Experiment set57IT023 for Escherichia coli BW25113
Ying_AminoAcid20 rep B; time point 2
Group: carbon sourceMedia: SDM_noCarbon + 1X Ying_AminoAcid20
Culturing: Keio_ML9a, tube, Aerobic, at 28 (C), shaken=180 rpm
By: Ying on 19-Oct-22
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 3 genes in this experiment
For carbon source Ying_AminoAcid20 in Escherichia coli BW25113
For carbon source Ying_AminoAcid20 across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Glycine and Serine Utilization | 1 |
| Polyamine Metabolism | 1 |
| Pyruvate Alanine Serine Interconversions | 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:
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| spermidine biosynthesis I | 2 | 2 | 1 |
| spermine biosynthesis | 2 | 1 | 1 |
| aminopropylcadaverine biosynthesis | 3 | 3 | 1 |
| spermidine biosynthesis III | 4 | 2 | 1 |
| superpathway of polyamine biosynthesis I | 8 | 7 | 1 |
| superpathway of polyamine biosynthesis II | 8 | 4 | 1 |
| L-methionine salvage cycle III | 11 | 5 | 1 |
| L-methionine salvage cycle I (bacteria and plants) | 12 | 5 | 1 |
| superpathway of arginine and polyamine biosynthesis | 17 | 16 | 1 |