Experiment set3S930 for Rhodanobacter sp. FW510-T8
NLDM_defined_nocarbon with D-Glucose and 20AA_mix 0.1X
Group: nutrientMedia: NLDM_defined_nocarbon + D-Glucose (20 mM) + 0.1X 20AA_mix, pH=7
Culturing: rhodanobacter_T8_ML1, 96 well deep well block, Aerobic, at 23 (C), shaken=700 rpm
By: Hira Lesea on 09/01/2025
Media components: 1 mM Ammonium chloride, 3.3 mM Potassium Chloride, 0.812 mM Magnesium Sulfate Heptahydrate, 0.68 mM Calcium chloride dihydrate, 4.05 mM Disodium phosphate, 0.95 mM Sodium phosphate monobasic, ATCC Wolfe's mineral mix (5 mg/L EDTA, 3 mg/L Magnesium Sulfate Heptahydrate, 5 mg/L Manganese (II) sulfate monohydrate, 10 mg/L Sodium Chloride, 1 mg/L Iron (II) sulfate heptahydrate, 1 mg/L Cobalt(II) nitrate hexahydrate, 1 mg/L Calcium chloride dihydrate, 1 mg/L Zinc sulfate heptahydrate, 0.1 mg/L Copper (II) sulfate pentahydrate, 0.1 mg/L Aluminum potassium sulfate dodecahydrate, 0.1 mg/L Boric Acid, 0.1 mg/L Sodium Molybdate Dihydrate, 0.01 mg/L Sodium selenite pentahydrate, 0.1 mg/L Sodium tungstate dihydrate, 0.2 mg/L Nickel (II) chloride hexahydrate), ATCC Wolfe's vitamin mix (20 ug/L Folic Acid, 100 ug/L Pyridoxine HCl, 50 ug/L Riboflavin, 20 ug/L biotin, 50 ug/L Thiamine HCl, 50 ug/L Nicotinic Acid, 50 ug/L calcium pantothenate, 1 ug/L Cyanocobalamin, 50 ug/L 4-Aminobenzoic acid, 50 ug/L Lipoic acid)
20AA_mix 0.1x includes: 0.05 mM L-Arginine, 0.05 mM L-Histidine, 0.05 mM L-Lysine, 0.05 mM L-Aspartic Acid, 0.05 mM L-Glutamic acid monopotassium salt monohydrate, 0.05 mM L-Serine, 0.05 mM L-Threonine, 0.05 mM L-Asparagine, 0.05 mM L-Glutamine, 0.05 mM L-Cysteine hydrochloride monohydrate, 0.05 mM Glycine, 0.05 mM L-Proline, 0.05 mM L-Alanine, 0.05 mM L-Valine, 0.05 mM L-Isoleucine, 0.05 mM L-Leucine, 0.05 mM L-Methionine, 0.05 mM L-Phenylalanine, 0.05 mM L-tyrosine disodium salt, 0.05 mM L-Tryptophan (final concentrations)
Specific Phenotypes
For 5 genes in this experiment
For nutrient D-Glucose in Rhodanobacter sp. FW510-T8
For nutrient D-Glucose across organisms
SEED Subsystems
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Tyrosine metabolism
- Fatty acid biosynthesis
- Lysine degradation
- Histidine metabolism
- Phenylalanine metabolism
- Glutathione metabolism
- Lipopolysaccharide biosynthesis
- Glycerophospholipid metabolism
- Ether lipid metabolism
- Glycosphingolipid biosynthesis - ganglio series
- 1- and 2-Methylnaphthalene degradation
- Benzoate degradation via CoA ligation
- Ethylbenzene degradation
- Styrene degradation
- Butanoate metabolism
- Limonene and pinene degradation
- Diterpenoid biosynthesis
- Carotenoid biosynthesis - General
- Anthocyanin biosynthesis
- Alkaloid biosynthesis I
- Alkaloid biosynthesis II
- Metabolism of xenobiotics by cytochrome P450
- Drug metabolism - cytochrome P450
- Biosynthesis of unsaturated fatty acids
- Biosynthesis of type II polyketide backbone
- Biosynthesis of terpenoids and steroids
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| gentisate degradation I | 3 | 2 | 1 |
| 4-hydroxy-2-nonenal detoxification | 4 | 1 | 1 |
| L-tyrosine degradation I | 5 | 4 | 1 |
| pentachlorophenol degradation | 10 | 3 | 2 |
| 5-nitroanthranilate degradation | 6 | 3 | 1 |
| glutathione-mediated detoxification I | 8 | 3 | 1 |
| gliotoxin biosynthesis | 9 | 1 | 1 |
| glutathione-mediated detoxification II | 9 | 1 | 1 |
| 3-phenylpropanoate degradation | 10 | 5 | 1 |
| indole glucosinolate activation (intact plant cell) | 12 | 3 | 1 |
| camalexin biosynthesis | 12 | 2 | 1 |