Experiment set17IT091 for Desulfovibrio vulgaris Hildenborough JW710
Hydrogen/Acetate-Sulfite (90%atm/5mM-20mM) with 0.1% Yeast Extract
Group: respiratory growthMedia: Dv_base_Y_medium + H2 (90 %atm) + Sodium acetate (5 mM) + sodium sulfite (20 mM), pH=7.2
Culturing: DvH_JW710, 15 mL tube, Anaerobic, at 30 (C), shaken=0 rpm
By: Kara on 5/22/2018
Media components: 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, 1 g/L Yeast Extract, 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 7 genes in this experiment
For respiratory growth H2 in Desulfovibrio vulgaris Hildenborough JW710
For respiratory growth H2 across organisms
SEED Subsystems
| Subsystem | #Specific |
|---|---|
| Bacterial Chemotaxis | 1 |
| Ketoisovalerate oxidoreductase | 1 |
| Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate | 1 |
| Two-component regulatory systems in Campylobacter | 1 |
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Glycolysis / Gluconeogenesis
- Pyruvate metabolism
- Propanoate metabolism
- Reductive carboxylate cycle (CO2 fixation)
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| acetate and ATP formation from acetyl-CoA III | 1 | 1 | 1 |
| acetate conversion to acetyl-CoA | 1 | 1 | 1 |
| superpathway of acetate utilization and formation | 3 | 3 | 1 |
| L-isoleucine biosynthesis V | 3 | 2 | 1 |
| ethanol degradation IV | 3 | 2 | 1 |
| ethanol degradation II | 3 | 2 | 1 |
| ethanol degradation III | 3 | 1 | 1 |
| chitin deacetylation | 4 | 2 | 1 |
| 2-methylcitrate cycle I | 5 | 1 | 1 |
| L-isoleucine biosynthesis IV | 6 | 4 | 1 |
| superpathway of bitter acids biosynthesis | 18 | 3 | 3 |
| lupulone and humulone biosynthesis | 6 | 1 | 1 |
| β-alanine biosynthesis II | 6 | 1 | 1 |
| colupulone and cohumulone biosynthesis | 6 | 1 | 1 |
| adlupulone and adhumulone biosynthesis | 6 | 1 | 1 |
| 2-methylcitrate cycle II | 6 | 1 | 1 |
| reductive glycine pathway of autotrophic CO2 fixation | 9 | 6 | 1 |
| cis-geranyl-CoA degradation | 9 | 1 | 1 |
| superpathway of coenzyme A biosynthesis II (plants) | 10 | 5 | 1 |