Experiment set25S542 for Pseudomonas fluorescens FW300-N2E2
Ying_AminoAcid20 rep C; time point 3
Group: carbon sourceMedia: SDM_noCarbon + 1X Ying_AminoAcid20
Culturing: pseudo6_N2E2_ML5b, tube, Aerobic, at 28 (C), shaken=180 rpm
By: Ying and Valentine on 1-Sep-23
Media components: 1.5 g/L Ammonium chloride, 0.6 g/L Potassium phosphate monobasic, 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)
Ying_AminoAcid20 1x includes: 128 uM L-Alanine, 128 uM L-Arginine, 128 uM L-Asparagine, 128 uM L-Aspartic Acid, 128 uM L-Cysteine, 128 uM L-Glutamic acid, 128 uM L-Glutamine, 128 uM Glycine, 128 uM L-Histidine, 128 uM L-Isoleucine, 128 uM L-Leucine, 128 uM L-Lysine, 128 uM L-Methionine, 128 uM L-Phenylalanine, 128 uM L-Proline, 128 uM L-Serine, 128 uM L-Threonine, 128 uM L-Tryptophan, 128 uM L-tyrosine, 128 uM L-Valine
Specific Phenotypes
For 5 genes in this experiment
For carbon source Ying_AminoAcid20 in Pseudomonas fluorescens FW300-N2E2
For carbon source Ying_AminoAcid20 across organisms
SEED Subsystems
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Urea cycle and metabolism of amino groups
- Arginine and proline metabolism
- Histidine metabolism
- Valine, leucine and isoleucine degradation
- Geraniol degradation
- Lysine biosynthesis
- Tryptophan metabolism
- 1- and 2-Methylnaphthalene degradation
- Naphthalene and anthracene degradation
- Glyoxylate and dicarboxylate metabolism
- Propanoate metabolism
- Limonene and pinene degradation
- Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| 2-oxoisovalerate decarboxylation to isobutanoyl-CoA | 3 | 3 | 1 |
| L-histidine degradation I | 4 | 4 | 1 |
| L-histidine degradation II | 5 | 5 | 1 |
| L-ornithine biosynthesis I | 5 | 5 | 1 |
| 2-methylcitrate cycle I | 5 | 5 | 1 |
| 2-methylcitrate cycle II | 6 | 5 | 1 |
| L-arginine biosynthesis I (via L-ornithine) | 9 | 9 | 1 |
| L-arginine biosynthesis III (via N-acetyl-L-citrulline) | 9 | 8 | 1 |
| L-arginine biosynthesis II (acetyl cycle) | 10 | 10 | 1 |
| superpathway of arginine and polyamine biosynthesis | 17 | 14 | 1 |