Experiment set7IT063 for Desulfovibrio vulgaris Miyazaki F
L-Serine nitrogen source
Group: nitrogen sourceMedia: MoLS4_no_ammonia + L-Serine
Culturing: Miya_ML3_a, 24 deep-well microplate, Anaerobic, at 30 (C), shaken=0 rpm
By: Jen on 4/6/2015
Media components: 30 mM Sodium sulfate, 60 mM Sodium D,L-Lactate, 30 mM Tris hydrochloride, 0.12 mM EDTA, 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 4 genes in this experiment
For nitrogen source L-Serine in Desulfovibrio vulgaris Miyazaki F
For nitrogen source L-Serine across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Ammonia assimilation | 3 |
| Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis | 1 |
| Glycine and Serine Utilization | 1 |
| Pyruvate Alanine Serine Interconversions | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Glutamate metabolism
- Glycine, serine and threonine metabolism
- Cysteine metabolism
- Nitrogen metabolism
- Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| L-serine degradation | 3 | 3 | 3 |
| L-glutamate biosynthesis I | 2 | 2 | 2 |
| L-glutamine degradation I | 1 | 1 | 1 |
| L-glutamine degradation II | 1 | 1 | 1 |
| ammonia assimilation cycle III | 3 | 3 | 2 |
| L-cysteine degradation II | 3 | 2 | 2 |
| L-tryptophan degradation II (via pyruvate) | 3 | 2 | 2 |
| D-serine degradation | 3 | 2 | 2 |
| glycine betaine degradation III | 7 | 4 | 3 |
| felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis | 5 | 2 | 2 |
| glycine betaine degradation I | 8 | 4 | 3 |
| L-methionine biosynthesis II | 6 | 4 | 2 |
| glycine degradation | 3 | 2 | 1 |
| 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-mimosine degradation | 8 | 4 | 2 |
| glutathione-mediated detoxification I | 8 | 2 | 2 |
| superpathway of L-lysine, L-threonine and L-methionine biosynthesis II | 15 | 13 | 2 |
| purine nucleobases degradation II (anaerobic) | 24 | 16 | 3 |
| L-citrulline biosynthesis | 8 | 5 | 1 |
| superpathway of L-citrulline metabolism | 12 | 7 | 1 |