Experiment set1IT083 for Acidovorax sp. GW101-3H11
D-Gluconic Acid carbon source
Group: carbon sourceMedia: RCH2_defined_noCarbon + D-Gluconic Acid sodium salt (20 mM), pH=7
Culturing: acidovorax_3H11_ML3a, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
By: Mark on 3/3/2015
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 30 mM PIPES sesquisodium salt, Wolfe's mineral mix (0.03 g/L Magnesium Sulfate Heptahydrate, 0.015 g/L Nitrilotriacetic acid, 0.01 g/L Sodium Chloride, 0.005 g/L Manganese (II) sulfate monohydrate, 0.001 g/L Cobalt chloride hexahydrate, 0.001 g/L Zinc sulfate heptahydrate, 0.001 g/L Calcium chloride dihydrate, 0.001 g/L Iron (II) sulfate heptahydrate, 0.00025 g/L Nickel (II) chloride hexahydrate, 0.0002 g/L Aluminum potassium sulfate dodecahydrate, 0.0001 g/L Copper (II) sulfate pentahydrate, 0.0001 g/L Boric Acid, 0.0001 g/L Sodium Molybdate Dihydrate, 0.003 mg/L Sodium selenite pentahydrate), Wolfe's vitamin mix (0.1 mg/L Pyridoxine HCl, 0.05 mg/L 4-Aminobenzoic acid, 0.05 mg/L Lipoic acid, 0.05 mg/L Nicotinic Acid, 0.05 mg/L Riboflavin, 0.05 mg/L Thiamine HCl, 0.05 mg/L calcium pantothenate, 0.02 mg/L biotin, 0.02 mg/L Folic Acid, 0.001 mg/L Cyanocobalamin)
Specific Phenotypes
For 18 genes in this experiment
For carbon source D-Gluconic Acid sodium salt in Acidovorax sp. GW101-3H11
For carbon source D-Gluconic Acid sodium salt across organisms
SEED Subsystems
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Nucleotide sugars metabolism
- Benzoate degradation via CoA ligation
- Fructose and mannose metabolism
- Fatty acid biosynthesis
- Purine metabolism
- Tyrosine metabolism
- Benzoate degradation via hydroxylation
- Tryptophan metabolism
- Phenylalanine, tyrosine and tryptophan biosynthesis
- Cyanoamino acid metabolism
- N-Glycan biosynthesis
- O-Glycan biosynthesis
- High-mannose type N-glycan biosynthesis
- O-Mannosyl glycan biosynthesis
- Aminosugars metabolism
- Keratan sulfate biosynthesis
- Lipopolysaccharide biosynthesis
- Peptidoglycan biosynthesis
- Glycerolipid metabolism
- Glycosylphosphatidylinositol(GPI)-anchor biosynthesis
- Sphingolipid metabolism
- Glycosphingolipid biosynthesis - lacto and neolacto series
- Glycosphingolipid biosynthesis - globo series
- Glycosphingolipid biosynthesis - ganglio series
- 1- and 2-Methylnaphthalene degradation
- Styrene degradation
- Butanoate metabolism
- Porphyrin and chlorophyll metabolism
- Limonene and pinene degradation
- Carotenoid biosynthesis - General
- Zeatin biosynthesis
- Nitrogen metabolism
- Flavonoid biosynthesis
- Anthocyanin biosynthesis
- Flavone and flavonol biosynthesis
- Biosynthesis of unsaturated fatty acids
- Biosynthesis of type II polyketide backbone
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| indole-3-acetate biosynthesis V (bacteria and fungi) | 1 | 1 | 1 |
| CMP-N-acetylneuraminate biosynthesis II (bacteria) | 3 | 2 | 1 |
| CMP-pseudaminate biosynthesis | 6 | 4 | 1 |
| indole-3-acetate biosynthesis II | 12 | 4 | 1 |
| indole glucosinolate activation (herbivore attack) | 13 | 8 | 1 |
| superpathway of CMP-sialic acids biosynthesis | 15 | 2 | 1 |