Experiment set6IT014 for Desulfovibrio vulgaris Hildenborough JW710

Formate/Acetate-Sulfite (60/30-40 mM) + 0.1% Yeast Extract

Group: respiratory growth
Media: Dv_base_Y_medium + Sodium Formate (60 mM) + Sodium acetate (30 mM) + sodium sulfite (20 mM), pH=7.2
Culturing: DvH_JW710, 24 deep-well microplate, 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, 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 25 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	5
Hydantoin metabolism	2
Molybdenum cofactor biosynthesis	2
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	2
Cysteine Biosynthesis	1
Formate hydrogenase	1
Ketoisovalerate oxidoreductase	1
Transport of Zinc	1
Zinc resistance	1

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 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
ethanol degradation II	3	2	1
L-isoleucine biosynthesis V	3	2	1
ethanol degradation IV	3	2	1
ethanol degradation III	3	1	1
chitin deacetylation	4	2	1
2-methylcitrate cycle I	5	1	1
creatinine degradation II	5	1	1
L-isoleucine biosynthesis IV	6	4	1
superpathway of bitter acids biosynthesis	18	3	3
2-methylcitrate cycle II	6	1	1
β-alanine biosynthesis II	6	1	1
lupulone and humulone biosynthesis	6	1	1
adlupulone and adhumulone biosynthesis	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