Experiment set32S134 for Bacteroides thetaiotaomicron VPI-5482

L-Serine nitrogen source; Varel_Bryant_medium_Glucose_DTT_NaS_noNitrogen

Group: nitrogen source
Media: Varel_Bryant_medium_Glucose_DTT_NaS_noNitrogen + L-Serine (10 mM)
Culturing: Btheta_ML6a, 96 deep-well microplate; 1.2 mL volume, Anaerobic, at 37 (C), shaken=0 rpm
By: Surya Tripathi on 3/20/24
Media components: 15 uM Hemin, 134 uM L-Methionine, 15 uM Iron (II) sulfate heptahydrate, 3 mM Dithiothreitol, 23.8 mM Sodium bicarbonate, 20 mM D-Glucose, 3 mM Sodium sulfide nonahydrate, Mineral 3B solution minus Nitrogen (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, 1.75 mM Sodium sulfate)

Specific Phenotypes

For 8 genes in this experiment

For nitrogen source L-Serine in Bacteroides thetaiotaomicron VPI-5482

For nitrogen source L-Serine across organisms

SEED Subsystems

Subsystem	#Specific
Cobalt-zinc-cadmium resistance	1
Cysteine Biosynthesis	1
D-Tagatose and Galactitol Utilization	1
Glycolysis and Gluconeogenesis	1
Glycolysis and Gluconeogenesis, including Archaeal enzymes	1
Methionine Biosynthesis	1
Methylglyoxal Metabolism	1
N-Acetyl-Galactosamine and Galactosamine Utilization	1
Rhamnose containing glycans	1
dTDP-rhamnose synthesis	1
linker unit-arabinogalactan synthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Histidine metabolism
• beta-Alanine metabolism
• Glycolysis / Gluconeogenesis
• Pentose phosphate pathway
• Fructose and mannose metabolism
• Galactose metabolism
• Urea cycle and metabolism of amino groups
• Alanine and aspartate metabolism
• Cysteine metabolism
• Arginine and proline metabolism
• Selenoamino acid metabolism
• Glutathione metabolism
• Streptomycin biosynthesis
• Polyketide sugar unit biosynthesis
• Pyruvate metabolism
• Sulfur 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
L-cysteine biosynthesis I	2	2	1
sedoheptulose bisphosphate bypass	2	2	1
glutathione degradation (DUG pathway)	2	1	1
dTDP-N-acetylviosamine biosynthesis	4	3	1
dTDP-6-deoxy-α-D-allose biosynthesis	4	2	1
muropeptide degradation	4	2	1
dTDP-β-D-fucofuranose biosynthesis	4	2	1
D-galactosamine and N-acetyl-D-galactosamine degradation	4	2	1
dTDP-N-acetylthomosamine biosynthesis	4	2	1
dTDP-β-L-rhamnose biosynthesis	5	5	1
dTDP-4-O-demethyl-β-L-noviose biosynthesis	5	3	1
N-acetyl-D-galactosamine degradation	5	2	1
seleno-amino acid biosynthesis (plants)	5	2	1
galactitol degradation	5	2	1
dTDP-3-acetamido-α-D-fucose biosynthesis	5	2	1
dTDP-α-D-mycaminose biosynthesis	5	2	1
dTDP-3-acetamido-3,6-dideoxy-α-D-glucose biosynthesis	5	2	1
lactose degradation I	5	1	1
dTDP-L-daunosamine biosynthesis	6	3	1
dTDP-D-desosamine biosynthesis	6	3	1
dTDP-sibirosamine biosynthesis	6	3	1
dTDP-α-D-ravidosamine and dTDP-4-acetyl-α-D-ravidosamine biosynthesis	6	2	1
γ-glutamyl cycle	6	1	1
dTDP-β-L-olivose biosynthesis	7	3	1
dTDP-β-L-digitoxose biosynthesis	7	3	1
dTDP-β-L-mycarose biosynthesis	7	2	1
dTDP-β-L-megosamine biosynthesis	8	3	1
dTDP-β-L-4-epi-vancosamine biosynthesis	8	3	1
superpathway of sulfate assimilation and cysteine biosynthesis	9	7	1
formaldehyde assimilation II (assimilatory RuMP Cycle)	9	7	1
superpathway of hexitol degradation (bacteria)	18	12	2
1,3-propanediol biosynthesis (engineered)	9	6	1
dTDP-α-D-olivose, dTDP-α-D-oliose and dTDP-α-D-mycarose biosynthesis	9	3	1
dTDP-α-D-forosamine biosynthesis	9	3	1
glycolysis IV	10	9	1
superpathway of enterobacterial common antigen biosynthesis	10	4	1
glycolysis III (from glucose)	11	11	1
glycolysis II (from fructose 6-phosphate)	11	10	1
O-antigen building blocks biosynthesis (E. coli)	11	8	1
homolactic fermentation	12	11	1
glycolysis I (from glucose 6-phosphate)	13	11	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	14	1
superpathway of anaerobic sucrose degradation	19	14	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	14	1
superpathway of dTDP-glucose-derived O-antigen building blocks biosynthesis	19	6	1
superpathway of seleno-compound metabolism	19	5	1
superpathway of novobiocin biosynthesis	19	4	1
superpathway of erythromycin biosynthesis	19	3	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	17	1
superpathway of N-acetylneuraminate degradation	22	16	1
superpathway of megalomicin A biosynthesis	22	4	1
superpathway of dTDP-glucose-derived antibiotic building blocks biosynthesis	23	3	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	18	1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	33	11	1