Experiment set8S96 for Rhodanobacter denitrificans FW104-10B01
D-Glucose carbon source and 20 AA mix; 30C
Group: carbon sourceMedia: RCH2_defined_noCarbon + D-Glucose (20 mM) + 0.1X 20AA_mix
Culturing: rhodanobacter_10B01_ML12, tube, Aerobic, at 30 (C), shaken=200 rpm
By: Hira on 03/01/2023
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 30 mM PIPES sesquisodium salt, 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)
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 2 genes in this experiment
For carbon source D-Glucose in Rhodanobacter denitrificans FW104-10B01
For carbon source D-Glucose across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Cysteine Biosynthesis | 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 |
|---|---|---|---|
| assimilatory sulfate reduction III | 3 | 3 | 1 |
| assimilatory sulfate reduction I | 4 | 4 | 1 |
| assimilatory sulfate reduction IV | 4 | 3 | 1 |
| 2-deoxy-D-glucose 6-phosphate degradation | 4 | 2 | 1 |
| superpathway of sulfate assimilation and cysteine biosynthesis | 9 | 8 | 1 |
| superpathway of sulfur amino acid biosynthesis (Saccharomyces cerevisiae) | 10 | 8 | 1 |
| superpathway of L-methionine biosynthesis (by sulfhydrylation) | 12 | 11 | 1 |