Experiment set1IT020 for Herbaspirillum seropedicae SmR1
D-Galacturonic Acid monohydrate carbon source
Group: carbon sourceMedia: RCH2_defined_noCarbon + D-Galacturonic Acid monohydrate (20 mM), pH=7
Culturing: HerbieS_ML4, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
Growth: about 2.7 generations
By: Mark on 3/10/2016
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)
Growth plate: CARBON3 A4
Specific Phenotypes
For 7 genes in this experiment
For carbon source D-Galacturonic Acid monohydrate in Herbaspirillum seropedicae SmR1
For carbon source D-Galacturonic Acid monohydrate across organisms
SEED Subsystems
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Ascorbate and aldarate metabolism
- Pentose phosphate pathway
- Fructose and mannose metabolism
- N-Glycan biosynthesis
- O-Glycan biosynthesis
- High-mannose type N-glycan biosynthesis
- O-Mannosyl glycan biosynthesis
- 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
- Carotenoid biosynthesis - General
- Zeatin biosynthesis
- Flavonoid biosynthesis
- Anthocyanin biosynthesis
- Flavone and flavonol biosynthesis
- Biosynthesis of alkaloids derived from histidine and purine
- Biosynthesis of plant hormones
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| D-galactarate degradation II | 3 | 3 | 2 |
| D-glucarate degradation II | 3 | 3 | 1 |
| pentose phosphate pathway (oxidative branch) I | 3 | 2 | 1 |
| D-galactarate degradation I | 4 | 4 | 1 |
| superpathway of D-glucarate and D-galactarate degradation | 5 | 5 | 1 |
| D-glucuronate degradation II | 5 | 4 | 1 |
| D-galacturonate degradation II | 5 | 3 | 1 |
| formaldehyde oxidation I | 6 | 3 | 1 |
| pentose phosphate pathway | 8 | 7 | 1 |
| Entner-Doudoroff pathway I | 9 | 9 | 1 |
| superpathway of microbial D-galacturonate and D-glucuronate degradation | 31 | 16 | 2 |
| superpathway of glycolysis and the Entner-Doudoroff pathway | 17 | 15 | 1 |
| superpathway of glucose and xylose degradation | 17 | 14 | 1 |
| heterolactic fermentation | 18 | 14 | 1 |