Experiment set12IT026 for Bacteroides thetaiotaomicron VPI-5482

Varel_Bryant_medium_Glucose with Deoxycholic acid 0.075 mg/ml

Group: stress
Media: Varel_Bryant_medium_Glucose + Deoxycholic acid (0.075 mg/ml) + Ethanol (0.15 vol%)
Culturing: Btheta_ML6a, 24-well transparent microplate, Anaerobic, at 37 (C), shaken=0 rpm
By: Adam on 6/29/18
Media components: 15 uM Hemin, 134 uM L-Methionine, 15 uM Iron (II) sulfate heptahydrate, 8.25 mM L-Cysteine, 23.8 mM Sodium bicarbonate, 20 mM D-Glucose, Mineral 3B solution (6.6 mM Potassium phosphate monobasic, 15.4 mM Sodium Chloride, 98 uM Magnesium chloride hexahydrate, 176.5 uM Calcium chloride dihydrate, 4.2 uM Cobalt chloride hexahydrate, 50.5 uM Manganese (II) chloride tetrahydrate, 9.3 mM Ammonium chloride, 1.75 mM Sodium sulfate)
Growth plate: 2050 B1

Specific Phenotypes

For 10 genes in this experiment

For stress Deoxycholic acid in Bacteroides thetaiotaomicron VPI-5482

For stress Deoxycholic acid across organisms

SEED Subsystems

Subsystem	#Specific
Lipid A-Ara4N pathway ( Polymyxin resistance )	1
Potassium homeostasis	1
TCA Cycle	1
Teichuronic acid biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Citrate cycle (TCA cycle)
• Pentose and glucuronate interconversions
• Ascorbate and aldarate metabolism
• Glutathione metabolism
• Starch and sucrose metabolism
• Nucleotide sugars metabolism
• Reductive carboxylate cycle (CO2 fixation)
• 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
UDP-α-D-glucuronate biosynthesis (from UDP-glucose)	1	1	1
UDP-α-D-xylose biosynthesis	2	2	1
cytosolic NADPH production (yeast)	5	3	1
superpathway of UDP-glucose-derived O-antigen building blocks biosynthesis	6	4	1
nitrogen remobilization from senescing leaves	8	5	1
partial TCA cycle (obligate autotrophs)	8	5	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	3	1
TCA cycle V (2-oxoglutarate synthase)	9	8	1
TCA cycle IV (2-oxoglutarate decarboxylase)	9	6	1
TCA cycle VII (acetate-producers)	9	6	1
TCA cycle VI (Helicobacter)	9	6	1
UDP-sugars interconversion	9	4	1
teichuronic acid biosynthesis (B. subtilis 168)	9	2	1
TCA cycle I (prokaryotic)	10	7	1
colanic acid building blocks biosynthesis	11	10	1
reductive TCA cycle I	11	9	1
reductive TCA cycle II	12	8	1
superpathway of glyoxylate bypass and TCA	12	7	1
mixed acid fermentation	16	12	1
methylaspartate cycle	19	11	1
ethene biosynthesis V (engineered)	25	15	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	18	1