Experiment set8IT055 for Pseudomonas fluorescens FW300-N1B4
Nitrate reduction, replicate C, timepoint 2
Group: denitrifyingMedia: Chakraborty_Basal + Sodium pyruvate (15 mM) + Sodium nitrate (30 mM)
Culturing: pseudo1_N1B4_ML1, 150mL Serum Bottle, Anaerobic, at 27 (C), shaken=0 rpm
Growth: about 3.0 generations
By: Alex Aaring on 03/13/16
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 0.3792 g/L Sodium phosphate monobasic, 0.9713 g/L Disodium phosphate, 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)
Specific Phenotypes
For 12 genes in this experiment
For denitrifying Sodium pyruvate in Pseudomonas fluorescens FW300-N1B4
For denitrifying Sodium pyruvate across organisms
SEED Subsystems
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Ubiquinone and menaquinone biosynthesis
- Oxidative phosphorylation
- Histidine metabolism
- Tyrosine metabolism
- Tryptophan metabolism
- Benzoxazinone biosynthesis
- Naphthalene and anthracene degradation
- Nicotinate and nicotinamide metabolism
- Porphyrin and chlorophyll metabolism
- Carotenoid biosynthesis - General
- Nitrogen metabolism
- Phenylpropanoid biosynthesis
- Flavonoid biosynthesis
- Anthocyanin biosynthesis
- Alkaloid biosynthesis I
- Insect hormone biosynthesis
- Biosynthesis of alkaloids derived from shikimate pathway
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| arsenite to oxygen electron transfer | 2 | 1 | 1 |
| heme d1 biosynthesis | 3 | 2 | 1 |
| ammonia oxidation II (anaerobic) | 3 | 1 | 1 |
| arsenite to oxygen electron transfer (via azurin) | 3 | 1 | 1 |
| nitrite-dependent anaerobic methane oxidation | 3 | 1 | 1 |
| aerobic respiration II (cytochrome c) (yeast) | 4 | 3 | 1 |
| aerobic respiration I (cytochrome c) | 4 | 3 | 1 |
| nitrate reduction I (denitrification) | 5 | 5 | 1 |
| nitrate reduction VII (denitrification) | 5 | 4 | 1 |
| nitrifier denitrification | 6 | 3 | 1 |
| NAD(P)/NADPH interconversion | 6 | 3 | 1 |
| Fe(II) oxidation | 6 | 3 | 1 |