Experiment set4IT048 for Herbaspirillum seropedicae SmR1
Defined media with L-Serine
Group: nutrientMedia: RCH2_defined_glucose + L-Serine (1 mM)
Culturing: HerbieS_ML4, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 5.8 generations
By: Adam on 20-Jun-16
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 20 mM D-Glucose, 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 1 genes in this experiment
For nutrient L-Serine in Herbaspirillum seropedicae SmR1
For nutrient L-Serine across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Branched-Chain Amino Acid Biosynthesis | 1 |
| Threonine degradation | 1 |
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 |
|---|---|---|---|
| L-methionine degradation II | 3 | 2 | 2 |
| L-threonine degradation I | 6 | 5 | 3 |
| L-threonine degradation V | 2 | 1 | 1 |
| L-isoleucine biosynthesis I (from threonine) | 7 | 7 | 3 |
| superpathway of L-isoleucine biosynthesis I | 13 | 13 | 3 |
| hypoglycin biosynthesis | 14 | 4 | 3 |
| superpathway of branched chain amino acid biosynthesis | 17 | 17 | 3 |
| superpathway of L-threonine metabolism | 18 | 13 | 3 |
| cyclosporin A biosynthesis | 15 | 2 | 1 |