Experiment set6IT003 for Paraburkholderia bryophila 376MFSha3.1
Malonic acid carbon source
Group: carbon sourceMedia: RCH2_defined_noCarbon + Malonic acid (10 mM) + Dimethyl Sulfoxide (1 vol%)
Culturing: Burk376_ML3, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C), shaken=700rpm
By: RobinH_and_TrentonO on 13-Feb-19
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 Malonic acid in Paraburkholderia bryophila 376MFSha3.1
For carbon source Malonic acid across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Malonate decarboxylase | 3 |
| Proline, 4-hydroxyproline uptake and utilization | 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 |
|---|---|---|---|
| malonate degradation I (biotin-independent) | 3 | 2 | 2 |
| fatty acid biosynthesis initiation (type II) | 3 | 3 | 1 |
| fatty acid biosynthesis initiation (mitochondria) | 4 | 2 | 1 |
| fatty acid biosynthesis initiation (plant mitochondria) | 4 | 1 | 1 |
| malonate degradation II (biotin-dependent) | 4 | 1 | 1 |
| superpathway of fatty acid biosynthesis initiation | 5 | 4 | 1 |
| pederin biosynthesis | 14 | 2 | 2 |
| bryostatin biosynthesis | 19 | 2 | 2 |
| mycobactin biosynthesis | 11 | 2 | 1 |
| superpathway of fatty acid biosynthesis I (E. coli) | 16 | 14 | 1 |
| mupirocin biosynthesis | 26 | 1 | 1 |
| corallopyronin A biosynthesis | 30 | 2 | 1 |
| superpathway of fatty acid biosynthesis II (plant) | 43 | 38 | 1 |
| superpathway of fatty acids biosynthesis (E. coli) | 53 | 50 | 1 |