Experiment set14IT061 for Pseudomonas fluorescens SBW25-INTG
D,L-Malic Acid (C) and Ammonium chloride (N); with MOPS; with Sodium chloride
Group: stressMedia: MME_noNitrogen_noCarbon + D,L-Malic Acid (20 mM) + Ammonium chloride (10 mM) + Sodium Chloride (400 mM), pH=7
Culturing: PseudoSBW25_INTG_ML3, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 33 (C), shaken=1200 rpm
By: Joshua Elmore on September 1, 2021
Media components: 9.1 mM Potassium phosphate dibasic trihydrate, 20 mM 3-(N-morpholino)propanesulfonic acid, 4.3 mM Sodium Chloride, 0.41 mM Magnesium Sulfate Heptahydrate, 0.07 mM Calcium chloride dihydrate, MME Trace Minerals (0.5 mg/L EDTA tetrasodium tetrahydrate salt, 2 mg/L Ferric chloride, 0.05 mg/L Boric Acid, 0.05 mg/L Zinc chloride, 0.03 mg/L copper (II) chloride dihydrate, 0.05 mg/L Manganese (II) chloride tetrahydrate, 0.05 mg/L Diammonium molybdate, 0.05 mg/L Cobalt chloride hexahydrate, 0.05 mg/L Nickel (II) chloride hexahydrate)
Specific Phenotypes
For 23 genes in this experiment
For stress D,L-Malic Acid in Pseudomonas fluorescens SBW25-INTG
For stress D,L-Malic Acid across organisms
SEED Subsystems
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Fatty acid metabolism
- Valine, leucine and isoleucine degradation
- Geraniol degradation
- Tyrosine metabolism
- Tryptophan metabolism
- 1- and 2-Methylnaphthalene degradation
- Naphthalene and anthracene degradation
- Butanoate metabolism
- Glycolysis / Gluconeogenesis
- Fructose and mannose metabolism
- Galactose metabolism
- Ascorbate and aldarate metabolism
- Ubiquinone and menaquinone biosynthesis
- Urea cycle and metabolism of amino groups
- Glutamate metabolism
- Lysine biosynthesis
- Lysine degradation
- Arginine and proline metabolism
- Histidine metabolism
- Benzoxazinone biosynthesis
- Starch and sucrose metabolism
- Nucleotide sugars metabolism
- Aminosugars metabolism
- Pyruvate metabolism
- Glyoxylate and dicarboxylate metabolism
- Benzoate degradation via CoA ligation
- Porphyrin and chlorophyll metabolism
- Limonene and pinene degradation
- Brassinosteroid biosynthesis
- Carotenoid biosynthesis - General
- Caprolactam degradation
- Phenylpropanoid biosynthesis
- Flavonoid biosynthesis
- Anthocyanin biosynthesis
- Alkaloid biosynthesis I
- Insect hormone biosynthesis
- Biosynthesis of terpenoids and steroids
- Biosynthesis of alkaloids derived from shikimate pathway
- Biosynthesis of plant hormones
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| 4-aminobutanoate degradation III | 2 | 2 | 1 |
| sucrose degradation I (sucrose phosphotransferase) | 3 | 2 | 1 |
| L-lysine degradation IV | 5 | 5 | 1 |
| fatty acid salvage | 6 | 6 | 1 |
| L-lysine degradation X | 6 | 5 | 1 |
| pyruvate fermentation to butanol II (engineered) | 6 | 4 | 1 |
| L-lysine degradation III | 6 | 2 | 1 |
| L-lysine degradation I | 7 | 4 | 1 |
| partial TCA cycle (obligate autotrophs) | 8 | 8 | 1 |
| TCA cycle VI (Helicobacter) | 9 | 7 | 1 |
| TCA cycle VII (acetate-producers) | 9 | 7 | 1 |
| TCA cycle I (prokaryotic) | 10 | 9 | 1 |
| pyruvate fermentation to hexanol (engineered) | 11 | 7 | 1 |
| superpathway of glyoxylate bypass and TCA | 12 | 11 | 1 |
| superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass | 26 | 22 | 1 |
| 1-butanol autotrophic biosynthesis (engineered) | 27 | 19 | 1 |
| oleate β-oxidation | 35 | 33 | 1 |
| superpathway of L-lysine degradation | 43 | 17 | 1 |