Experiment set8IT043 for Bacteroides thetaiotaomicron VPI-5482

BHIS with Trimethoprim 0.00625 mM

Group: stress
Media: BHIS + Trimethoprim (0.00625 mM) + Dimethyl Sulfoxide (0.0625 vol%)
Culturing: Btheta_ML6a, 96 deep-well microplate; 1.2 mL volume, Anaerobic, at 37 (C), shaken=0 rpm
By: Hans on 6/18/18
Media components: 7.7 g/L Calf brains, 9.8 g/L Beef heart, 10 g/L Proteose Peptone, 5 g/L Sodium Chloride, 2.5 g/L Disodium phosphate, 1 g/L L-Cysteine, 2 g/L Sodium bicarbonate, 0.005 g/L Hemin

Specific Phenotypes

For 12 genes in this experiment

For stress Trimethoprim in Bacteroides thetaiotaomicron VPI-5482

For stress Trimethoprim across organisms

SEED Subsystems

Subsystem	#Specific
Butanol Biosynthesis	1
De Novo Purine Biosynthesis	1
Fermentations: Mixed acid	1
Glycine and Serine Utilization	1
Multidrug Resistance Efflux Pumps	1
Purine Utilization	1
Pyruvate Alanine Serine Interconversions	1
Respiratory Complex I	1
Ribosome biogenesis bacterial	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glycine, serine and threonine metabolism
• Pyruvate metabolism
• Biosynthesis of alkaloids derived from shikimate pathway
• Glycolysis / Gluconeogenesis
• Citrate cycle (TCA cycle)
• Ubiquinone and menaquinone biosynthesis
• Oxidative phosphorylation
• Purine metabolism
• Glutamate metabolism
• Cysteine metabolism
• Valine, leucine and isoleucine degradation
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• Naphthalene and anthracene degradation
• Propanoate metabolism
• Butanoate metabolism
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• 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
L-serine degradation	3	3	3
L-tryptophan degradation II (via pyruvate)	3	3	2
L-cysteine degradation II	3	2	2
D-serine degradation	3	2	2
reductive monocarboxylic acid cycle	2	2	1
NADH to cytochrome bd oxidase electron transfer I	2	1	1
NADH to cytochrome bo oxidase electron transfer I	2	1	1
phenylmercury acetate degradation	2	1	1
glycine betaine degradation III	7	4	3
felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis	5	2	2
glycine betaine degradation I	8	4	3
glycine biosynthesis II	3	3	1
pyruvate fermentation to acetate IV	3	3	1
glycine cleavage	3	3	1
pyruvate fermentation to ethanol I	3	2	1
pyruvate decarboxylation to acetyl CoA I	3	2	1
glycine degradation	3	2	1
2-oxoisovalerate decarboxylation to isobutanoyl-CoA	3	2	1
2-oxoglutarate decarboxylation to succinyl-CoA	3	2	1
aerobic respiration III (alternative oxidase pathway)	3	2	1
L-methionine biosynthesis II	6	3	2
L-mimosine degradation	8	4	2
aerobic respiration I (cytochrome c)	4	2	1
glutathione-mediated detoxification I	8	2	2
5-aminoimidazole ribonucleotide biosynthesis I	5	5	1
5-aminoimidazole ribonucleotide biosynthesis II	5	5	1
superpathway of 5-aminoimidazole ribonucleotide biosynthesis	6	6	1
L-threonine degradation I	6	5	1
NAD(P)/NADPH interconversion	6	2	1
Fe(II) oxidation	6	1	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	12	2
purine nucleobases degradation II (anaerobic)	24	12	3
superpathway of fermentation (Chlamydomonas reinhardtii)	9	7	1
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	10	1
mixed acid fermentation	16	12	1
superpathway of L-threonine metabolism	18	13	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	14	1
superpathway of purine nucleotides de novo biosynthesis I	21	21	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	17	1
superpathway of N-acetylneuraminate degradation	22	16	1
superpathway of purine nucleotides de novo biosynthesis II	26	23	1
superpathway of histidine, purine, and pyrimidine biosynthesis	46	42	1