Experiment set2IT005 for Paraburkholderia graminis OAS925
D-Serine carbon source
Group: carbon sourceMedia: RCH2_defined_noCarbon + D-Serine (20 mM)
Culturing: Burkholderia_OAS925_ML2, 96 deep-well microplate; 0.8 mL volume, Aerobic, at 30 (C), shaken=700 rpm
By: Marta on 10-Apr-21
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 4 genes in this experiment
For carbon source D-Serine in Paraburkholderia graminis OAS925
For carbon source D-Serine across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Branched-Chain Amino Acid Biosynthesis | 1 |
| Glycine and Serine Utilization | 1 |
| Pyruvate Alanine Serine Interconversions | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Glycine, serine and threonine metabolism
- Cysteine metabolism
- Valine, leucine and isoleucine biosynthesis
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| D-serine degradation | 3 | 3 | 3 |
| L-serine degradation | 3 | 3 | 3 |
| L-cysteine degradation II | 3 | 2 | 2 |
| L-methionine degradation II | 3 | 2 | 2 |
| L-tryptophan degradation II (via pyruvate) | 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 |
| glycine betaine degradation III | 7 | 6 | 3 |
| felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis | 5 | 2 | 2 |
| glycine betaine degradation I | 8 | 6 | 3 |
| L-methionine biosynthesis II | 6 | 4 | 2 |
| glycine degradation | 3 | 2 | 1 |
| L-mimosine degradation | 8 | 4 | 2 |
| glutathione-mediated detoxification I | 8 | 3 | 2 |
| 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 | 14 | 3 |
| superpathway of L-lysine, L-threonine and L-methionine biosynthesis II | 15 | 12 | 2 |
| purine nucleobases degradation II (anaerobic) | 24 | 16 | 3 |
| cyclosporin A biosynthesis | 15 | 2 | 1 |