Experiment set6IT011 for Desulfovibrio vulgaris Hildenborough JW710

MoYLS4 with FCCP 10uM

Group: stress
Media: MoYLS4 + FCCP (10 uM), 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: 1 g/L Yeast Extract, 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, 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 16 genes in this experiment

For stress FCCP in Desulfovibrio vulgaris Hildenborough JW710

For stress FCCP across organisms

SEED Subsystems

Subsystem	#Specific
Molybdenum cofactor biosynthesis	5
Glycerol and Glycerol-3-phosphate Uptake and Utilization	2
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	2
Multidrug Resistance Efflux Pumps	2
Multidrug efflux pump in Campylobacter jejuni (CmeABC operon)	2
Respiratory dehydrogenases 1	2
Entner-Doudoroff Pathway	1
Glycine reductase, sarcosine reductase and betaine reductase	1
Glycolysis and Gluconeogenesis	1
Glycolysis and Gluconeogenesis, including Archaeal enzymes	1
Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria	1
Thioredoxin-disulfide reductase	1
Transport of Molybdenum	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:

• Glycolysis / Gluconeogenesis
• Pentose phosphate pathway
• Fructose and mannose metabolism
• Pyrimidine metabolism
• Glycerophospholipid metabolism
• 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
glycerol-3-phosphate to fumarate electron transfer	2	2	1
glycerophosphodiester degradation	2	2	1
glycerol-3-phosphate shuttle	2	2	1
glycerol 3-phosphate to cytochrome aa3 oxidase electron transfer	2	1	1
thioredoxin pathway	2	1	1
glycerol-3-phosphate to cytochrome bo oxidase electron transfer	2	1	1
nitrate reduction IX (dissimilatory)	2	1	1
glycerol-3-phosphate to hydrogen peroxide electron transport	2	1	1
glycerol degradation I	3	2	1
Rapoport-Luebering glycolytic shunt	3	1	1
sn-glycerol 3-phosphate anaerobic respiration	3	1	1
glycerol and glycerophosphodiester degradation	4	3	1
glycolysis IV	10	8	2
glycolysis II (from fructose 6-phosphate)	11	10	2
glycolysis III (from glucose)	11	10	2
glycolysis VI (from fructose)	11	8	2
pentose phosphate pathway (non-oxidative branch) II	6	6	1
homolactic fermentation	12	11	2
glycolysis I (from glucose 6-phosphate)	13	11	2
superpathway of glycolysis and the Entner-Doudoroff pathway	17	12	2
Entner-Doudoroff pathway I	9	6	1
superpathway of hexitol degradation (bacteria)	18	11	2
Entner-Doudoroff pathway III (semi-phosphorylative)	9	4	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	16	2
superpathway of anaerobic sucrose degradation	19	15	2
Rubisco shunt	10	8	1
glycolysis V (Pyrococcus)	10	7	1
photorespiration II	10	6	1
superpathway of N-acetylneuraminate degradation	22	15	2
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	14	2
gluconeogenesis III	12	9	1
gluconeogenesis I	13	10	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	18	2
formaldehyde assimilation I (serine pathway)	13	7	1
Bifidobacterium shunt	15	13	1
glycerol degradation to butanol	16	9	1
superpathway of glucose and xylose degradation	17	12	1
heterolactic fermentation	18	13	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	1
ethene biosynthesis V (engineered)	25	17	1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	14	1
1-butanol autotrophic biosynthesis (engineered)	27	15	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	22	1