Experiment set8IT056 for Desulfovibrio vulgaris Hildenborough JW710
MoLS4 with L-Arginine nitrogen source
Group: nitrogen sourceMedia: MoLS4_no_ammonium + L-Arginine (20 mM), pH=7.2
Culturing: DvH_JW710, 24 deep-well microplate, Anaerobic, at 30 (C), shaken=0 rpm
By: Valentine on 3/3/2017
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 (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 21 genes in this experiment
For nitrogen source L-Arginine in Desulfovibrio vulgaris Hildenborough JW710
For nitrogen source L-Arginine across organisms
SEED Subsystems
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Glycine, serine and threonine metabolism
- Lysine biosynthesis
- Aminophosphonate metabolism
- Starch and sucrose metabolism
- High-mannose type N-glycan biosynthesis
- Nucleotide sugars metabolism
- Glycerophospholipid metabolism
- Sphingolipid metabolism
- One carbon pool by folate
- 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 |
|---|---|---|---|
| glycine biosynthesis II | 3 | 3 | 2 |
| glycine cleavage | 3 | 3 | 2 |
| cardiolipin biosynthesis II | 3 | 3 | 1 |
| cardiolipin and phosphatidylethanolamine biosynthesis (Xanthomonas) | 4 | 3 | 1 |
| glycogen biosynthesis I (from ADP-D-Glucose) | 4 | 3 | 1 |
| L-lysine biosynthesis VI | 7 | 7 | 1 |
| L-lysine biosynthesis I | 9 | 7 | 1 |
| L-lysine biosynthesis II | 9 | 6 | 1 |
| starch biosynthesis | 10 | 5 | 1 |
| superpathway of cardiolipin biosynthesis (bacteria) | 13 | 9 | 1 |
| superpathway of L-lysine, L-threonine and L-methionine biosynthesis II | 15 | 13 | 1 |
| superpathway of L-lysine, L-threonine and L-methionine biosynthesis I | 18 | 13 | 1 |
| aspartate superpathway | 25 | 20 | 1 |