Experiment set2S321 for Desulfovibrio vulgaris Hildenborough JW710

Formate/Acetate-Sulfate (60/30-30 mM) minimal without Molybdate

Group: respiratory growth
Media: Dv_base_medium_no_Mo + Sodium Formate (60 mM) + Sodium acetate (30 mM) + Sodium sulfate (30 mM), pH=7.2
Culturing: DvH_JW710, 15 mL tube, Anaerobic, at 30 (C), shaken=0 rpm
By: Valentine on 4/18/2016
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 minus Sodium molybdate (15 uM Manganese (II) chloride tetrahydrate, 7.8 uM Cobalt chloride hexahydrate, 9 uM Zinc chloride, 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 Sodium Formate in Desulfovibrio vulgaris Hildenborough JW710

For respiratory growth Sodium Formate across organisms

SEED Subsystems

Subsystem	#Specific
Na(+)-translocating NADH-quinone oxidoreductase and rnf-like group of electron transport complexes	4
Calvin-Benson cycle	1
Entner-Doudoroff Pathway	1
Glycolysis and Gluconeogenesis	1
Hydantoin metabolism	1
Pyridoxin (Vitamin B6) Biosynthesis	1
Redox-dependent regulation of nucleus processes	1

Metabolic Maps

Color code by fitness: see overview map or list of maps.

Maps containing gene(s) with specific phenotypes:

• Glycolysis / Gluconeogenesis
• Urea cycle and metabolism of amino groups
• Geraniol degradation
• Lysine biosynthesis
• Arginine and proline metabolism
• Tryptophan metabolism
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Limonene and pinene degradation
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
pyridoxal 5'-phosphate biosynthesis I	7	5	1
sucrose biosynthesis I (from photosynthesis)	9	7	1
Entner-Doudoroff pathway I	9	6	1
glycolysis IV	10	8	1
glycolysis II (from fructose 6-phosphate)	11	10	1
glycolysis III (from glucose)	11	10	1
glycolysis VI (from fructose)	11	8	1
homolactic fermentation	12	11	1
formaldehyde assimilation III (dihydroxyacetone cycle)	12	10	1
gluconeogenesis III	12	9	1
superpathway of pyridoxal 5'-phosphate biosynthesis and salvage	12	9	1
glycolysis I (from glucose 6-phosphate)	13	11	1
gluconeogenesis I	13	10	1
Bifidobacterium shunt	15	13	1
glycerol degradation to butanol	16	9	1
superpathway of glucose and xylose degradation	17	12	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	12	1
heterolactic fermentation	18	13	1
superpathway of hexitol degradation (bacteria)	18	11	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	16	1
superpathway of anaerobic sucrose degradation	19	15	1
superpathway of N-acetylneuraminate degradation	22	15	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	14	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	18	1