Experiment set9IT062 for Desulfovibrio vulgaris Hildenborough JW710

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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 (40 mM), pH=7.2
Culturing: DvH_JW710, 15 mL tube, Anaerobic, at 30 (C), shaken=0 rpm
By: Valentine on 4/17/2017
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 24 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
Flagellum 2
Formate hydrogenase 2
Cysteine Biosynthesis 1
Flagellar motility 1
Flagellum in Campylobacter 1
Glycine reductase, sarcosine reductase and betaine reductase 1
Hydantoin metabolism 1
Ketoisovalerate oxidoreductase 1
Molybdenum cofactor biosynthesis 1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate 1
Thioredoxin-disulfide reductase 1
Wyeosine-MimG Biosynthesis 1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

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
formate oxidation to CO2 1 1 1
thioredoxin pathway 2 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
oxalate degradation VI 4 1 1
oxalate degradation III 5 1 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
colupulone and cohumulone biosynthesis 6 1 1
β-alanine biosynthesis II 6 1 1
lupulone and humulone biosynthesis 6 1 1
adlupulone and adhumulone 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
superpathway of C1 compounds oxidation to CO2 12 2 1
purine nucleobases degradation I (anaerobic) 15 5 1
purine nucleobases degradation II (anaerobic) 24 16 1