient 1. | crotonoyl-CoA(4-)
CHEBI:57332 | |
4-hydroxybutanoyl-CoA => (2E)-butenoyl-CoA + H2O
RHEA:26531 | produces Stoichiometric coefficient 1. | water
CHEBI:15377 | |
crotonoyl-CoA(4-)
CHEBI:57332 | consumes Stoichiometric coefficient 1. | (2E)-butenoyl-CoA + H2O => (3S)-3-hydroxybutanoyl-CoA
RHEA:26560 | |
water
CHEBI:15377 | consumes Stoichiometric coefficient 1. | (2E)-butenoyl-CoA + H2O => (3S)-3-hydroxybutanoyl-CoA
RHEA:26560 | |
(2E)-butenoyl-CoA + H2O => (3S)-3-hydroxybutanoyl-CoA
RHEA:26560 | produces Stoichiometric coefficient 1. | (S)-3-hydroxybutanoyl-CoA(4-)
CHEBI:57316 | |
(S)-3-hydroxybutanoyl-CoA(4-)
CHEBI:57316 | consumes Stoichiometric coefficient 1. | (3S)-3-hydroxybutanoyl-CoA + NAD(+) => acetoacetyl-CoA + NADH + H(+)
RHEA:30800 | |
NAD(1-)
CHEBI:57540 | consumes Stoichiometric coefficient 1. | (3S)-3-hydroxybutanoyl-CoA + NAD(+) => acetoacetyl-CoA + NADH + H(+)
RHEA:30800 | |
(3S)-3-hydroxybutanoyl-CoA + NAD(+) => acetoacetyl-CoA + NADH + H(+)
RHEA:30800 | produces Stoichiometric coefficient 1. | acetoacetyl-CoA(4-)
CHEBI:57286 | |
(3S)-3-hydroxybutanoyl-CoA + NAD(+) => acetoacetyl-CoA + NADH + H(+)
RHEA:30800 | produces Stoichiometric coefficient 1. | NADH(2-)
CHEBI:57945 | |
(3S)-3-hydroxybutanoyl-CoA + NAD(+) => acetoacetyl-CoA + NADH + H(+)
RHEA:30800 | produces Stoichiometric coefficient 1. | hydron
CHEBI:15378 | |
acetoacetyl-CoA(4-)
CHEBI:57286 | consumes Stoichiometric coefficient 1. | acetoacetyl-CoA + CoA => 2 acetyl-CoA
RHEA:21038 | |
coenzyme A(4-)
CHEBI:57287 | consumes Stoichiometric coefficient 1. | acetoacetyl-CoA + CoA => 2 acetyl-CoA
RHEA:21038 | |
acetoacetyl-CoA + CoA => 2 acetyl-CoA
RHEA:21038 | produces Stoichiometric coefficient 2. | acetyl-CoA(4-)
CHEBI:57288 | |
pyruvate:ferredoxin 2-oxidoreductase (CoA-acetylating)
KEGG:R01196 | part_of Cycle step 1. Cell-extract activity; four alternative locus groups are proposed. Do not choose one exact complex or prove its composition from name matching. Rhea formal 2Fe-2S carrier class is not measured Tneu cluster identity; native KEGG uses generic ferredoxin. Preserve assay/carrier distinction. | KEGG:M00374 | - KEGG:M00374
Source assertion: The complete module includes native KEGG:R01196; its fourteen reaction objects define the full cycle. The organism-specific step 1 is separately supported by the primary activity study, rather than inferred from module membership alone. Source locationOriginal flatfile ENTRY M00374; REACTION R01196; DEFINITION - PMID:19411323
Source assertion: Pyruvate-acceptor oxidoreductase was measured with methyl viologen; pyruvate-carboxyl 14CO2 exchange was also measured. These assays do not identify the physiological ferredoxin or select among the candidate locus groups. Source locationPMC2698501 HTML //*[@id="sec5"]/p[2] - PMID:19411323
Source assertion: Figure 1 identifies cycle enzyme 1; Table 1 reports the corresponding activity in autotrophic T. neutrophilus extracts and lists candidate loci. Temperature-extrapolated values are distinguished from measured activities. Source locationPMC2698501 HTML //*[@id="f1"]; //table[1] and its footnotes
|
pyruvate + ATP + H2O => phosphoenolpyruvate + AMP + phosphate + 2 H(+)
RHEA:11365 | part_of Cycle step 2. ATP/AMP + phosphate reaction; primary observes PEP formation with extract. Current protein assignment is annotation/candidate tier, not a purified construct. | KEGG:M00374 | - KEGG:M00374
Source assertion: The complete module includes native KEGG:R00199; its fourteen reaction objects define the full cycle. The organism-specific step 2 is separately supported by the primary activity study, rather than inferred from module membership alone. Source locationOriginal flatfile ENTRY M00374; REACTION R00199; DEFINITION - PMID:19411323
Source assertion: Extract pyruvate-water dikinase formed PEP with ATP; a discontinuous PEP assay was used. This is the AMP/phosphate-forming reaction, not an inferred pyruvate-kinase reversal. Source locationPMC2698501 HTML //*[@id="sec5"]/p[3] - PMID:19411323
Source assertion: Figure 1 identifies cycle enzyme 2; Table 1 reports the corresponding activity in autotrophic T. neutrophilus extracts and lists candidate loci. Temperature-extrapolated values are distinguished from measured activities. Source locationPMC2698501 HTML //*[@id="f1"]; //table[1] and its footnotes - RHEA:11365
Source assertion: Rhea master 11364 explicitly includes directional member 11365; its current sides supply the selected chemical microstates. This grounds chemical orientation, not T. neutrophilus activity. Source locationRDF142 <http://rdf.rhea-db.org/11364> rh:directionalReaction <http://rdf.rhea-db.org/11365>; <http://rdf.rhea-db.org/11365> rh:substrates/rh:products/rdfs:label; official rhea-directions.tsv master 11364
|
phosphoenolpyruvate + hydrogencarbonate => oxaloacetate + phosphate
RHEA:28372 | part_of Cycle step 3. Cell-extract direct activity; exact locus is a primary candidate/current HAMAP assignment. Mn2+ is present in assay, not automatically a demonstrated native occupancy requirement. | KEGG:M00374 | - KEGG:M00374
Source assertion: The complete module includes native KEGG:R00345; its fourteen reaction objects define the full cycle. The organism-specific step 3 is separately supported by the primary activity study, rather than inferred from module membership alone. Source locationOriginal flatfile ENTRY M00374; REACTION R00345; DEFINITION - PMID:19411323
Source assertion: PEP carboxylase activity was measured by coupled NADH oxidation and radiochemical bicarbonate incorporation. MnCl2 was an assay component, not a demonstrated native metal-occupancy result. Source locationPMC2698501 HTML //*[@id="sec5"]/p[6] - PMID:19411323
Source assertion: Figure 1 identifies cycle enzyme 3; Table 1 reports the corresponding activity in autotrophic T. neutrophilus extracts and lists candidate loci. Temperature-extrapolated values are distinguished from measured activities. Source locationPMC2698501 HTML //*[@id="f1"]; //table[1] and its footnotes - RHEA:28372
Source assertion: Rhea master 28370 explicitly includes directional member 28372; its current sides supply the selected chemical microstates. This grounds chemical orientation, not T. neutrophilus activity. Source locationRDF142 <http://rdf.rhea-db.org/28370> rh:directionalReaction <http://rdf.rhea-db.org/28372>; <http://rdf.rhea-db.org/28372> rh:substrates/rh:products/rdfs:label; official rhea-directions.tsv master 28370
|
oxaloacetate + NADH + H(+) => (S)-malate + NAD(+)
RHEA:21434 | part_of Cycle step 4. NADH-dependent extract assay; use the NADH-specific reaction, not the preferred NADPH function of different I. hospitalis Mdh. | KEGG:M00374 | - KEGG:M00374
Source assertion: The complete module includes native KEGG:R00342; its fourteen reaction objects define the full cycle. The organism-specific step 4 is separately supported by the primary activity study, rather than inferred from module membership alone. Source locationOriginal flatfile ENTRY M00374; REACTION R00342; DEFINITION - PMID:19411323
Source assertion: Extract malate dehydrogenase was measured by oxaloacetate-dependent NADH oxidation. This record preserves that NADH-dependent chemistry. Source locationPMC2698501 HTML //*[@id="sec5"]/p[8] - PMID:19411323
Source assertion: Figure 1 identifies cycle enzyme 4; Table 1 reports the corresponding activity in autotrophic T. neutrophilus extracts and lists candidate loci. Temperature-extrapolated values are distinguished from measured activities. Source locationPMC2698501 HTML //*[@id="f1"]; //table[1] and its footnotes - RHEA:21434
Source assertion: Rhea master 21432 explicitly includes directional member 21434; its current sides supply the selected chemical microstates. This grounds chemical orientation, not T. neutrophilus activity. Source locationRDF142 <http://rdf.rhea-db.org/21432> rh:directionalReaction <http://rdf.rhea-db.org/21434>; <http://rdf.rhea-db.org/21434> rh:substrates/rh:products/rdfs:label; official rhea-directions.tsv master 21432
|
(S)-malate => fumarate + H2O
RHEA:12461 | part_of Cycle step 5. Cell-extract activity, candidate two-subunit locus. Current names are tartrate/fumarate-family proteins, including submitted EC4.2.1.32; no direct purified Tneu assembly or obligatory stoichiometry established. | KEGG:M00374 | - KEGG:M00374
Source assertion: The complete module includes native KEGG:R01082; its fourteen reaction objects define the full cycle. The organism-specific step 5 is separately supported by the primary activity study, rather than inferred from module membership alone. Source locationOriginal flatfile ENTRY M00374; REACTION R01082; DEFINITION - PMID:19411323
Source assertion: Extract fumarate hydratase was assayed anaerobically with D,L-malate. The selected stereospecific physiological malate reaction is separately grounded in Rhea. Source locationPMC2698501 HTML //*[@id="sec5"]/p[9] - PMID:19411323
Source assertion: Figure 1 identifies cycle enzyme 5; Table 1 reports the corresponding activity in autotrophic T. neutrophilus extracts and lists candidate loci. Temperature-extrapolated values are distinguished from measured activities. Source locationPMC2698501 HTML //*[@id="f1"]; //table[1] and its footnotes - RHEA:12461
Source assertion: Rhea master 12460 explicitly includes directional member 12461; its current sides supply the selected chemical microstates. This grounds chemical orientation, not T. neutrophilus activity. Source locationRDF142 <http://rdf.rhea-db.org/12460> rh:directionalReaction <http://rdf.rhea-db.org/12461>; <http://rdf.rhea-db.org/12461> rh:substrates/rh:products/rdfs:label; official rhea-directions.tsv master 12460
|
fumarate + AH2 => succinate + A
RHEA:16359 | part_of Cycle step 6. Reduced methyl viologen works in vitro; NAD(P)H does not. Soluble activity and putative induced subunits are supported. Disposition KEGG quinol equation R02164; use source-issued generic A/AH2 Rhea chemistry with an unknown physiological-donor qualification. No quinol or particular ferredoxin claim. | KEGG:M00374 | - KEGG:M00374
Source assertion: The complete module includes native KEGG:R02164; its fourteen reaction objects define the full cycle. The organism-specific step 6 is separately supported by the primary activity study, rather than inferred from module membership alone. Source locationOriginal flatfile ENTRY M00374; REACTION R02164; DEFINITION - PMID:19411323
Source assertion: Extract fumarate reductase used reduced methyl viologen. This assay does not establish quinol or a specific ferredoxin as its physiological electron donor. Source locationPMC2698501 HTML //*[@id="sec5"]/p[10] - PMID:19411323
Source assertion: Figure 1 identifies cycle enzyme 6; Table 1 reports the corresponding activity in autotrophic T. neutrophilus extracts and lists candidate loci. Temperature-extrapolated values are distinguished from measured activities. Source locationPMC2698501 HTML //*[@id="f1"]; //table[1] and its footnotes - RHEA:16359
Source assertion: Rhea master 16357 explicitly includes directional member 16359; its current sides supply the selected chemical microstates. This grounds chemical orientation, not T. neutrophilus activity. Source locationRDF142 <http://rdf.rhea-db.org/16357> rh:directionalReaction <http://rdf.rhea-db.org/16359>; <http://rdf.rhea-db.org/16359> rh:substrates/rh:products/rdfs:label; official rhea-directions.tsv master 16357 - PMID:21169482
Source assertion: T. neutrophilus fumarate reductase was soluble and active with reduced viologens but not NAD(P)H. Tneu_0423/0424 are putative induced subunits. Generic A/AH2 retains the unresolved physiological donor instead of native module quinol chemistry. Source locationPMC3067573 HTML //*[@id="sec27"]/p[1]
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succinate + ATP + CoA => succinyl-CoA + ADP + phosphate
RHEA:17662 | part_of Cycle step 7. Direct extract reaction with M. sedula coupling enzyme. Current HAMAP subunits are inferred; do not attribute the coupling enzyme or its NADPH to Tneu synthetase. | KEGG:M00374 | - KEGG:M00374
Source assertion: The complete module includes native KEGG:R00405; its fourteen reaction objects define the full cycle. The organism-specific step 7 is separately supported by the primary activity study, rather than inferred from module membership alone. Source locationOriginal flatfile ENTRY M00374; REACTION R00405; DEFINITION - PMID:19411323
Source assertion: Extract succinyl-CoA synthetase used succinate, ATP and CoA, coupled to recombinant M. sedula reductase. NADPH belonged to the coupling reaction, not the synthetase stoichiometry. Source locationPMC2698501 HTML //*[@id="sec5"]/p[11] - PMID:19411323
Source assertion: Figure 1 identifies cycle enzyme 7; Table 1 reports the corresponding activity in autotrophic T. neutrophilus extracts and lists candidate loci. Temperature-extrapolated values are distinguished from measured activities. Source locationPMC2698501 HTML //*[@id="f1"]; //table[1] and its footnotes - RHEA:17662
Source assertion: Rhea master 17661 explicitly includes directional member 17662; its current sides supply the selected chemical microstates. This grounds chemical orientation, not T. neutrophilus activity. Source locationRDF142 <http://rdf.rhea-db.org/17661> rh:directionalReaction <http://rdf.rhea-db.org/17662>; <http://rdf.rhea-db.org/17662> rh:substrates/rh:products/rdfs:label; official rhea-directions.tsv master 17661
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succinyl-CoA + NADPH + H(+) => succinate semialdehyde + NADP(+) + CoA
RHEA:26452 | part_of Cycle step 8. Direct purified N-terminal His10-tagged Tneu_0421 expressed in E. coli. NADPH preferred, NADH10%; no malonyl-/methylmalonyl-CoA activity. Current homotetramer is ARBA inference, not the measured experiment. Exact I. hospitalis function/donor cannot be transferred. | KEGG:M00374 | - KEGG:M00374
Source assertion: The complete module includes native KEGG:R09280; its fourteen reaction objects define the full cycle. The organism-specific step 8 is separately supported by the primary activity study, rather than inferred from module membership alone. Source locationOriginal flatfile ENTRY M00374; REACTION R09280; DEFINITION - PMID:19411323
Source assertion: Extract succinyl-CoA reductase was measured with succinyl-CoA and NADPH. The T. neutrophilus reaction is distinguished from the donor-unspecified I. hospitalis activity. Source locationPMC2698501 HTML //*[@id="sec5"]/p[12] - PMID:19411323
Source assertion: Figure 1 identifies cycle enzyme 8; Table 1 reports the corresponding activity in autotrophic T. neutrophilus extracts and lists candidate loci. Temperature-extrapolated values are distinguished from measured activities. Source locationPMC2698501 HTML //*[@id="f1"]; //table[1] and its footnotes - RHEA:26452
Source assertion: Rhea master 26450 explicitly includes directional member 26452; its current sides supply the selected chemical microstates. This grounds chemical orientation, not T. neutrophilus activity. Source locationRDF142 <http://rdf.rhea-db.org/26450> rh:directionalReaction <http://rdf.rhea-db.org/26452>; <http://rdf.rhea-db.org/26452> rh:substrates/rh:products/rdfs:label; official rhea-directions.tsv master 26450
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succinate semialdehyde + NADPH + H(+) => 4-hydroxybutanoate + NADP(+)
RHEA:26383 | part_of Cycle step 9. Direct purified N-terminal His10-tagged Tneu_0419. NADPH is supported; Zn2+ in current UniProt is ARBA/RuleBase inference, not direct primary metal analysis. | KEGG:M00374 | - KEGG:M00374
Source assertion: The complete module includes native KEGG:R09281; its fourteen reaction objects define the full cycle. The organism-specific step 9 is separately supported by the primary activity study, rather than inferred from module membership alone. Source locationOriginal flatfile ENTRY M00374; REACTION R09281; DEFINITION - PMID:19411323
Source assertion: Extract succinic semialdehyde reductase was measured with succinic semialdehyde and NADPH. Source locationPMC2698501 HTML //*[@id="sec5"]/p[12] - PMID:19411323
Source assertion: Figure 1 identifies cycle enzyme 9; Table 1 reports the corresponding activity in autotrophic T. neutrophilus extracts and lists candidate loci. Temperature-extrapolated values are distinguished from measured activities. Source locationPMC2698501 HTML //*[@id="f1"]; //table[1] and its footnotes - RHEA:26383
Source assertion: Rhea master 26381 explicitly includes directional member 26383; its current sides supply the selected chemical microstates. This grounds chemical orientation, not T. neutrophilus activity. Source locationRDF142 <http://rdf.rhea-db.org/26381> rh:directionalReaction <http://rdf.rhea-db.org/26383>; <http://rdf.rhea-db.org/26383> rh:substrates/rh:products/rdfs:label; official rhea-directions.tsv master 26381
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4-hydroxybutanoate + ATP + CoA => 4-hydroxybutanoyl-CoA + AMP + diphosphate
RHEA:23129 | part_of Cycle step 10. Purified recombinant protein acts on4HB; low activity linked to Lys594 acetylation in E. coli expression. Native archaeal regulation by acetylation is not established. This verified Tneu ligase must not inherit the failed I. hospitalis0256/0257 assignment. | KEGG:M00374 | - KEGG:M00374
Source assertion: The complete module includes native KEGG:R09279; its fourteen reaction objects define the full cycle. The organism-specific step 10 is separately supported by the primary activity study, rather than inferred from module membership alone. Source locationOriginal flatfile ENTRY M00374; REACTION R09279; DEFINITION - PMID:19411323
Source assertion: 4-Hydroxybutyrate-CoA ligase was measured with 4-hydroxybutyrate, ATP and CoA by discontinuous CoA consumption. Source locationPMC2698501 HTML //*[@id="sec5"]/p[13] - PMID:19411323
Source assertion: Figure 1 identifies cycle enzyme 10; Table 1 reports the corresponding activity in autotrophic T. neutrophilus extracts and lists candidate loci. Temperature-extrapolated values are distinguished from measured activities. Source locationPMC2698501 HTML //*[@id="f1"]; //table[1] and its footnotes - RHEA:23129
Source assertion: Rhea master 23128 explicitly includes directional member 23129; its current sides supply the selected chemical microstates. This grounds chemical orientation, not T. neutrophilus activity. Source locationRDF142 <http://rdf.rhea-db.org/23128> rh:directionalReaction <http://rdf.rhea-db.org/23129>; <http://rdf.rhea-db.org/23129> rh:substrates/rh:products/rdfs:label; official rhea-directions.tsv master 23128
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4-hydroxybutanoyl-CoA => (2E)-butenoyl-CoA + H2O
RHEA:26531 | part_of Cycle step 11. Direct extract conversion/coupled assay plus sequence-based Tneu_0422 attribution. No purified Tneu cofactor or assembly measurement in these sources; do not transfer clostridial Fe-S/FAD occupancy or oligomeric data as direct Tneu evidence. | KEGG:M00374 | - KEGG:M00374
Source assertion: The complete module includes native KEGG:R10782; its fourteen reaction objects define the full cycle. The organism-specific step 11 is separately supported by the primary activity study, rather than inferred from module membership alone. Source locationOriginal flatfile ENTRY M00374; REACTION R10782; DEFINITION - PMID:19411323
Source assertion: Extract 4-hydroxybutyryl-CoA dehydratase was assayed by detecting crotonyl-CoA with an added R. sphaeroides coupling enzyme; coupling-enzyme cofactors are not transferred. Source locationPMC2698501 HTML //*[@id="sec5"]/p[14] - PMID:19411323
Source assertion: Figure 1 identifies cycle enzyme 11; Table 1 reports the corresponding activity in autotrophic T. neutrophilus extracts and lists candidate loci. Temperature-extrapolated values are distinguished from measured activities. Source locationPMC2698501 HTML //*[@id="f1"]; //table[1] and its footnotes - RHEA:26531
Source assertion: Rhea master 26530 explicitly includes directional member 26531; its current sides supply the selected chemical microstates. This grounds chemical orientation, not T. neutrophilus activity. Source locationRDF142 <http://rdf.rhea-db.org/26530> rh:directionalReaction <http://rdf.rhea-db.org/26531>; <http://rdf.rhea-db.org/26531> rh:substrates/rh:products/rdfs:label; official rhea-directions.tsv master 26530
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(2E)-butenoyl-CoA + H2O => (3S)-3-hydroxybutanoyl-CoA
RHEA:26560 | part_of Cycle step 12. S-specific cell-extract activity is direct. The2011 purified bifunctional protein was Msed_0399; Tneu_0541 role is inferred from orthology/domain structure and unique candidate, not direct Tneu recombinant demonstration. Current monomer annotation is inferred. | KEGG:M00374 | - KEGG:M00374
Source assertion: The complete module includes native KEGG:R03026; its fourteen reaction objects define the full cycle. The organism-specific step 12 is separately supported by the primary activity study, rather than inferred from module membership alone. Source locationOriginal flatfile ENTRY M00374; REACTION R03026; DEFINITION - PMID:19411323
Source assertion: Crotonyl-CoA hydratase was assayed in reverse with (R)- or (S)-3-hydroxybutyryl-CoA. Activity occurred only with the (S) substrate. Source locationPMC2698501 HTML //*[@id="sec5"]/p[15] - PMID:19411323
Source assertion: Figure 1 identifies cycle enzyme 12; Table 1 reports the corresponding activity in autotrophic T. neutrophilus extracts and lists candidate loci. Temperature-extrapolated values are distinguished from measured activities. Source locationPMC2698501 HTML //*[@id="f1"]; //table[1] and its footnotes - RHEA:26560
Source assertion: Rhea master 26558 explicitly includes directional member 26560; its current sides supply the selected chemical microstates. This grounds chemical orientation, not T. neutrophilus activity. Source locationRDF142 <http://rdf.rhea-db.org/26558> rh:directionalReaction <http://rdf.rhea-db.org/26560>; <http://rdf.rhea-db.org/26560> rh:substrates/rh:products/rdfs:label; official rhea-directions.tsv master 26558
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(3S)-3-hydroxybutanoyl-CoA + NAD(+) => acetoacetyl-CoA + NADH + H(+)
RHEA:30800 | part_of Cycle step 13. NAD+ and S substrate supported in Tneu extract; NADP+ and R stereoisomer inactive. Same exact Tneu fusion-protein assignment limit as step12; no direct Msed construct transfer. | KEGG:M00374 | - KEGG:M00374
Source assertion: The complete module includes native KEGG:R01975; its fourteen reaction objects define the full cycle. The organism-specific step 13 is separately supported by the primary activity study, rather than inferred from module membership alone. Source locationOriginal flatfile ENTRY M00374; REACTION R01975; DEFINITION - PMID:19411323
Source assertion: Extract (S)-3-hydroxybutyryl-CoA dehydrogenase reduced NAD+. No activity was detected with NADP+ or the (R) substrate. Source locationPMC2698501 HTML //*[@id="sec5"]/p[16] - PMID:19411323
Source assertion: Figure 1 identifies cycle enzyme 13; Table 1 reports the corresponding activity in autotrophic T. neutrophilus extracts and lists candidate loci. Temperature-extrapolated values are distinguished from measured activities. Source locationPMC2698501 HTML //*[@id="f1"]; //table[1] and its footnotes - RHEA:30800
Source assertion: Rhea master 30799 explicitly includes directional member 30800; its current sides supply the selected chemical microstates. This grounds chemical orientation, not T. neutrophilus activity. Source locationRDF142 <http://rdf.rhea-db.org/30799> rh:directionalReaction <http://rdf.rhea-db.org/30800>; <http://rdf.rhea-db.org/30800> rh:substrates/rh:products/rdfs:label; official rhea-directions.tsv master 30799
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acetoacetyl-CoA + CoA => 2 acetyl-CoA
RHEA:21038 | part_of Cycle step 14. Direct soluble N-terminal His10-tagged Tneu_0249 expressed in E. coli, purified thiolytic cleavage. No arbitrary standalone monomer sufficiency/complex ID. | KEGG:M00374 | - KEGG:M00374
Source assertion: The complete module includes native KEGG:R00238; its fourteen reaction objects define the full cycle. The organism-specific step 14 is separately supported by the primary activity study, rather than inferred from module membership alone. Source locationOriginal flatfile ENTRY M00374; REACTION R00238; DEFINITION - PMID:19411323
Source assertion: Thiolase activity was measured by HPLC detection of acetyl-CoA from acetoacetyl-CoA and CoA. Source locationPMC2698501 HTML //*[@id="sec5"]/p[17] - PMID:19411323
Source assertion: Figure 1 identifies cycle enzyme 14; Table 1 reports the corresponding activity in autotrophic T. neutrophilus extracts and lists candidate loci. Temperature-extrapolated values are distinguished from measured activities. Source locationPMC2698501 HTML //*[@id="f1"]; //table[1] and its footnotes - RHEA:21038
Source assertion: Rhea master 21036 explicitly includes directional member 21038; its current sides supply the selected chemical microstates. This grounds chemical orientation, not T. neutrophilus activity. Source locationRDF142 <http://rdf.rhea-db.org/21036> rh:directionalReaction <http://rdf.rhea-db.org/21038>; <http://rdf.rhea-db.org/21038> rh:substrates/rh:products/rdfs:label; official rhea-directions.tsv master 21036
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Phosphoenolpyruvate synthase
UniProtKB:B1Y8Q3 | enables Functional assignment of Tneu_1204; ATP/AMP + phosphate reaction; primary observes PEP formation with extract. Current protein assignment is annotation/candidate tier, not a purified construct. | pyruvate + ATP + H2O => phosphoenolpyruvate + AMP + phosphate + 2 H(+)
RHEA:11365 | - PMID:19411323
Source assertion: Tneu_1204 is a candidate pyruvate-water dikinase in Table 1; the measured activity is from extract, not purified Tneu_1204. Source locationPMC2698501 HTML //*[@id="sec5"]/p[3]; (//table)[1] column Putative gene(s) in T. neutrophilus - UniProtKB:B1Y8Q3
Source assertion: This unreviewed entry identifies Tneu_1204 as UniProtKB:B1Y8Q3 in strain DSM 2338/V24Sta (taxon 444157). The locus/sequence bridge supports identity; it does not independently turn the primary candidate assignment into a purified-protein result. Source location/results/2/primaryAccession; /results/2/genes; /results/2/organism; /results/2/sequence; /results/2/uniProtKBCrossReferences - PMID:19411323
Source assertion: Table 1 lists Tneu_1204 among the putative genes for cycle activity 2; direct activity is measured in cell extract. Source locationPMC2698501 HTML //table[1] column Putative gene(s) in T. neutrophilus - UniProtKB:B1Y8Q3
Source assertion: The current unreviewed catalytic annotation cites RHEA:11364 with ECO:0000256 automated rule inference. It supports a qualified functional assignment, not direct experimental validation of this protein. Source location/results/2/comments/1/reaction
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Phosphoenolpyruvate carboxylase
UniProtKB:B1YBY2 | enables Functional assignment of Tneu_0418; Cell-extract direct activity; exact locus is a primary candidate/current HAMAP assignment. Mn2+ is present in assay, not automatically a demonstrated native occupancy requirement. | phosphoenolpyruvate + hydrogencarbonate => oxaloacetate + phosphate
RHEA:28372 | - PMID:19411323
Source assertion: Tneu_0418 is the Table 1 candidate PEP carboxylase; activity is demonstrated in extract, not purified Tneu_0418. Source locationPMC2698501 HTML //*[@id="sec5"]/p[6]; (//table)[1] column Putative gene(s) in T. neutrophilus - UniProtKB:B1YBY2
Source assertion: This unreviewed entry identifies Tneu_0418 as UniProtKB:B1YBY2 in strain DSM 2338/V24Sta (taxon 444157). The locus/sequence bridge supports identity; it does not independently turn the primary candidate assignment into a purified-protein result. Source location/results/12/primaryAccession; /results/12/genes; /results/12/organism; /results/12/sequence; /results/12/uniProtKBCrossReferences - PMID:19411323
Source assertion: Table 1 lists Tneu_0418 among the putative genes for cycle activity 3; direct activity is measured in cell extract. Source locationPMC2698501 HTML //table[1] column Putative gene(s) in T. neutrophilus - UniProtKB:B1YBY2
Source assertion: The current unreviewed catalytic annotation cites RHEA:28370 with ECO:0000256 automated rule inference. It supports a qualified functional assignment, not direct experimental validation of this protein. Source location/results/12/comments/1/reaction - UniProtKB:B1YBY2
Source assertion: The current homotetramer annotation is HAMAP ECO:0000256 inference, not an assembly measurement in the primary extract assays. Source location/results/12/comments/3
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Malate dehydrogenase
UniProtKB:B1Y9K4 | enables Functional assignment of Tneu_1509; NADH-dependent extract assay; use the NADH-specific reaction, not the preferred NADPH function of different I. hospitalis Mdh. | oxaloacetate + NADH + H(+) => (S)-malate + NAD(+)
RHEA:21434 | - PMID:19411323
Source assertion: Tneu_1509 is the Table 1 candidate malate dehydrogenase; the NADH-dependent reaction is demonstrated in extract. Source locationPMC2698501 HTML //*[@id="sec5"]/p[8]; (//table)[1] column Putative gene(s) in T. neutrophilus - UniProtKB:B1Y9K4
Source assertion: This unreviewed entry identifies Tneu_1509 as UniProtKB:B1Y9K4 in strain DSM 2338/V24Sta (taxon 444157). The locus/sequence bridge supports identity; it does not independently turn the primary candidate assignment into a purified-protein result. Source location/results/9/primaryAccession; /results/9/genes; /results/9/organism; /results/9/sequence; /results/9/uniProtKBCrossReferences - PMID:19411323
Source assertion: Table 1 lists Tneu_1509 among the putative genes for cycle activity 4; direct activity is measured in cell extract. Source locationPMC2698501 HTML //table[1] column Putative gene(s) in T. neutrophilus
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Hydro-lyase, Fe-S type, tartrate/fumarate subfamily, beta subunit
UniProtKB:B1Y931 | enables Functional assignment of Tneu_1334; Cell-extract activity, candidate two-subunit locus. Current names are tartrate/fumarate-family proteins, including submitted EC4.2.1.32; no direct purified Tneu assembly or obligatory stoichiometry established. | (S)-malate => fumarate + H2O
RHEA:12461 | - PMID:19411323
Source assertion: Table 1 assigns Tneu_1334/1335 as putative fumarate-hydratase subunits. The direct activity is in extract; individual subunit sufficiency and exact assembly stoichiometry were not measured. Source locationPMC2698501 HTML //*[@id="sec5"]/p[9]; (//table)[1] column Putative gene(s) in T. neutrophilus - UniProtKB:B1Y931
Source assertion: This unreviewed entry identifies Tneu_1334 as UniProtKB:B1Y931 in strain DSM 2338/V24Sta (taxon 444157). The locus/sequence bridge supports identity; it does not independently turn the primary candidate assignment into a purified-protein result. Source location/results/14/primaryAccession; /results/14/genes; /results/14/organism; /results/14/sequence; /results/14/uniProtKBCrossReferences - PMID:19411323
Source assertion: Table 1 lists Tneu_1334 among the putative genes for cycle activity 5; direct activity is measured in cell extract. Source locationPMC2698501 HTML //table[1] column Putative gene(s) in T. neutrophilus
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Hydro-lyase, Fe-S type, tartrate/fumarate subfamily, alpha subunit
UniProtKB:B1Y932 | enables Functional assignment of Tneu_1335; Cell-extract activity, candidate two-subunit locus. Current names are tartrate/fumarate-family proteins, including submitted EC4.2.1.32; no direct purified Tneu assembly or obligatory stoichiometry established. | (S)-malate => fumarate + H2O
RHEA:12461 | - PMID:19411323
Source assertion: Table 1 assigns Tneu_1334/1335 as putative fumarate-hydratase subunits. The direct activity is in extract; individual subunit sufficiency and exact assembly stoichiometry were not measured. Source locationPMC2698501 HTML //*[@id="sec5"]/p[9]; (//table)[1] column Putative gene(s) in T. neutrophilus - UniProtKB:B1Y932
Source assertion: This unreviewed entry identifies Tneu_1335 as UniProtKB:B1Y932 in strain DSM 2338/V24Sta (taxon 444157). The locus/sequence bridge supports identity; it does not independently turn the primary candidate assignment into a purified-protein result. Source location/results/22/primaryAccession; /results/22/genes; /results/22/organism; /results/22/sequence; /results/22/uniProtKBCrossReferences - PMID:19411323
Source assertion: Table 1 lists Tneu_1335 among the putative genes for cycle activity 5; direct activity is measured in cell extract. Source locationPMC2698501 HTML //table[1] column Putative gene(s) in T. neutrophilus
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succinate dehydrogenase
UniProtKB:B1YBY7 | enables Functional assignment of Tneu_0423; Reduced methyl viologen works in vitro; NAD(P)H does not. Soluble activity and putative induced subunits are supported. Disposition KEGG quinol equation R02164; use source-issued generic A/AH2 Rhea chemistry with an unknown physiological-donor qualification. No quinol or particular ferredoxin claim. | fumarate + AH2 => succinate + A
RHEA:16359 | - PMID:21169482
Source assertion: Tneu_0423/0424 are putative fumarate-reductase subunits induced during autotrophic growth. Soluble extract activity uses reduced viologens, not NAD(P)H; neither isolated subunit is asserted to catalyze the whole reaction. Source locationPMC3067573 HTML //*[@id="sec27"]/p[1] - UniProtKB:B1YBY7
Source assertion: This unreviewed entry identifies Tneu_0423 as UniProtKB:B1YBY7 in strain DSM 2338/V24Sta (taxon 444157). The locus/sequence bridge supports identity; it does not independently turn the primary candidate assignment into a purified-protein result. Source location/results/13/primaryAccession; /results/13/genes; /results/13/organism; /results/13/sequence; /results/13/uniProtKBCrossReferences
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Ferredoxin
UniProtKB:B1YBY8 | enables Functional assignment of Tneu_0424; Reduced methyl viologen works in vitro; NAD(P)H does not. Soluble activity and putative induced subunits are supported. Disposition KEGG quinol equation R02164; use source-issued generic A/AH2 Rhea chemistry with an unknown physiological-donor qualification. No quinol or particular ferredoxin claim. | fumarate + AH2 => succinate + A
RHEA:16359 | - PMID:21169482
Source assertion: Tneu_0423/0424 are putative fumarate-reductase subunits induced during autotrophic growth. Soluble extract activity uses reduced viologens, not NAD(P)H; neither isolated subunit is asserted to catalyze the whole reaction. Source locationPMC3067573 HTML //*[@id="sec27"]/p[1] - UniProtKB:B1YBY8
Source assertion: This unreviewed entry identifies Tneu_0424 as UniProtKB:B1YBY8 in strain DSM 2338/V24Sta (taxon 444157). The locus/sequence bridge supports identity; it does not independently turn the primary candidate assignment into a purified-protein result. Source location/results/18/primaryAccession; /results/18/genes; /results/18/organism; /results/18/sequence; /results/18/uniProtKBCrossReferences
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Succinate--CoA ligase [ADP-forming] subunit beta
UniProtKB:B1Y9F9 | enables Functional assignment of Tneu_1463; Direct extract reaction with M. sedula coupling enzyme. Current HAMAP subunits are inferred; do not attribute the coupling enzyme or its NADPH to Tneu synthetase. | succinate + ATP + CoA => succinyl-CoA + ADP + phosphate
RHEA:17662 | - PMID:21169482
Source assertion: Tneu_1463 and Tneu_1464 are the two autotrophy-induced succinyl-CoA synthetase subunits. Their joint role does not establish that each independently catalyzes the reaction. Source locationPMC3067573 HTML //*[@id="sec29"]/p[1] - UniProtKB:B1Y9F9
Source assertion: This unreviewed entry identifies Tneu_1463 as UniProtKB:B1Y9F9 in strain DSM 2338/V24Sta (taxon 444157). The locus/sequence bridge supports identity; it does not independently turn the primary candidate assignment into a purified-protein result. Source location/results/0/primaryAccession; /results/0/genes; /results/0/organism; /results/0/sequence; /results/0/uniProtKBCrossReferences - UniProtKB:B1Y9F9
Source assertion: The current unreviewed catalytic annotation cites RHEA:17661 with ECO:0000256 automated rule inference. It supports a qualified functional assignment, not direct experimental validation of this protein. Source location/results/0/comments/2/reaction - UniProtKB:B1Y9F9
Source assertion: Current HAMAP/RuleBase annotation describes a heterotetramer with two alpha and two beta subunits. This is ECO:0000256 inference, not a demonstrated native Tneu assembly. Source location/results/0/comments/5
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Succinate--CoA ligase [ADP-forming] subunit alpha
UniProtKB:B1Y9G0 | enables Functional assignment of Tneu_1464; Direct extract reaction with M. sedula coupling enzyme. Current HAMAP subunits are inferred; do not attribute the coupling enzyme or its NADPH to Tneu synthetase. | succinate + ATP + CoA => succinyl-CoA + ADP + phosphate
RHEA:17662 | - PMID:21169482
Source assertion: Tneu_1463 and Tneu_1464 are the two autotrophy-induced succinyl-CoA synthetase subunits. Their joint role does not establish that each independently catalyzes the reaction. Source locationPMC3067573 HTML //*[@id="sec29"]/p[1] - UniProtKB:B1Y9G0
Source assertion: This unreviewed entry identifies Tneu_1464 as UniProtKB:B1Y9G0 in strain DSM 2338/V24Sta (taxon 444157). The locus/sequence bridge supports identity; it does not independently turn the primary candidate assignment into a purified-protein result. Source location/results/1/primaryAccession; /results/1/genes; /results/1/organism; /results/1/sequence; /results/1/uniProtKBCrossReferences - UniProtKB:B1Y9G0
Source assertion: The current unreviewed catalytic annotation cites RHEA:17661 with ECO:0000256 automated rule inference. It supports a qualified functional assignment, not direct experimental validation of this protein. Source location/results/1/comments/2/reaction - UniProtKB:B1Y9G0
Source assertion: Current HAMAP/RuleBase annotation describes a heterotetramer with two alpha and two beta subunits. This is ECO:0000256 inference, not a demonstrated native Tneu assembly. Source location/results/1/comments/4
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Aldehyde Dehydrogenase
UniProtKB:B1YBY5 | enables Functional assignment of Tneu_0421; Direct purified N-terminal His10-tagged Tneu_0421 expressed in E. coli. NADPH preferred, NADH10%; no malonyl-/methylmalonyl-CoA activity. Current homotetramer is ARBA inference, not the measured experiment. Exact I. hospitalis function/donor cannot be transferred. | succinyl-CoA + NADPH + H(+) => succinate semialdehyde + NADP(+) + CoA
RHEA:26452 | - PMID:21169482
Source assertion: Tneu_0421 was expressed in E. coli as soluble N-terminal His10-tagged protein and purified. It reduced succinyl-CoA with NADPH, with 10% activity using NADH; malonyl-CoA and methylmalonyl-CoA were inactive. Source locationPMC3067573 HTML //*[@id="sec20"]/p[1] - UniProtKB:B1YBY5
Source assertion: This unreviewed entry identifies Tneu_0421 as UniProtKB:B1YBY5 in strain DSM 2338/V24Sta (taxon 444157). The locus/sequence bridge supports identity; it does not independently turn the primary candidate assignment into a purified-protein result. Source location/results/27/primaryAccession; /results/27/genes; /results/27/organism; /results/27/sequence; /results/27/uniProtKBCrossReferences - UniProtKB:B1YBY5
Source assertion: The current homotetramer annotation is ARBA ECO:0000256 inference. The functional edge neither asserts a measured assembly nor a catalytically sufficient monomer. Source location/results/27/comments/0
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Alcohol dehydrogenase zinc-binding domain protein
UniProtKB:B1YBY3 | enables Functional assignment of Tneu_0419; Direct purified N-terminal His10-tagged Tneu_0419. NADPH is supported; Zn2+ in current UniProt is ARBA/RuleBase inference, not direct primary metal analysis. | succinate semialdehyde + NADPH + H(+) => 4-hydroxybutanoate + NADP(+)
RHEA:26383 | - PMID:21169482
Source assertion: Tneu_0419 was expressed in E. coli as soluble N-terminal His10-tagged protein and purified. It catalyzed NADPH-dependent reduction of succinic semialdehyde. Source locationPMC3067573 HTML //*[@id="sec21"]/p[1] - UniProtKB:B1YBY3
Source assertion: This unreviewed entry identifies Tneu_0419 as UniProtKB:B1YBY3 in strain DSM 2338/V24Sta (taxon 444157). The locus/sequence bridge supports identity; it does not independently turn the primary candidate assignment into a purified-protein result. Source location/results/17/primaryAccession; /results/17/genes; /results/17/organism; /results/17/sequence; /results/17/uniProtKBCrossReferences
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AMP-dependent synthetase and ligase
UniProtKB:B1YBY4 | enables Functional assignment of Tneu_0420; Purified recombinant protein acts on4HB; low activity linked to Lys594 acetylation in E. coli expression. Native archaeal regulation by acetylation is not established. This verified Tneu ligase must not inherit the failed I. hospitalis0256/0257 assignment. | 4-hydroxybutanoate + ATP + CoA => 4-hydroxybutanoyl-CoA + AMP + diphosphate
RHEA:23129 | - PMID:21169482
Source assertion: Purified recombinant Tneu_0420 acted on 4-hydroxybutyrate. Lys594 acetylation was detected in the E. coli-produced protein and may be an expression artifact; native archaeal regulatory acetylation is not established. Source locationPMC3067573 HTML //*[@id="sec22"]/p[1] - UniProtKB:B1YBY4
Source assertion: This unreviewed entry identifies Tneu_0420 as UniProtKB:B1YBY4 in strain DSM 2338/V24Sta (taxon 444157). The locus/sequence bridge supports identity; it does not independently turn the primary candidate assignment into a purified-protein result. Source location/results/26/primaryAccession; /results/26/genes; /results/26/organism; /results/26/sequence; /results/26/uniProtKBCrossReferences
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Vinylacetyl-CoA Delta-isomerase
UniProtKB:B1YBY6 | enables Functional assignment of Tneu_0422; Direct extract conversion/coupled assay plus sequence-based Tneu_0422 attribution. No purified Tneu cofactor or assembly measurement in these sources; do not transfer clostridial Fe-S/FAD occupancy or oligomeric data as direct Tneu evidence. | 4-hydroxybutanoyl-CoA => (2E)-butenoyl-CoA + H2O
RHEA:26531 | - PMID:21169482
Source assertion: Tneu_0422 is assigned by sequence similarity alongside extract dehydratase activity. Purified T. neutrophilus enzyme, assembly and Fe-S/FAD occupancy were not demonstrated in this study. Source locationPMC3067573 HTML //*[@id="sec23"]/p[1] - UniProtKB:B1YBY6
Source assertion: This unreviewed entry identifies Tneu_0422 as UniProtKB:B1YBY6 in strain DSM 2338/V24Sta (taxon 444157). The locus/sequence bridge supports identity; it does not independently turn the primary candidate assignment into a purified-protein result. Source location/results/20/primaryAccession; /results/20/genes; /results/20/organism; /results/20/sequence; /results/20/uniProtKBCrossReferences
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3-hydroxyacyl-CoA dehydrogenase NAD-binding
UniProtKB:B1YCH1 | enables Functional assignment of Tneu_0541; S-specific cell-extract activity is direct. The2011 purified bifunctional protein was Msed_0399; Tneu_0541 role is inferred from orthology/domain structure and unique candidate, not direct Tneu recombinant demonstration. Current monomer annotation is inferred. | (2E)-butenoyl-CoA + H2O => (3S)-3-hydroxybutanoyl-CoA
RHEA:26560 | - PMID:21169482
Source assertion: Tneu_0541 is a candidate hydratase/dehydrogenase fusion identified by domain similarity. The purified native and recombinant enzyme tested in this section is Msed_0399, not Tneu_0541. Source locationPMC3067573 HTML //*[@id="sec24"]/p[1] for the candidate fusion; //*[@id="sec24"]/p[2] for native and recombinant Msed_0399 characterization - UniProtKB:B1YCH1
Source assertion: This unreviewed entry identifies Tneu_0541 as UniProtKB:B1YCH1 in strain DSM 2338/V24Sta (taxon 444157). The locus/sequence bridge supports identity; it does not independently turn the primary candidate assignment into a purified-protein result. Source location/results/21/primaryAccession; /results/21/genes; /results/21/organism; /results/21/sequence; /results/21/uniProtKBCrossReferences - UniProtKB:B1YCH1
Source assertion: The current monomer annotation is ARBA ECO:0000256 inference; no experimental Tneu_0541 oligomeric state is claimed. Source location/results/21/comments/1
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3-hydroxyacyl-CoA dehydrogenase NAD-binding
UniProtKB:B1YCH1 | enables Functional assignment of Tneu_0541; NAD+ and S substrate supported in Tneu extract; NADP+ and R stereoisomer inactive. Same exact Tneu fusion-protein assignment limit as step12; no direct Msed construct transfer. | (3S)-3-hydroxybutanoyl-CoA + NAD(+) => acetoacetyl-CoA + NADH + H(+)
RHEA:30800 | - PMID:21169482
Source assertion: The authors infer that the fusion protein operates in anaerobic crenarchaeal carbon fixation because it is the only candidate for these two activities; this is not a purified Tneu_0541 experiment. Source locationPMC3067573 HTML //*[@id="sec24"]/p[3] - UniProtKB:B1YCH1
Source assertion: This unreviewed entry identifies Tneu_0541 as UniProtKB:B1YCH1 in strain DSM 2338/V24Sta (taxon 444157). The locus/sequence bridge supports identity; it does not independently turn the primary candidate assignment into a purified-protein result. Source location/results/21/primaryAccession; /results/21/genes; /results/21/organism; /results/21/sequence; /results/21/uniProtKBCrossReferences - UniProtKB:B1YCH1
Source assertion: The current monomer annotation is ARBA ECO:0000256 inference; no experimental Tneu_0541 oligomeric state is claimed. Source location/results/21/comments/1
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Acetyl-CoA acetyltransferase
UniProtKB:B1YB71 | enables Functional assignment of Tneu_0249; Direct soluble N-terminal His10-tagged Tneu_0249 expressed in E. coli, purified thiolytic cleavage. No arbitrary standalone monomer sufficiency/complex ID. | acetoacetyl-CoA + CoA => 2 acetyl-CoA
RHEA:21038 | - PMID:21169482
Source assertion: Tneu_0249 was expressed as soluble N-terminal His10-tagged protein in E. coli. The purified enzyme cleaved acetoacetyl-CoA thiolytically into two acetyl-CoA molecules. Source locationPMC3067573 HTML //*[@id="sec25"]/p[1] - UniProtKB:B1YB71
Source assertion: This unreviewed entry identifies Tneu_0249 as UniProtKB:B1YB71 in strain DSM 2338/V24Sta (taxon 444157). The locus/sequence bridge supports identity; it does not independently turn the primary candidate assignment into a purified-protein result. Source location/results/25/primaryAccession; /results/25/genes; /results/25/organism; /results/25/sequence; /results/25/uniProtKBCrossReferences
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Phosphoenolpyruvate synthase
UniProtKB:B1Y8Q3 | has_cofactor Automated cofactor inference retained at its source tier; assay ingredients alone are not treated as a native requirement. | magnesium(2+)
CHEBI:18420 | |
Phosphoenolpyruvate carboxylase
UniProtKB:B1YBY2 | has_cofactor Automated cofactor inference retained at its source tier; assay ingredients alone are not treated as a native requirement. | magnesium(2+)
CHEBI:18420 | |
Succinate--CoA ligase [ADP-forming] subunit beta
UniProtKB:B1Y9F9 | has_cofactor Automated cofactor inference retained at its source tier; assay ingredients alone are not treated as a native requirement. | magnesium(2+)
CHEBI:18420 | |
succinate dehydrogenase
UniProtKB:B1YBY7 | has_cofactor Automated cofactor inference retained at its source tier; assay ingredients alone are not treated as a native requirement. | FAD(3-)
CHEBI:57692 | |
Alcohol dehydrogenase zinc-binding domain protein
UniProtKB:B1YBY3 | has_cofactor Automated cofactor inference retained at its source tier; assay ingredients alone are not treated as a native requirement. | zinc(2+)
CHEBI:29105 | |
pyruvate:ferredoxin 2-oxidoreductase (CoA-acetylating)
KEGG:R01196 | provides_input_for Material continuity through CHEBI:15361; physiological cycle context, not a new thermodynamic irreversibility claim. | pyruvate + ATP + H2O => phosphoenolpyruvate + AMP + phosphate + 2 H(+)
RHEA:11365 | - PMID:19411323
Source assertion: The Figure 1 cycle places activity 1 before activity 2 through the named carbon intermediate. The selected CHEBI:15361 microstate comes from the separately cited current reaction definitions, not from a primary ChEBI identifier. Source locationPMC2698501 HTML //*[@id="f1"] caption and depicted cycle; Results //*[@id="sec18"] - KEGG:R01196
Source assertion: Native R01196 connects acetyl-CoA C00024 and pyruvate C00022 using two generic ferredoxin redox partners and two H+ in its acid-form reference equation. Selected anion normalization is supported by separately cited compound and ChEBI bodies. Source locationOriginal flatfile ENTRY R01196; DEFINITION; EQUATION; RCLASS C00022_C00024 - RHEA:11365
Source assertion: Rhea directed reaction 11365 places CHEBI:15361 on its substrates side with coefficient 1. Source locationRDF142 <http://rdf.rhea-db.org/11365> rh:substrates <http://rdf.rhea-db.org/11364_L>; <http://rdf.rhea-db.org/11364_L> rh:contains1 <http://rdf.rhea-db.org/Participant_11364_compound_3719>; <http://rdf.rhea-db.org/Participant_11364_compound_3719> rh:compound <http://rdf.rhea-db.org/Compound_3719>; compound rh:accession - KEGG:C00024
Source assertion: The original compound batch gives C00024/C00010/C00022 formulas and ChEBI links to acetyl-CoA, CoA and pyruvic acid. These are native acid reference forms; this body alone does not define the selected deprotonated ChEBI forms. Source locationOriginal five-entry batch ENTRY C00024/C00010/C00022; FORMULA; DBLINKS ChEBI:15351/15346/32816 - CHEBI:15361
Source assertion: Original ChEBI forms differ only in protonation: 15351→57288 and 15346→57287 each lose four H; 32816→15361 loses one H. The CoA shifts cancel and product pyruvate deprotonation reduces native input two H+ to one. This is derived bookkeeping, not measured flux. Source locationOriginal ChEBI255 semantic SQL statements for CHEBI:15351/57288, CHEBI:15346/57287, CHEBI:32816/15361; chemrof:generalized_empirical_formula, chemrof:charge, chemrof:inchi_string
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pyruvate + ATP + H2O => phosphoenolpyruvate + AMP + phosphate + 2 H(+)
RHEA:11365 | provides_input_for Material continuity through CHEBI:58702; physiological cycle context, not a new thermodynamic irreversibility claim. | phosphoenolpyruvate + hydrogencarbonate => oxaloacetate + phosphate
RHEA:28372 | - PMID:19411323
Source assertion: The Figure 1 cycle places activity 2 before activity 3 through the named carbon intermediate. The selected CHEBI:58702 microstate comes from the separately cited current reaction definitions, not from a primary ChEBI identifier. Source locationPMC2698501 HTML //*[@id="f1"] caption and depicted cycle; Results //*[@id="sec18"] - RHEA:11365
Source assertion: Rhea directed reaction 11365 places CHEBI:58702 on its products side with coefficient 1. Source locationRDF142 <http://rdf.rhea-db.org/11365> rh:products <http://rdf.rhea-db.org/11364_R>; <http://rdf.rhea-db.org/11364_R> rh:contains1 <http://rdf.rhea-db.org/Participant_11364_compound_3582>; <http://rdf.rhea-db.org/Participant_11364_compound_3582> rh:compound <http://rdf.rhea-db.org/Compound_3582>; compound rh:accession - RHEA:28372
Source assertion: Rhea directed reaction 28372 places CHEBI:58702 on its substrates side with coefficient 1. Source locationRDF142 <http://rdf.rhea-db.org/28372> rh:substrates <http://rdf.rhea-db.org/28370_R>; <http://rdf.rhea-db.org/28370_R> rh:contains1 <http://rdf.rhea-db.org/Participant_28370_compound_3582>; <http://rdf.rhea-db.org/Participant_28370_compound_3582> rh:compound <http://rdf.rhea-db.org/Compound_3582>; compound rh:accession
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phosphoenolpyruvate + hydrogencarbonate => oxaloacetate + phosphate
RHEA:28372 | provides_input_for Material continuity through CHEBI:16452; physiological cycle context, not a new thermodynamic irreversibility claim. | oxaloacetate + NADH + H(+) => (S)-malate + NAD(+)
RHEA:21434 | - PMID:19411323
Source assertion: The Figure 1 cycle places activity 3 before activity 4 through the named carbon intermediate. The selected CHEBI:16452 microstate comes from the separately cited current reaction definitions, not from a primary ChEBI identifier. Source locationPMC2698501 HTML //*[@id="f1"] caption and depicted cycle; Results //*[@id="sec18"] - RHEA:28372
Source assertion: Rhea directed reaction 28372 places CHEBI:16452 on its products side with coefficient 1. Source locationRDF142 <http://rdf.rhea-db.org/28372> rh:products <http://rdf.rhea-db.org/28370_L>; <http://rdf.rhea-db.org/28370_L> rh:contains1 <http://rdf.rhea-db.org/Participant_28370_compound_5219>; <http://rdf.rhea-db.org/Participant_28370_compound_5219> rh:compound <http://rdf.rhea-db.org/Compound_5219>; compound rh:accession - RHEA:21434
Source assertion: Rhea directed reaction 21434 places CHEBI:16452 on its substrates side with coefficient 1. Source locationRDF142 <http://rdf.rhea-db.org/21434> rh:substrates <http://rdf.rhea-db.org/21432_R>; <http://rdf.rhea-db.org/21432_R> rh:contains1 <http://rdf.rhea-db.org/Participant_21432_compound_5219>; <http://rdf.rhea-db.org/Participant_21432_compound_5219> rh:compound <http://rdf.rhea-db.org/Compound_5219>; compound rh:accession
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oxaloacetate + NADH + H(+) => (S)-malate + NAD(+)
RHEA:21434 | provides_input_for Material continuity through CHEBI:15589; physiological cycle context, not a new thermodynamic irreversibility claim. | (S)-malate => fumarate + H2O
RHEA:12461 | - PMID:19411323
Source assertion: The Figure 1 cycle places activity 4 before activity 5 through the named carbon intermediate. The selected CHEBI:15589 microstate comes from the separately cited current reaction definitions, not from a primary ChEBI identifier. Source locationPMC2698501 HTML //*[@id="f1"] caption and depicted cycle; Results //*[@id="sec18"] - RHEA:21434
Source assertion: Rhea directed reaction 21434 places CHEBI:15589 on its products side with coefficient 1. Source locationRDF142 <http://rdf.rhea-db.org/21434> rh:products <http://rdf.rhea-db.org/21432_L>; <http://rdf.rhea-db.org/21432_L> rh:contains1 <http://rdf.rhea-db.org/Participant_21432_compound_3953>; <http://rdf.rhea-db.org/Participant_21432_compound_3953> rh:compound <http://rdf.rhea-db.org/Compound_3953>; compound rh:accession - RHEA:12461
Source assertion: Rhea directed reaction 12461 places CHEBI:15589 on its substrates side with coefficient 1. Source locationRDF142 <http://rdf.rhea-db.org/12461> rh:substrates <http://rdf.rhea-db.org/12460_L>; <http://rdf.rhea-db.org/12460_L> rh:contains1 <http://rdf.rhea-db.org/Participant_12460_compound_3953>; <http://rdf.rhea-db.org/Participant_12460_compound_3953> rh:compound <http://rdf.rhea-db.org/Compound_3953>; compound rh:accession
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(S)-malate => fumarate + H2O
RHEA:12461 | provides_input_for Material continuity through CHEBI:29806; physiological cycle context, not a new thermodynamic irreversibility claim. | fumarate + AH2 => succinate + A
RHEA:16359 | - PMID:19411323
Source assertion: The Figure 1 cycle places activity 5 before activity 6 through the named carbon intermediate. The selected CHEBI:29806 microstate comes from the separately cited current reaction definitions, not from a primary ChEBI identifier. Source locationPMC2698501 HTML //*[@id="f1"] caption and depicted cycle; Results //*[@id="sec18"] - RHEA:12461
Source assertion: Rhea directed reaction 12461 places CHEBI:29806 on its products side with coefficient 1. Source locationRDF142 <http://rdf.rhea-db.org/12461> rh:products <http://rdf.rhea-db.org/12460_R>; <http://rdf.rhea-db.org/12460_R> rh:contains1 <http://rdf.rhea-db.org/Participant_12460_compound_3031>; <http://rdf.rhea-db.org/Participant_12460_compound_3031> rh:compound <http://rdf.rhea-db.org/Compound_3031>; compound rh:accession - RHEA:16359
Source assertion: Rhea directed reaction 16359 places CHEBI:29806 on its substrates side with coefficient 1. Source locationRDF142 <http://rdf.rhea-db.org/16359> rh:substrates <http://rdf.rhea-db.org/16357_R>; <http://rdf.rhea-db.org/16357_R> rh:contains1 <http://rdf.rhea-db.org/Participant_16357_compound_3031>; <http://rdf.rhea-db.org/Participant_16357_compound_3031> rh:compound <http://rdf.rhea-db.org/Compound_3031>; compound rh:accession
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fumarate + AH2 => succinate + A
RHEA:16359 | provides_input_for Material continuity through CHEBI:30031; physiological cycle context, not a new thermodynamic irreversibility claim. | succinate + ATP + CoA => succinyl-CoA + ADP + phosphate
RHEA:17662 | - PMID:19411323
Source assertion: The Figure 1 cycle places activity 6 before activity 7 through the named carbon intermediate. The selected CHEBI:30031 microstate comes from the separately cited current reaction definitions, not from a primary ChEBI identifier. Source locationPMC2698501 HTML //*[@id="f1"] caption and depicted cycle; Results //*[@id="sec18"] - RHEA:16359
Source assertion: Rhea directed reaction 16359 places CHEBI:30031 on its products side with coefficient 1. Source locationRDF142 <http://rdf.rhea-db.org/16359> rh:products <http://rdf.rhea-db.org/16357_L>; <http://rdf.rhea-db.org/16357_L> rh:contains1 <http://rdf.rhea-db.org/Participant_16357_compound_2501>; <http://rdf.rhea-db.org/Participant_16357_compound_2501> rh:compound <http://rdf.rhea-db.org/Compound_2501>; compound rh:accession - RHEA:17662
Source assertion: Rhea directed reaction 17662 places CHEBI:30031 on its substrates side with coefficient 1. Source locationRDF142 <http://rdf.rhea-db.org/17662> rh:substrates <http://rdf.rhea-db.org/17661_L>; <http://rdf.rhea-db.org/17661_L> rh:contains1 <http://rdf.rhea-db.org/Participant_17661_compound_2501>; <http://rdf.rhea-db.org/Participant_17661_compound_2501> rh:compound <http://rdf.rhea-db.org/Compound_2501>; compound rh:accession
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succinate + ATP + CoA => succinyl-CoA + ADP + phosphate
RHEA:17662 | provides_input_for Material continuity through CHEBI:57292; physiological cycle context, not a new thermodynamic irreversibility claim. | succinyl-CoA + NADPH + H(+) => succinate semialdehyde + NADP(+) + CoA
RHEA:26452 | - PMID:19411323
Source assertion: The Figure 1 cycle places activity 7 before activity 8 through the named carbon intermediate. The selected CHEBI:57292 microstate comes from the separately cited current reaction definitions, not from a primary ChEBI identifier. Source locationPMC2698501 HTML //*[@id="f1"] caption and depicted cycle; Results //*[@id="sec18"] - RHEA:17662
Source assertion: Rhea directed reaction 17662 places CHEBI:57292 on its products side with coefficient 1. Source locationRDF142 <http://rdf.rhea-db.org/17662> rh:products <http://rdf.rhea-db.org/17661_R>; <http://rdf.rhea-db.org/17661_R> rh:contains1 <http://rdf.rhea-db.org/Participant_17661_compound_4684>; <http://rdf.rhea-db.org/Participant_17661_compound_4684> rh:compound <http://rdf.rhea-db.org/Compound_4684>; compound rh:accession - RHEA:26452
Source assertion: Rhea directed reaction 26452 places CHEBI:57292 on its substrates side with coefficient 1. Source locationRDF142 <http://rdf.rhea-db.org/26452> rh:substrates <http://rdf.rhea-db.org/26450_R>; <http://rdf.rhea-db.org/26450_R> rh:contains1 <http://rdf.rhea-db.org/Participant_26450_compound_4684>; <http://rdf.rhea-db.org/Participant_26450_compound_4684> rh:compound <http://rdf.rhea-db.org/Compound_4684>; compound rh:accession
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succinyl-CoA + NADPH + H(+) => succinate semialdehyde + NADP(+) + CoA
RHEA:26452 | provides_input_for Material continuity through CHEBI:57706; physiological cycle context, not a new thermodynamic irreversibility claim. | succinate semialdehyde + NADPH + H(+) => 4-hydroxybutanoate + NADP(+)
RHEA:26383 | - PMID:19411323
Source assertion: The Figure 1 cycle places activity 8 before activity 9 through the named carbon intermediate. The selected CHEBI:57706 microstate comes from the separately cited current reaction definitions, not from a primary ChEBI identifier. Source locationPMC2698501 HTML //*[@id="f1"] caption and depicted cycle; Results //*[@id="sec18"] - RHEA:26452
Source assertion: Rhea directed reaction 26452 places CHEBI:57706 on its products side with coefficient 1. Source locationRDF142 <http://rdf.rhea-db.org/26452> rh:products <http://rdf.rhea-db.org/26450_L>; <http://rdf.rhea-db.org/26450_L> rh:contains1 <http://rdf.rhea-db.org/Participant_26450_compound_4279>; <http://rdf.rhea-db.org/Participant_26450_compound_4279> rh:compound <http://rdf.rhea-db.org/Compound_4279>; compound rh:accession - RHEA:26383
Source assertion: Rhea directed reaction 26383 places CHEBI:57706 on its substrates side with coefficient 1. Source locationRDF142 <http://rdf.rhea-db.org/26383> rh:substrates <http://rdf.rhea-db.org/26381_R>; <http://rdf.rhea-db.org/26381_R> rh:contains1 <http://rdf.rhea-db.org/Participant_26381_compound_4279>; <http://rdf.rhea-db.org/Participant_26381_compound_4279> rh:compound <http://rdf.rhea-db.org/Compound_4279>; compound rh:accession
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succinate semialdehyde + NADPH + H(+) => 4-hydroxybutanoate + NADP(+)
RHEA:26383 | provides_input_for Material continuity through CHEBI:16724; physiological cycle context, not a new thermodynamic irreversibility claim. | 4-hydroxybutanoate + ATP + CoA => 4-hydroxybutanoyl-CoA + AMP + diphosphate
RHEA:23129 | - PMID:19411323
Source assertion: The Figure 1 cycle places activity 9 before activity 10 through the named carbon intermediate. The selected CHEBI:16724 microstate comes from the separately cited current reaction definitions, not from a primary ChEBI identifier. Source locationPMC2698501 HTML //*[@id="f1"] caption and depicted cycle; Results //*[@id="sec18"] - RHEA:26383
Source assertion: Rhea directed reaction 26383 places CHEBI:16724 on its products side with coefficient 1. Source locationRDF142 <http://rdf.rhea-db.org/26383> rh:products <http://rdf.rhea-db.org/26381_L>; <http://rdf.rhea-db.org/26381_L> rh:contains1 <http://rdf.rhea-db.org/Participant_26381_compound_5278>; <http://rdf.rhea-db.org/Participant_26381_compound_5278> rh:compound <http://rdf.rhea-db.org/Compound_5278>; compound rh:accession - RHEA:23129
Source assertion: Rhea directed reaction 23129 places CHEBI:16724 on its substrates side with coefficient 1. Source locationRDF142 <http://rdf.rhea-db.org/23129> rh:substrates <http://rdf.rhea-db.org/23128_L>; <http://rdf.rhea-db.org/23128_L> rh:contains1 <http://rdf.rhea-db.org/Participant_23128_compound_5278>; <http://rdf.rhea-db.org/Participant_23128_compound_5278> rh:compound <http://rdf.rhea-db.org/Compound_5278>; compound rh:accession
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4-hydroxybutanoate + ATP + CoA => 4-hydroxybutanoyl-CoA + AMP + diphosphate
RHEA:23129 | provides_input_for Material continuity through CHEBI:58574; physiological cycle context, not a new thermodynamic irreversibility claim. | 4-hydroxybutanoyl-CoA => (2E)-butenoyl-CoA + H2O
RHEA:26531 | - PMID:19411323
Source assertion: The Figure 1 cycle places activity 10 before activity 11 through the named carbon intermediate. The selected CHEBI:58574 microstate comes from the separately cited current reaction definitions, not from a primary ChEBI identifier. Source locationPMC2698501 HTML //*[@id="f1"] caption and depicted cycle; Results //*[@id="sec18"] - RHEA:23129
Source assertion: Rhea directed reaction 23129 places CHEBI:58574 on its products side with coefficient 1. Source locationRDF142 <http://rdf.rhea-db.org/23129> rh:products <http://rdf.rhea-db.org/23128_R>; <http://rdf.rhea-db.org/23128_R> rh:contains1 <http://rdf.rhea-db.org/Participant_23128_compound_6032>; <http://rdf.rhea-db.org/Participant_23128_compound_6032> rh:compound <http://rdf.rhea-db.org/Compound_6032>; compound rh:accession - RHEA:26531
Source assertion: Rhea directed reaction 26531 places CHEBI:58574 on its substrates side with coefficient 1. Source locationRDF142 <http://rdf.rhea-db.org/26531> rh:substrates <http://rdf.rhea-db.org/26530_L>; <http://rdf.rhea-db.org/26530_L> rh:contains1 <http://rdf.rhea-db.org/Participant_26530_compound_6032>; <http://rdf.rhea-db.org/Participant_26530_compound_6032> rh:compound <http://rdf.rhea-db.org/Compound_6032>; compound rh:accession
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4-hydroxybutanoyl-CoA => (2E)-butenoyl-CoA + H2O
RHEA:26531 | provides_input_for Material continuity through CHEBI:57332; physiological cycle context, not a new thermodynamic irreversibility claim. | (2E)-butenoyl-CoA + H2O => (3S)-3-hydroxybutanoyl-CoA
RHEA:26560 | - PMID:19411323
Source assertion: The Figure 1 cycle places activity 11 before activity 12 through the named carbon intermediate. The selected CHEBI:57332 microstate comes from the separately cited current reaction definitions, not from a primary ChEBI identifier. Source locationPMC2698501 HTML //*[@id="f1"] caption and depicted cycle; Results //*[@id="sec18"] - RHEA:26531
Source assertion: Rhea directed reaction 26531 places CHEBI:57332 on its products side with coefficient 1. Source locationRDF142 <http://rdf.rhea-db.org/26531> rh:products <http://rdf.rhea-db.org/26530_R>; <http://rdf.rhea-db.org/26530_R> rh:contains1 <http://rdf.rhea-db.org/Participant_26530_compound_2633>; <http://rdf.rhea-db.org/Participant_26530_compound_2633> rh:compound <http://rdf.rhea-db.org/Compound_2633>; compound rh:accession - RHEA:26560
Source assertion: Rhea directed reaction 26560 places CHEBI:57332 on its substrates side with coefficient 1. Source locationRDF142 <http://rdf.rhea-db.org/26560> rh:substrates <http://rdf.rhea-db.org/26558_R>; <http://rdf.rhea-db.org/26558_R> rh:contains1 <http://rdf.rhea-db.org/Participant_26558_compound_2633>; <http://rdf.rhea-db.org/Participant_26558_compound_2633> rh:compound <http://rdf.rhea-db.org/Compound_2633>; compound rh:accession
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(2E)-butenoyl-CoA + H2O => (3S)-3-hydroxybutanoyl-CoA
RHEA:26560 | provides_input_for Material continuity through CHEBI:57316; physiological cycle context, not a new thermodynamic irreversibility claim. | (3S)-3-hydroxybutanoyl-CoA + NAD(+) => acetoacetyl-CoA + NADH + H(+)
RHEA:30800 | - PMID:19411323
Source assertion: The Figure 1 cycle places activity 12 before activity 13 through the named carbon intermediate. The selected CHEBI:57316 microstate comes from the separately cited current reaction definitions, not from a primary ChEBI identifier. Source locationPMC2698501 HTML //*[@id="f1"] caption and depicted cycle; Results //*[@id="sec18"] - RHEA:26560
Source assertion: Rhea directed reaction 26560 places CHEBI:57316 on its products side with coefficient 1. Source locationRDF142 <http://rdf.rhea-db.org/26560> rh:products <http://rdf.rhea-db.org/26558_L>; <http://rdf.rhea-db.org/26558_L> rh:contains1 <http://rdf.rhea-db.org/Participant_26558_compound_2192>; <http://rdf.rhea-db.org/Participant_26558_compound_2192> rh:compound <http://rdf.rhea-db.org/Compound_2192>; compound rh:accession - RHEA:30800
Source assertion: Rhea directed reaction 30800 places CHEBI:57316 on its substrates side with coefficient 1. Source locationRDF142 <http://rdf.rhea-db.org/30800> rh:substrates <http://rdf.rhea-db.org/30799_L>; <http://rdf.rhea-db.org/30799_L> rh:contains1 <http://rdf.rhea-db.org/Participant_30799_compound_2192>; <http://rdf.rhea-db.org/Participant_30799_compound_2192> rh:compound <http://rdf.rhea-db.org/Compound_2192>; compound rh:accession
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(3S)-3-hydroxybutanoyl-CoA + NAD(+) => acetoacetyl-CoA + NADH + H(+)
RHEA:30800 | provides_input_for Material continuity through CHEBI:57286; physiological cycle context, not a new thermodynamic irreversibility claim. | acetoacetyl-CoA + CoA => 2 acetyl-CoA
RHEA:21038 | - PMID:19411323
Source assertion: The Figure 1 cycle places activity 13 before activity 14 through the named carbon intermediate. The selected CHEBI:57286 microstate comes from the separately cited current reaction definitions, not from a primary ChEBI identifier. Source locationPMC2698501 HTML //*[@id="f1"] caption and depicted cycle; Results //*[@id="sec18"] - RHEA:30800
Source assertion: Rhea directed reaction 30800 places CHEBI:57286 on its products side with coefficient 1. Source locationRDF142 <http://rdf.rhea-db.org/30800> rh:products <http://rdf.rhea-db.org/30799_R>; <http://rdf.rhea-db.org/30799_R> rh:contains1 <http://rdf.rhea-db.org/Participant_30799_compound_4872>; <http://rdf.rhea-db.org/Participant_30799_compound_4872> rh:compound <http://rdf.rhea-db.org/Compound_4872>; compound rh:accession - RHEA:21038
Source assertion: Rhea directed reaction 21038 places CHEBI:57286 on its substrates side with coefficient 1. Source locationRDF142 <http://rdf.rhea-db.org/21038> rh:substrates <http://rdf.rhea-db.org/21036_R>; <http://rdf.rhea-db.org/21036_R> rh:contains1 <http://rdf.rhea-db.org/Participant_21036_compound_4872>; <http://rdf.rhea-db.org/Participant_21036_compound_4872> rh:compound <http://rdf.rhea-db.org/Compound_4872>; compound rh:accession
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acetoacetyl-CoA + CoA => 2 acetyl-CoA
RHEA:21038 | provides_input_for Material continuity through CHEBI:57288; physiological cycle context, not a new thermodynamic irreversibility claim. | pyruvate:ferredoxin 2-oxidoreductase (CoA-acetylating)
KEGG:R01196 | - PMID:19411323
Source assertion: The Figure 1 cycle places activity 14 before activity 1 through the named carbon intermediate. The selected CHEBI:57288 microstate comes from the separately cited current reaction definitions, not from a primary ChEBI identifier. Source locationPMC2698501 HTML //*[@id="f1"] caption and depicted cycle; Results //*[@id="sec18"] - RHEA:21038
Source assertion: Rhea directed reaction 21038 places CHEBI:57288 on its products side with coefficient 2. Source locationRDF142 <http://rdf.rhea-db.org/21038> rh:products <http://rdf.rhea-db.org/21036_L>; <http://rdf.rhea-db.org/21036_L> rh:contains2 <http://rdf.rhea-db.org/Participant_21036_compound_4271>; <http://rdf.rhea-db.org/Participant_21036_compound_4271> rh:compound <http://rdf.rhea-db.org/Compound_4271>; compound rh:accession - KEGG:R01196
Source assertion: Native R01196 connects acetyl-CoA C00024 and pyruvate C00022 using two generic ferredoxin redox partners and two H+ in its acid-form reference equation. Selected anion normalization is supported by separately cited compound and ChEBI bodies. Source locationOriginal flatfile ENTRY R01196; DEFINITION; EQUATION; RCLASS C00022_C00024 - KEGG:C00024
Source assertion: The original compound batch gives C00024/C00010/C00022 formulas and ChEBI links to acetyl-CoA, CoA and pyruvic acid. These are native acid reference forms; this body alone does not define the selected deprotonated ChEBI forms. Source locationOriginal five-entry batch ENTRY C00024/C00010/C00022; FORMULA; DBLINKS ChEBI:15351/15346/32816 - CHEBI:57288
Source assertion: Original ChEBI forms differ only in protonation: 15351→57288 and 15346→57287 each lose four H; 32816→15361 loses one H. The CoA shifts cancel and product pyruvate deprotonation reduces native input two H+ to one. This is derived bookkeeping, not measured flux. Source locationOriginal ChEBI255 semantic SQL statements for CHEBI:15351/57288, CHEBI:15346/57287, CHEBI:32816/15361; chemrof:generalized_empirical_formula, chemrof:charge, chemrof:inchi_string
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