Experiment set27S309 for Bacteroides thetaiotaomicron VPI-5482

carbon source Mucin from porcine stomach type III 10 mg/ml

Group: carbon source
Media: Varel_Bryant_medium + Mucin from porcine stomach type III (10 mg/ml)
Culturing: Btheta_ML6a, tube, Anaerobic, at 37 (C), shaken=0 rpm
By: Didier Ndeh on 10/7/23
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, 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)

Specific Phenotypes

For 4 genes in this experiment

For carbon source Mucin from porcine stomach type III in Bacteroides thetaiotaomicron VPI-5482

For carbon source Mucin from porcine stomach type III across organisms

SEED Subsystems

Subsystem	#Specific
Carboxysome	1
Glycolysis and Gluconeogenesis	1
Respiratory dehydrogenases 1	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
• Oxidative phosphorylation
• Urea cycle and metabolism of amino groups
• Alanine and aspartate metabolism
• Arginine and proline metabolism
• Glutathione metabolism
• Carbon fixation in photosynthetic organisms
• Biosynthesis of phenylpropanoids

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
NADH to cytochrome bd oxidase electron transfer I	2	1	1
glutathione degradation (DUG pathway)	2	1	1
NADH to cytochrome bo oxidase electron transfer I	2	1	1
aerobic respiration III (alternative oxidase pathway)	3	2	1
aerobic respiration I (cytochrome c)	4	2	1
muropeptide degradation	4	2	1
NAD(P)/NADPH interconversion	6	2	1
γ-glutamyl cycle	6	1	1
Fe(II) oxidation	6	1	1
sucrose biosynthesis I (from photosynthesis)	9	6	1
glycolysis II (from fructose 6-phosphate)	11	10	1
gluconeogenesis III	12	10	1
formaldehyde assimilation III (dihydroxyacetone cycle)	12	10	1
glycolysis I (from glucose 6-phosphate)	13	11	1
gluconeogenesis I	13	11	1
Calvin-Benson-Bassham cycle	13	9	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	14	1
oxygenic photosynthesis	17	9	1
superpathway of hexitol degradation (bacteria)	18	12	1
superpathway of anaerobic sucrose degradation	19	14	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	14	1
superpathway of N-acetylneuraminate degradation	22	16	1
ethene biosynthesis V (engineered)	25	15	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	18	1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	12	1
1-butanol autotrophic biosynthesis (engineered)	27	12	1