MetaCyc Pathway: superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle in Variovorax sp. SCN45

MetaCyc Pathway: superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle in Variovorax sp. SCN45

Diphosphate--fructose-6-phosphate 1-phosphotransferase:
β-D-fructofuranose 6-phosphate + diphosphate→β-D-fructofuranose 1,6-bisphosphate + H⁺ + phosphate (EC 2.7.1.90)

No genes

6-phosphofructokinase:
β-D-fructofuranose 6-phosphate + ATP→β-D-fructofuranose 1,6-bisphosphate + ADP + H⁺ (EC 2.7.1.11)

Fructose-bisphosphate aldolase:
β-D-fructofuranose 1,6-bisphosphate→glycerone phosphate + D-glyceraldehyde 3-phosphate (EC 4.1.2.13)

Triose-phosphate isomerase (in reverse):
glycerone phosphate→D-glyceraldehyde 3-phosphate (EC 5.3.1.1)

Glyceraldehyde-3-phosphate dehydrogenase (NADP(+)):
D-glyceraldehyde 3-phosphate + NADP⁺ + H₂O→3-phospho-D-glycerate + NADPH + 2 H⁺ (EC 1.2.1.9)

No genes

Glyceraldehyde-3-phosphate dehydrogenase (phosphorylating):
D-glyceraldehyde 3-phosphate + NAD⁺ + phosphate→3-phospho-D-glyceroyl phosphate + NADH + H⁺ (EC 1.2.1.12)

Phosphoglycerate kinase (in reverse):
3-phospho-D-glyceroyl phosphate + ADP→3-phospho-D-glycerate + ATP (EC 2.7.2.3)

3-phospho-D-glycerate→2-phospho-D-glycerate (EC 5.4.2.12)

Phosphopyruvate hydratase:
2-phospho-D-glycerate→phosphoenolpyruvate + H₂O (EC 4.2.1.11)

Pyruvate kinase (in reverse):
phosphoenolpyruvate + ADP + H⁺→pyruvate + ATP (EC 2.7.1.40)

pyruvate + a [pyruvate dehydrogenase E2 protein] N⁶-lipoyl-L-lysine + H⁺→a [pyruvate dehydrogenase E2 protein] N⁶-S-acetyldihydrolipoyl-L-lysine + CO₂ (EC 1.2.1.104; 1.2.4.1)

a [pyruvate dehydrogenase E2 protein] N⁶-S-acetyldihydrolipoyl-L-lysine + coenzyme A→acetyl-CoA + a [pyruvate dehydrogenase E2 protein] N⁶-dihydrolipoyl-L-lysine (EC 1.2.1.104; 2.3.1.12)

Citrate (Si)-synthase:
oxaloacetate + acetyl-CoA + H₂O→citrate + coenzyme A + H⁺ (EC 2.3.3.1; 2.3.3.16; 2.3.3.3)

a [pyruvate dehydrogenase E2 protein] N⁶-dihydrolipoyl-L-lysine + NAD⁺→a [pyruvate dehydrogenase E2 protein] N⁶-lipoyl-L-lysine + NADH + H⁺ (EC 1.2.1.104; 1.8.1.4)

Aconitate hydratase:
citrate→cis-aconitate + H₂O (EC 4.2.1.3)

Aconitate hydratase:
cis-aconitate + H₂O→D-threo-isocitrate (EC 4.2.1.3)

Isocitrate--homoisocitrate dehydrogenase:
D-threo-isocitrate + NAD⁺→2-oxoglutarate + CO₂ + NADH (EC 1.1.1.286; 1.1.1.41)

2-oxoglutarate + coenzyme A + NAD⁺→succinyl-CoA + CO₂ + NADH (EC 1.2.1.105)

Succinate--CoA ligase (ADP-forming) (in reverse):
succinyl-CoA + ADP + phosphate→succinate + ATP + coenzyme A (EC 6.2.1.5)

Succinate dehydrogenase (ubiquinone):
succinate_[in] + an electron-transfer quinone→fumarate_[in] + an electron-transfer quinol (EC 1.3.5.1)

Fumarate hydratase (in reverse):
fumarate + H₂O→(S)-malate (EC 4.2.1.2)

Malate dehydrogenase:
(S)-malate + NAD⁺→oxaloacetate + NADH + H⁺ (EC 1.1.1.37; 1.1.1.38)

Links:

Pathway details at MetaCyc
Fitness data for 47 genes
Select organism:
All MetaCyc pathways for Variovorax sp. SCN45

Candidate genes for each reaction are identified from best hits to MetaCyc; by matching EC numbers (which are assigned by TIGRFam, SEED, or best hits to KEGG); or by matching SEED roles to KEGG reactions to MetaCyc reactions. See the "Protein" tab of each gene for more information