Experiment set11IT005 for Desulfovibrio vulgaris Hildenborough JW710
MoLS4 with L-Tryptophan as nutrient source 10mM
Group: nutrientMedia: MoLS4 + L-Tryptophan (10 mM), pH=7.2
Culturing: DvH_JW710, 24 deep-well microplate, Anaerobic, at 30 (C), shaken=0 rpm
By: Valentine on 5/5/2017
Media components: 30 mM Sodium sulfate, 60 mM Sodium D,L-Lactate, 20 mM Ammonium chloride, 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 4 genes in this experiment
For nutrient L-Tryptophan in Desulfovibrio vulgaris Hildenborough JW710
For nutrient L-Tryptophan across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Coenzyme A Biosynthesis | 1 |
| Glycolate, glyoxylate interconversions | 1 |
| Photorespiration (oxidative C2 cycle) | 1 |
| Pyridoxin (Vitamin B6) Biosynthesis | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Glyoxylate and dicarboxylate metabolism
- beta-Alanine metabolism
- Vitamin B6 metabolism
- Pantothenate and CoA biosynthesis
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| glycolate and glyoxylate degradation II | 2 | 2 | 1 |
| glycolate and glyoxylate degradation III | 3 | 1 | 1 |
| phosphopantothenate biosynthesis I | 4 | 4 | 1 |
| glycolate and glyoxylate degradation I | 4 | 1 | 1 |
| pyridoxal 5'-phosphate biosynthesis I | 7 | 5 | 1 |
| superpathway of glycol metabolism and degradation | 7 | 2 | 1 |
| superpathway of coenzyme A biosynthesis I (bacteria) | 9 | 8 | 1 |
| photorespiration I | 9 | 6 | 1 |
| photorespiration III | 9 | 6 | 1 |
| photorespiration II | 10 | 6 | 1 |
| superpathway of coenzyme A biosynthesis II (plants) | 10 | 5 | 1 |
| superpathway of pyridoxal 5'-phosphate biosynthesis and salvage | 12 | 9 | 1 |