Experiment set9IT016 for Desulfovibrio vulgaris Miyazaki F
MoYLS4 media with N2 no edta
Group: nitrogen sourceMedia: MoLS4_no_ammonnia_noEDTA + N2 (90 % atm), pH=7.2
Culturing: Miya_ML3_a, SerumBottle, Anaerobic, at 30 (C), shaken=0 rpm
By: Wetmore (Baker) on 22-Apr-19
Media components: 30 mM Sodium sulfate, 60 mM Sodium D,L-Lactate, 30 mM Tris hydrochloride, 1 mM Sodium sulfide nonahydrate, 8 mM Magnesium chloride hexahydrate, 0.6 mM Calcium chloride, 2 mM Potassium phosphate dibasic, 60 uM Iron (II) chloride tetrahydrate, 15 uM Manganese (II) chloride tetrahydrate, 7.8 uM Cobalt chloride hexahydrate, 9 uM Zinc chloride, 1.26 uM Sodium molybdate, 1.92 uM Boric Acid, 2.28 uM Nickel (II) sulfate hexahydrate, 0.06 uM copper (II) chloride dihydrate, 0.21 uM Sodium selenite pentahydrate, 0.144 uM Sodium tungstate dihydrate, Thauer's vitamin mix (0.01 mg/L Pyridoxine HCl, 0.005 mg/L 4-Aminobenzoic acid, 0.005 mg/L Lipoic acid, 0.005 mg/L Nicotinic Acid, 0.005 mg/L Riboflavin, 0.005 mg/L Thiamine HCl, 0.005 mg/L calcium pantothenate, 0.002 mg/L biotin, 0.002 mg/L Folic Acid, 0.0001 mg/L Cyanocobalamin, 0.2 mg/L Choline chloride)
Specific Phenotypes
For 12 genes in this experiment
For nitrogen source N2 in Desulfovibrio vulgaris Miyazaki F
For nitrogen source N2 across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Nitrogen fixation | 7 |
| Ammonia assimilation | 3 |
| Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis | 1 |
| Potassium homeostasis | 1 |
| Zinc resistance | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Nitrogen metabolism
- Glutamate metabolism
- Tetrachloroethene degradation
- Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| L-glutamate biosynthesis I | 2 | 2 | 2 |
| nitrogen fixation I (ferredoxin) | 1 | 1 | 1 |
| L-glutamine degradation I | 1 | 1 | 1 |
| L-glutamine degradation II | 1 | 1 | 1 |
| ammonia assimilation cycle III | 3 | 3 | 2 |
| L-glutamate and L-glutamine biosynthesis | 7 | 4 | 2 |
| L-asparagine biosynthesis III (tRNA-dependent) | 4 | 4 | 1 |
| glutaminyl-tRNAgln biosynthesis via transamidation | 4 | 3 | 1 |
| L-citrulline biosynthesis | 8 | 5 | 1 |
| superpathway of L-citrulline metabolism | 12 | 7 | 1 |