Experiment set7IT061 for Desulfovibrio vulgaris Miyazaki F

MoLS4 with Sodium Chlorate 6.25 mM

Group: stress
Media: MoLS4 + Sodium Chlorate (6.25 mM)
Culturing: Miya_ML3_a, 24 deep-well microplate, Anaerobic, at 30 (C), shaken=0 rpm
By: Jen on 4/6/2015
Media components: 30 mM Sodium sulfate, 60 mM Sodium D,L-Lactate, 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 17 genes in this experiment

For stress Sodium Chlorate in Desulfovibrio vulgaris Miyazaki F

For stress Sodium Chlorate across organisms

SEED Subsystems

Subsystem	#Specific
Anaerobic respiratory reductases	2
Dihydroxyacetone kinases	2
Molybdenum cofactor biosynthesis	2
Bacterial Chemotaxis	1
Chorismate Synthesis	1
Flagellar motility	1
Folate Biosynthesis	1
Formate hydrogenase	1
Phenylalanine and Tyrosine Branches from Chorismate	1
Two-component regulatory systems in Campylobacter	1
Zinc resistance	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Phenylalanine, tyrosine and tryptophan biosynthesis
• Lipopolysaccharide biosynthesis
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Glycolysis / Gluconeogenesis
• Pentose phosphate pathway
• Fructose and mannose metabolism
• Galactose metabolism
• Ascorbate and aldarate metabolism
• Starch and sucrose metabolism
• Nucleotide sugars metabolism
• Aminosugars metabolism
• Glycosylphosphatidylinositol(GPI)-anchor biosynthesis
• Glyoxylate and dicarboxylate metabolism
• Methane metabolism
• Nicotinate and nicotinamide metabolism
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
formate oxidation to CO2	1	1	1
NADH to dimethyl sulfoxide electron transfer	2	2	1
hydrogen to dimethyl sulfoxide electron transfer	2	1	1
formate to dimethyl sulfoxide electron transfer	2	1	1
glycerol degradation V	2	1	1
L-phenylalanine biosynthesis I	3	3	1
L-tyrosine biosynthesis I	3	3	1
L-tyrosine biosynthesis III	4	2	1
L-tyrosine biosynthesis II	4	1	1
oxalate degradation VI	4	1	1
L-phenylalanine biosynthesis II	4	1	1
chorismate biosynthesis from 3-dehydroquinate	5	5	1
superpathway of L-phenylalanine biosynthesis	10	9	2
superpathway of L-tyrosine biosynthesis	10	9	2
oxalate degradation III	5	1	1
superpathway of L-phenylalanine and L-tyrosine biosynthesis	5	1	1
chorismate biosynthesis I	7	6	1
superpathway of aromatic amino acid biosynthesis	18	17	2
bacilysin biosynthesis	10	1	1
chorismate biosynthesis II (archaea)	12	9	1
superpathway of C1 compounds oxidation to CO2	12	2	1
superpathway of L-tryptophan biosynthesis	13	12	1
purine nucleobases degradation I (anaerobic)	15	5	1
salinosporamide A biosynthesis	15	3	1
purine nucleobases degradation II (anaerobic)	24	16	1
superpathway of chorismate metabolism	59	31	2