Experiment set67S86 for Escherichia coli BW25113

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Uridine 0.4095 mM carbon source

Group: carbon source
Media: Chakraborty_Basal + Uridine (0.4095 mM), pH=7
Culturing: Keio_ML9a, tube, Aerobic, at 29 (C), shaken=200 rpm
By: Bri Finley on 9/16/24
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 0.3792 g/L Sodium phosphate monobasic, 0.9713 g/L Disodium phosphate, Wolfe's mineral mix (0.03 g/L Magnesium Sulfate Heptahydrate, 0.015 g/L Nitrilotriacetic acid, 0.01 g/L Sodium Chloride, 0.005 g/L Manganese (II) sulfate monohydrate, 0.001 g/L Cobalt chloride hexahydrate, 0.001 g/L Zinc sulfate heptahydrate, 0.001 g/L Calcium chloride dihydrate, 0.001 g/L Iron (II) sulfate heptahydrate, 0.00025 g/L Nickel (II) chloride hexahydrate, 0.0002 g/L Aluminum potassium sulfate dodecahydrate, 0.0001 g/L Copper (II) sulfate pentahydrate, 0.0001 g/L Boric Acid, 0.0001 g/L Sodium Molybdate Dihydrate, 0.003 mg/L Sodium selenite pentahydrate), Wolfe's vitamin mix (0.1 mg/L Pyridoxine HCl, 0.05 mg/L 4-Aminobenzoic acid, 0.05 mg/L Lipoic acid, 0.05 mg/L Nicotinic Acid, 0.05 mg/L Riboflavin, 0.05 mg/L Thiamine HCl, 0.05 mg/L calcium pantothenate, 0.02 mg/L biotin, 0.02 mg/L Folic Acid, 0.001 mg/L Cyanocobalamin)

Specific Phenotypes

For 16 genes in this experiment

For carbon source Uridine in Escherichia coli BW25113

For carbon source Uridine across organisms

SEED Subsystems

Subsystem #Specific
Curli production 4
CytR regulation 1
DNA-binding regulatory proteins, strays 1
Deoxyribose and Deoxynucleoside Catabolism 1
Entner-Doudoroff Pathway 1
Glycolysis and Gluconeogenesis 1
Glycolysis and Gluconeogenesis, including Archaeal enzymes 1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway #Steps #Present #Specific
pyrimidine ribonucleosides degradation 2 2 1
superpathway of pyrimidine deoxyribonucleosides degradation 6 6 2
2-deoxy-α-D-ribose 1-phosphate degradation 3 3 1
pyrimidine deoxyribonucleosides degradation 3 3 1
superpathway of pyrimidine ribonucleosides degradation 5 4 1
purine ribonucleosides degradation 6 6 1
superpathway of purine deoxyribonucleosides degradation 7 7 1
Entner-Doudoroff pathway III (semi-phosphorylative) 9 6 1
Rubisco shunt 10 9 1
glycolysis IV 10 8 1
glycolysis V (Pyrococcus) 10 7 1
photorespiration II 10 6 1
nucleoside and nucleotide degradation (archaea) 10 4 1
glycolysis II (from fructose 6-phosphate) 11 11 1
glycolysis III (from glucose) 11 11 1
glycolysis VI (from fructose) 11 8 1
homolactic fermentation 12 12 1
glycolysis I (from glucose 6-phosphate) 13 13 1
gluconeogenesis I 13 13 1
Bifidobacterium shunt 15 13 1
glycerol degradation to butanol 16 11 1
superpathway of glucose and xylose degradation 17 17 1
superpathway of glycolysis and the Entner-Doudoroff pathway 17 17 1
superpathway of hexitol degradation (bacteria) 18 18 1
gluconeogenesis II (Methanobacterium thermoautotrophicum) 18 9 1
hexitol fermentation to lactate, formate, ethanol and acetate 19 19 1
superpathway of anaerobic sucrose degradation 19 17 1
superpathway of N-acetylneuraminate degradation 22 22 1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle 22 18 1
ethene biosynthesis V (engineered) 25 18 1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass 26 25 1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered) 26 19 1
1-butanol autotrophic biosynthesis (engineered) 27 19 1
Methanobacterium thermoautotrophicum biosynthetic metabolism 56 22 1