Experiment set6S93 for Pseudomonas sp. RS175
methyl ferulate carbon source
Group: carbon sourceMedia: MME_noCarbon + methyl ferulate (2 mM)
Culturing: Pseudomonas_RS175_ML2, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C)
By: Andrew Frank on 1/31/23
Media components: 9.1 mM Potassium phosphate dibasic trihydrate, 20 mM 3-(N-morpholino)propanesulfonic acid, 4.3 mM Sodium Chloride, 10 mM Ammonium 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 21 genes in this experiment
For carbon source methyl ferulate in Pseudomonas sp. RS175
For carbon source methyl ferulate across organisms
SEED Subsystems
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Ubiquinone and menaquinone biosynthesis
- Methane metabolism
- Ascorbate and aldarate metabolism
- Methionine metabolism
- Histidine metabolism
- Phenylalanine metabolism
- gamma-Hexachlorocyclohexane degradation
- Bisphenol A degradation
- Tryptophan metabolism
- Cyanoamino acid metabolism
- Starch and sucrose metabolism
- Nucleotide sugars metabolism
- Glycosaminoglycan degradation
- Peptidoglycan biosynthesis
- Toluene and xylene degradation
- 2,4-Dichlorobenzoate degradation
- 1- and 2-Methylnaphthalene degradation
- Naphthalene and anthracene degradation
- 1,4-Dichlorobenzene degradation
- Benzoate degradation via CoA ligation
- Styrene degradation
- Limonene and pinene degradation
- Brassinosteroid biosynthesis
- Carotenoid biosynthesis - General
- Phenylpropanoid biosynthesis
- Flavonoid biosynthesis
- Isoflavonoid biosynthesis
- Alkaloid biosynthesis I
- Biosynthesis of phenylpropanoids
- 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 |
|---|---|---|---|
| 3-methylthiopropanoate biosynthesis | 1 | 1 | 1 |
| vanillin and vanillate degradation II | 2 | 2 | 1 |
| formaldehyde oxidation II (glutathione-dependent) | 3 | 3 | 1 |
| trehalose biosynthesis V | 3 | 3 | 1 |
| methylglyoxal degradation I | 3 | 2 | 1 |
| methylglyoxal degradation VIII | 3 | 2 | 1 |
| nylon-6 oligomer degradation | 7 | 3 | 2 |
| starch degradation V | 4 | 3 | 1 |
| peptidoglycan maturation (meso-diaminopimelate containing) | 12 | 4 | 2 |
| S-methyl-5-thio-α-D-ribose 1-phosphate degradation I | 7 | 2 | 1 |
| glycogen degradation I | 8 | 7 | 1 |
| sucrose biosynthesis II | 8 | 6 | 1 |
| superpathway of methylglyoxal degradation | 8 | 3 | 1 |
| starch degradation II | 9 | 1 | 1 |
| L-methionine salvage cycle III | 11 | 5 | 1 |
| L-methionine salvage cycle II (plants) | 11 | 3 | 1 |
| superpathway of C1 compounds oxidation to CO2 | 12 | 5 | 1 |
| L-methionine salvage cycle I (bacteria and plants) | 12 | 4 | 1 |
| peptidoglycan biosynthesis II (staphylococci) | 17 | 12 | 1 |
| peptidoglycan biosynthesis IV (Enterococcus faecium) | 17 | 12 | 1 |