Experiment set1S312 for Rhodopseudomonas palustris CGA009
4-Aminobutyric acid carbon source; anaerobic
Group: carbon sourceMedia: PM + 4-Aminobutyric acid (10 mM) + Sodium bicarbonate (10 mM) + Light intensity (30 µmol photons/m2/s from a 60-W incandescent light bulb)
Culturing: RPal_CGA009_ML8, tube, Anaerobic, at 30 (C)
By: Rpal_Yasu on 9/1/24
Media components: 12.5 mM Disodium phosphate, 12.5 mM Potassium phosphate monobasic, 1 g/L Ammonium Sulfate, 0.1 mM Sodium thiosulfate pentahydrate, 0.002 g/L 4-Aminobenzoic acid, UW concentrated base (0.02 g/L Nitrilotriacetic acid, 0.0289 g/L Magnesium sulfate, 0.00667 g/L Calcium chloride dihydrate, 1.85e-05 g/L ammonium molybdate tetrahydrate, 0.000698 g/L Iron (II) sulfate heptahydrate, 0.00025 g/L EDTA, 0.001095 g/L Zinc sulfate heptahydrate, 0.000154 g/L Manganese (II) sulfate monohydrate, 3.92e-05 g/L Copper (II) sulfate pentahydrate, 2.5e-05 g/L Cobalt(II) nitrate hexahydrate, 1.77e-05 g/L sodium tetraborate decahydrate)
Specific Phenotypes
For 9 genes in this experiment
For carbon source 4-Aminobutyric acid in Rhodopseudomonas palustris CGA009
For carbon source 4-Aminobutyric acid across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Utilization of glutathione as a sulphur source | 4 |
| Biotin biosynthesis | 1 |
| Glycogen metabolism | 1 |
| Trehalose Biosynthesis | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Propanoate metabolism
- Alanine and aspartate metabolism
- Valine, leucine and isoleucine degradation
- beta-Alanine metabolism
- Ascorbate and aldarate metabolism
- Ubiquinone and menaquinone biosynthesis
- Glutamate metabolism
- Geraniol degradation
- Tyrosine metabolism
- Nucleotide sugars metabolism
- Glycosaminoglycan degradation
- alpha-Linolenic acid metabolism
- Benzoate degradation via CoA ligation
- Ethylbenzene degradation
- Butanoate metabolism
- Biotin metabolism
- Limonene and pinene degradation
- Caprolactam degradation
- Alkaloid biosynthesis II
- Biosynthesis of plant hormones
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| 4-aminobutanoate degradation III | 2 | 2 | 1 |
| β-alanine degradation II | 2 | 2 | 1 |
| 4-aminobutanoate degradation II | 2 | 1 | 1 |
| 4-aminobutanoate degradation I | 2 | 1 | 1 |
| superpathway of 4-aminobutanoate degradation | 3 | 1 | 1 |
| biotin biosynthesis from 8-amino-7-oxononanoate I | 4 | 4 | 1 |
| GABA shunt II | 4 | 2 | 1 |
| GABA shunt I | 4 | 1 | 1 |
| L-lysine degradation IV | 5 | 2 | 1 |
| L-lysine degradation X | 6 | 4 | 1 |
| β-alanine biosynthesis II | 6 | 4 | 1 |
| L-lysine degradation III | 6 | 2 | 1 |
| L-lysine degradation I | 7 | 4 | 1 |
| 4-aminobutanoate degradation V | 7 | 1 | 1 |
| L-valine degradation I | 8 | 6 | 1 |
| superpathway of coenzyme A biosynthesis II (plants) | 10 | 8 | 1 |
| superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation | 11 | 3 | 1 |
| superpathway of L-arginine and L-ornithine degradation | 13 | 5 | 1 |
| biotin biosynthesis I | 15 | 13 | 1 |
| nicotine degradation I (pyridine pathway) | 17 | 4 | 1 |
| superpathway of L-lysine degradation | 43 | 13 | 1 |