Sodium pyruvate 20 mM
Group:
carbon source
Media:
Hans_Basal_Media_plus_0.2x_20AA_mix +
Sodium pyruvate (20 mM)
Culturing: rhodanobacter_10B01_ML12, 96 deep-well microplate; 0.8 mL volume, Aerobic, at 28 (C), shaken=700 rpm
By: Hans Carlson and Trenton Owens on
24-Aug-21
Media components: 0.03 M
PIPES sesquisodium salt, 0.1 g/L
Potassium Chloride, 0.01 g/L
Sodium Chloride, 0.01 g/L
Calcium chloride dihydrate, 0.1 g/L
Magnesium chloride hexahydrate, 0.1 g/L
Sodium sulfate, 0.25 g/L
Ammonium chloride, 0.1 g/L
Disodium phosphate, 20AA_mix
(0.1 mM L-Arginine, 0.1 mM L-Histidine, 0.1 mM L-Lysine, 0.1 mM L-Aspartic Acid, 0.1 mM L-Glutamic acid monopotassium salt monohydrate, 0.1 mM L-Serine, 0.1 mM L-Threonine, 0.1 mM L-Asparagine, 0.1 mM L-Glutamine, 0.1 mM L-Cysteine hydrochloride monohydrate, 0.1 mM Glycine, 0.1 mM L-Proline, 0.1 mM L-Alanine, 0.1 mM L-Valine, 0.1 mM L-Isoleucine, 0.1 mM L-Leucine, 0.1 mM L-Methionine, 0.1 mM L-Phenylalanine, 0.1 mM L-tyrosine disodium salt, 0.1 mM L-Tryptophan), DL vitamins
(0.0002 mg/L biotin, 0.0002 mg/L Folic Acid, 0.001 mg/L Pyridoxine HCl, 0.0005 mg/L Riboflavin, 0.0005 mg/L Thiamine HCl, 0.0005 mg/L Nicotinic Acid, 0.0005 mg/L calcium pantothenate, 1e-05 mg/L Cyanocobalamin, 0.0005 mg/L 4-Aminobenzoic acid, 0.0005 mg/L Lipoic acid), Sulfur-free DL minerals
(0.0003 g/L Magnesium chloride hexahydrate, 0.00015 g/L Nitrilotriacetic acid disodium salt, 0.0001 g/L Sodium Chloride, 5e-05 g/L Manganese (II) chloride tetrahydrate, 1e-05 g/L Cobalt chloride hexahydrate, 1.3e-05 g/L Zinc chloride, 1e-05 g/L Calcium chloride dihydrate, 1e-05 g/L Iron (II) chloride tetrahydrate, 2.5e-06 g/L Nickel (II) chloride hexahydrate, 2e-06 g/L Aluminum chloride hydrate, 1e-06 g/L copper (II) chloride dihydrate, 1e-06 g/L Boric Acid, 1e-06 g/L Sodium Molybdate Dihydrate, 3e-05 g/L Sodium selenite pentahydrate, 2.5e-05 g/L Sodium tungstate dihydrate)
Growth plate: 1 F4
Specific Phenotypes
For 11 genes in this experiment
For carbon source Sodium pyruvate in Rhodanobacter denitrificans FW104-10B01
For carbon source Sodium pyruvate across organisms
SEED Subsystems
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|
| siroheme biosynthesis | 4 | 4 | 4 |
| CO2 fixation into oxaloacetate (anaplerotic) | 2 | 2 | 1 |
| factor 430 biosynthesis | 7 | 3 | 3 |
| L-serine degradation | 3 | 3 | 1 |
| assimilatory sulfate reduction III | 3 | 3 | 1 |
| L-cysteine degradation II | 3 | 3 | 1 |
| D-serine degradation | 3 | 3 | 1 |
| L-methionine degradation II | 3 | 2 | 1 |
| L-tryptophan degradation II (via pyruvate) | 3 | 2 | 1 |
| assimilatory sulfate reduction I | 4 | 4 | 1 |
| gondoate biosynthesis (anaerobic) | 4 | 4 | 1 |
| octanoyl-[acyl-carrier protein] biosynthesis (mitochondria, yeast) | 12 | 9 | 3 |
| palmitate biosynthesis III | 29 | 21 | 7 |
| tetradecanoate biosynthesis (mitochondria) | 25 | 17 | 6 |
| palmitate biosynthesis II (type II fatty acid synthase) | 31 | 29 | 7 |
| palmitoleate biosynthesis I (from (5Z)-dodec-5-enoate) | 9 | 8 | 2 |
| oleate biosynthesis IV (anaerobic) | 14 | 13 | 3 |
| superpathway of fatty acids biosynthesis (E. coli) | 53 | 49 | 11 |
| superpathway of unsaturated fatty acids biosynthesis (E. coli) | 20 | 18 | 4 |
| cis-vaccenate biosynthesis | 5 | 4 | 1 |
| fatty acid elongation -- saturated | 5 | 4 | 1 |
| 8-amino-7-oxononanoate biosynthesis IV | 5 | 4 | 1 |
| felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis | 5 | 2 | 1 |
| cob(II)yrinate a,c-diamide biosynthesis I (early cobalt insertion) | 15 | 3 | 3 |
| superpathway of fatty acid biosynthesis II (plant) | 43 | 38 | 8 |
| 8-amino-7-oxononanoate biosynthesis I | 11 | 10 | 2 |
| odd iso-branched-chain fatty acid biosynthesis | 34 | 24 | 6 |
| anteiso-branched-chain fatty acid biosynthesis | 34 | 24 | 6 |
| even iso-branched-chain fatty acid biosynthesis | 34 | 24 | 6 |
| (5Z)-dodecenoate biosynthesis I | 6 | 6 | 1 |
| L-methionine biosynthesis II | 6 | 5 | 1 |
| stearate biosynthesis II (bacteria and plants) | 6 | 5 | 1 |
| L-threonine degradation I | 6 | 5 | 1 |
| (5Z)-dodecenoate biosynthesis II | 6 | 5 | 1 |
| stearate biosynthesis IV | 6 | 4 | 1 |
| petroselinate biosynthesis | 6 | 2 | 1 |
| cob(II)yrinate a,c-diamide biosynthesis II (late cobalt incorporation) | 13 | 2 | 2 |
| streptorubin B biosynthesis | 34 | 20 | 5 |
| L-isoleucine biosynthesis I (from threonine) | 7 | 7 | 1 |
| C4 photosynthetic carbon assimilation cycle, NADP-ME type | 7 | 4 | 1 |
| glycine betaine degradation III | 7 | 4 | 1 |
| biotin biosynthesis I | 15 | 14 | 2 |
| superpathway of fatty acid biosynthesis I (E. coli) | 16 | 14 | 2 |
| partial TCA cycle (obligate autotrophs) | 8 | 7 | 1 |
| nitrogen remobilization from senescing leaves | 8 | 7 | 1 |
| glycine betaine degradation I | 8 | 4 | 1 |
| L-mimosine degradation | 8 | 4 | 1 |
| glutathione-mediated detoxification I | 8 | 3 | 1 |
| 2-allylmalonyl-CoA biosynthesis | 8 | 2 | 1 |
| superpathway of sulfate assimilation and cysteine biosynthesis | 9 | 8 | 1 |
| gluconeogenesis II (Methanobacterium thermoautotrophicum) | 18 | 8 | 2 |
| superpathway of sulfur amino acid biosynthesis (Saccharomyces cerevisiae) | 10 | 8 | 1 |
| glycolysis V (Pyrococcus) | 10 | 7 | 1 |
| glycolysis II (from fructose 6-phosphate) | 11 | 11 | 1 |
| C4 photosynthetic carbon assimilation cycle, NAD-ME type | 11 | 7 | 1 |
| superpathway of L-methionine biosynthesis (by sulfhydrylation) | 12 | 11 | 1 |
| adenosylcobalamin biosynthesis I (anaerobic) | 36 | 12 | 3 |
| superpathway of L-isoleucine biosynthesis I | 13 | 13 | 1 |
| glycolysis I (from glucose 6-phosphate) | 13 | 12 | 1 |
| gluconeogenesis I | 13 | 11 | 1 |
| formaldehyde assimilation I (serine pathway) | 13 | 6 | 1 |
| C4 photosynthetic carbon assimilation cycle, PEPCK type | 14 | 8 | 1 |
| hypoglycin biosynthesis | 14 | 4 | 1 |
| superpathway of L-lysine, L-threonine and L-methionine biosynthesis II | 15 | 13 | 1 |
| mixed acid fermentation | 16 | 12 | 1 |
| adenosylcobalamin biosynthesis II (aerobic) | 33 | 12 | 2 |
| superpathway of branched chain amino acid biosynthesis | 17 | 17 | 1 |
| superpathway of glycolysis and the Entner-Doudoroff pathway | 17 | 16 | 1 |
| superpathway of hexitol degradation (bacteria) | 18 | 14 | 1 |
| superpathway of L-threonine metabolism | 18 | 13 | 1 |
| superpathway of anaerobic sucrose degradation | 19 | 16 | 1 |
| hexitol fermentation to lactate, formate, ethanol and acetate | 19 | 14 | 1 |
| superpathway of N-acetylneuraminate degradation | 22 | 16 | 1 |
| purine nucleobases degradation II (anaerobic) | 24 | 9 | 1 |
| ethene biosynthesis V (engineered) | 25 | 17 | 1 |
| superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass | 26 | 23 | 1 |
| Methanobacterium thermoautotrophicum biosynthetic metabolism | 56 | 25 | 2 |
| mycolate biosynthesis | 205 | 20 | 5 |
| superpathway of mycolate biosynthesis | 239 | 21 | 5 |