Experiment set57IT032 for Escherichia coli BW25113

Compare to:

Ying_Nucleobase14 rep B; time point 2

Group: carbon source
Media: SDM_noCarbon + 1X Ying_Nucleobase14
Culturing: Keio_ML9a, tube, Aerobic, at 28 (C), shaken=180 rpm
By: Ying on 19-Oct-22
Media components: 1.5 g/L Ammonium chloride, 0.6 g/L Potassium phosphate monobasic, 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)

Ying_Nucleobase14 1x includes: 183 uM 5-methyluridine, 183 uM Adenine, 183 uM Adenosine, 183 uM Cytidine, 183 uM Cytosine, 183 uM Guanine, 183 uM Guanosine, 183 uM Hypoxanthine, 183 uM Inosine, 183 uM Thymine, 183 uM Uracil, 183 uM Uridine, 183 uM Xanthine, 183 uM Xanthosine

Specific Phenotypes

For 28 genes in this experiment

For carbon source Ying_Nucleobase14 in Escherichia coli BW25113

For carbon source Ying_Nucleobase14 across organisms

SEED Subsystems

Subsystem #Specific
Deoxyribose and Deoxynucleoside Catabolism 3
Purine conversions 2
2-phosphoglycolate salvage 1
Adenosyl nucleosidases 1
Alanine biosynthesis 1
Arginine and Ornithine Degradation 1
CytR regulation 1
DNA-binding regulatory proteins, strays 1
Entner-Doudoroff Pathway 1
Glycolate, glyoxylate interconversions 1
Glycolysis and Gluconeogenesis 1
Glycolysis and Gluconeogenesis, including Archaeal enzymes 1
Mannitol Utilization 1
Multidrug Resistance Efflux Pumps 1
Photorespiration (oxidative C2 cycle) 1
Pyruvate Alanine Serine Interconversions 1
cAMP signaling in bacteria 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
adenine and adenosine salvage I 2 2 2
guanine and guanosine salvage I 2 2 2
L-alanine degradation III 1 1 1
L-alanine biosynthesis II 1 1 1
alanine racemization 1 1 1
purine ribonucleosides degradation 6 6 5
purine deoxyribonucleosides degradation I 4 4 3
purine deoxyribonucleosides degradation II 3 3 2
superpathway of guanine and guanosine salvage 3 3 2
superpathway of purine deoxyribonucleosides degradation 7 7 4
superpathway of L-alanine biosynthesis 4 4 2
adenine and adenosine salvage III 4 4 2
L-alanine degradation V (oxidative Stickland reaction) 2 2 1
adenine and adenosine salvage II 2 2 1
L-alanine biosynthesis I 2 2 1
xanthine and xanthosine salvage 2 2 1
glutathione degradation (DUG pathway) 2 2 1
L-alanine degradation I 2 2 1
guanine and guanosine salvage II 2 2 1
pyrimidine ribonucleosides degradation 2 2 1
superpathway of pyrimidine deoxyribonucleosides degradation 6 6 2
adenine and adenosine salvage V 3 3 1
adenine salvage 3 3 1
pyrimidine deoxyribonucleosides degradation 3 3 1
2-deoxy-α-D-ribose 1-phosphate degradation 3 3 1
L-alanine degradation II (to D-lactate) 3 2 1
pyruvate fermentation to acetate and alanine 3 2 1
nucleoside and nucleotide degradation (archaea) 10 4 3
superpathway of purine nucleotide salvage 14 13 4
anaerobic energy metabolism (invertebrates, cytosol) 7 5 2
purine nucleotides degradation II (aerobic) 11 11 3
inosine 5'-phosphate degradation 4 4 1
guanosine nucleotides degradation III 4 4 1
adenosine nucleotides degradation II 5 5 1
superpathway of pyrimidine ribonucleosides degradation 5 4 1
photorespiration II 10 6 2
C4 photosynthetic carbon assimilation cycle, NAD-ME type 11 8 2
γ-glutamyl cycle 6 5 1
nucleoside and nucleotide degradation (halobacteria) 6 3 1
L-alanine degradation VI (reductive Stickland reaction) 6 2 1
fluoroacetate and fluorothreonine biosynthesis 6 1 1
ureide biosynthesis 7 5 1
C4 photosynthetic carbon assimilation cycle, PEPCK type 14 9 2
glyphosate degradation III 7 4 1
(aminomethyl)phosphonate degradation 8 8 1
superpathway of anaerobic energy metabolism (invertebrates) 17 12 2
Entner-Doudoroff pathway III (semi-phosphorylative) 9 6 1
photorespiration III 9 5 1
photorespiration I 9 5 1
superpathway of L-alanine fermentation (Stickland reaction) 9 5 1
ansatrienin biosynthesis 9 1 1
Rubisco shunt 10 9 1
glycolysis IV 10 8 1
glycolysis V (Pyrococcus) 10 7 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
salinosporamide A biosynthesis 15 3 1
cyclosporin A biosynthesis 15 2 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
arsenic detoxification (mammals) 17 8 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 2