Experiment set12IT018 for Bacteroides thetaiotaomicron VPI-5482

Varel_Bryant_medium_Glucose with Indolicidin 0.002 mg/ml

Group: stress
Media: Varel_Bryant_medium_Glucose + Indolicidin (0.002 mg/ml)
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: 2048 D2

Specific Phenotypes

For 4 genes in this experiment

For stress Indolicidin in Bacteroides thetaiotaomicron VPI-5482

For stress Indolicidin across organisms

SEED Subsystems

Subsystem	#Specific
TCA Cycle	2
Serine-glyoxylate cycle	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)
• 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
• Glutathione metabolism
• Glyoxylate and dicarboxylate metabolism
• Reductive carboxylate cycle (CO2 fixation)

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
partial TCA cycle (obligate autotrophs)	8	5	2
nitrogen remobilization from senescing leaves	8	5	2
TCA cycle V (2-oxoglutarate synthase)	9	8	2
TCA cycle IV (2-oxoglutarate decarboxylase)	9	6	2
TCA cycle VI (Helicobacter)	9	6	2
TCA cycle VII (acetate-producers)	9	6	2
TCA cycle I (prokaryotic)	10	7	2
cytosolic NADPH production (yeast)	5	3	1
glyoxylate cycle	6	4	1
superpathway of glyoxylate bypass and TCA	12	7	2
mixed acid fermentation	16	12	2
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	3	1
TCA cycle II (plants and fungi)	9	6	1
methylaspartate cycle	19	11	2
TCA cycle III (animals)	10	7	1
reductive TCA cycle I	11	9	1
reductive TCA cycle II	12	8	1
ethene biosynthesis V (engineered)	25	15	2
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	18	2
superpathway of glyoxylate cycle and fatty acid degradation	14	6	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	17	1