Experiment set11IT017 for Burkholderia phytofirmans PsJN
Malonic acid carbon source
Group: carbon sourceMedia: MOPS minimal media_noCarbon + Malonic acid (10 mM)
Culturing: BFirm_ML3_JBEI, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 1.2 generations
By: Allie Pearson on 8/26/19
Media components: 40 mM 3-(N-morpholino)propanesulfonic acid, 4 mM Tricine, 1.32 mM Potassium phosphate dibasic, 0.01 mM Iron (II) sulfate heptahydrate, 9.5 mM Ammonium chloride, 0.276 mM Aluminum potassium sulfate dodecahydrate, 0.0005 mM Calcium chloride, 0.525 mM Magnesium chloride hexahydrate, 50 mM Sodium Chloride, 3e-09 M Ammonium heptamolybdate tetrahydrate, 4e-07 M Boric Acid, 3e-08 M Cobalt chloride hexahydrate, 1e-08 M Copper (II) sulfate pentahydrate, 8e-08 M Manganese (II) chloride tetrahydrate, 1e-08 M Zinc sulfate heptahydrate
Specific Phenotypes
For 2 genes in this experiment
For carbon source Malonic acid in Burkholderia phytofirmans PsJN
For carbon source Malonic acid across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Ketoisovalerate oxidoreductase | 1 |
| Malonate decarboxylase | 1 |
| Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Glycolysis / Gluconeogenesis
- Pyruvate metabolism
- Propanoate metabolism
- Reductive carboxylate cycle (CO2 fixation)
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| acetate and ATP formation from acetyl-CoA III | 1 | 1 | 1 |
| acetate conversion to acetyl-CoA | 1 | 1 | 1 |
| ethanol degradation II | 3 | 3 | 1 |
| ethanol degradation IV | 3 | 3 | 1 |
| superpathway of acetate utilization and formation | 3 | 3 | 1 |
| ethanol degradation III | 3 | 2 | 1 |
| malonate degradation I (biotin-independent) | 3 | 2 | 1 |
| L-isoleucine biosynthesis V | 3 | 2 | 1 |
| chitin deacetylation | 4 | 2 | 1 |
| malonate degradation II (biotin-dependent) | 4 | 1 | 1 |
| 2-methylcitrate cycle I | 5 | 5 | 1 |
| 2-methylcitrate cycle II | 6 | 5 | 1 |
| L-isoleucine biosynthesis IV | 6 | 4 | 1 |
| β-alanine biosynthesis II | 6 | 4 | 1 |
| superpathway of bitter acids biosynthesis | 18 | 3 | 3 |
| adlupulone and adhumulone biosynthesis | 6 | 1 | 1 |
| colupulone and cohumulone biosynthesis | 6 | 1 | 1 |
| lupulone and humulone biosynthesis | 6 | 1 | 1 |
| reductive glycine pathway of autotrophic CO2 fixation | 9 | 4 | 1 |
| cis-geranyl-CoA degradation | 9 | 2 | 1 |
| superpathway of coenzyme A biosynthesis II (plants) | 10 | 8 | 1 |