Experiment set4IT020 for Desulfovibrio vulgaris Hildenborough JW710
MoLS4 with L-Serine nitrogen source, without W
Group: nitrogen sourceMedia: MoLS4_no_ammonium_no_W + L-Serine (20 mM), pH=7.2
Culturing: DvH_JW710, 24 deep-well microplate, Anaerobic, at 30 (C), shaken=0 rpm
By: Valentine on 11/10/2016
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, Desulfovibrio trace elements minus Sodium tungstate dihydrate (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), 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 5 genes in this experiment
For nitrogen source L-Serine in Desulfovibrio vulgaris Hildenborough JW710
For nitrogen source L-Serine across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Zinc resistance | 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 |
|---|---|---|---|
| L-serine degradation | 3 | 3 | 3 |
| L-tryptophan degradation II (via pyruvate) | 3 | 3 | 2 |
| L-cysteine degradation II | 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 |
| spermidine biosynthesis II | 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 |
| superpathway of polyamine biosynthesis III | 8 | 3 | 1 |
| L-lysine biosynthesis IV | 9 | 3 | 1 |