Experiment set6IT033 for Desulfovibrio vulgaris Hildenborough JW710
Formate/Acetate-Sulfate (60/10-30 mM) minimal
Group: respiratory growthMedia: Dv_base_medium + Sodium Formate (60 mM) + Sodium acetate (10 mM) + Sodium sulfate (30 mM), pH=7.2
Culturing: DvH_JW710, 15 mL tube, Anaerobic, at 30 (C), shaken=0 rpm
By: Valentine on 12/12/2016
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, 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 respiratory growth Sodium Formate in Desulfovibrio vulgaris Hildenborough JW710
For respiratory growth Sodium Formate across organisms
SEED Subsystems
Metabolic Maps
Color code by fitness: see overview map or list of maps.
Maps containing gene(s) with specific phenotypes:
- Glycolysis / Gluconeogenesis
- Arginine and proline metabolism
- Pyruvate metabolism
- Propanoate metabolism
- Reductive carboxylate cycle (CO2 fixation)
MetaCyc Pathways
Pathways that contain genes with specific phenotypes:
| Pathway | #Steps | #Present | #Specific |
|---|---|---|---|
| acetate conversion to acetyl-CoA | 1 | 1 | 1 |
| acetate and ATP formation from acetyl-CoA III | 1 | 1 | 1 |
| superpathway of acetate utilization and formation | 3 | 3 | 1 |
| ethanol degradation IV | 3 | 2 | 1 |
| ethanol degradation II | 3 | 2 | 1 |
| L-isoleucine biosynthesis V | 3 | 2 | 1 |
| ethanol degradation III | 3 | 1 | 1 |
| chitin deacetylation | 4 | 2 | 1 |
| creatinine degradation II | 5 | 1 | 1 |
| 2-methylcitrate cycle I | 5 | 1 | 1 |
| L-isoleucine biosynthesis IV | 6 | 4 | 1 |
| superpathway of bitter acids biosynthesis | 18 | 3 | 3 |
| β-alanine biosynthesis II | 6 | 1 | 1 |
| adlupulone and adhumulone biosynthesis | 6 | 1 | 1 |
| lupulone and humulone biosynthesis | 6 | 1 | 1 |
| 2-methylcitrate cycle II | 6 | 1 | 1 |
| colupulone and cohumulone biosynthesis | 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 |