Experiment set57IT050 for Escherichia coli BW25113

Compare to:

Ying_Nucleobase14 rep B; time point 3

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 46 genes in this experiment

For carbon source Ying_Nucleobase14 in Escherichia coli BW25113

For carbon source Ying_Nucleobase14 across organisms

SEED Subsystems

Subsystem #Specific
Curli production 3
Deoxyribose and Deoxynucleoside Catabolism 3
D-Galacturonate and D-Glucuronate Utilization 2
2-phosphoglycolate salvage 1
Adenosyl nucleosidases 1
Alanine biosynthesis 1
Arginine and Ornithine Degradation 1
Cysteine Biosynthesis 1
CytR regulation 1
DNA-binding regulatory proteins, strays 1
Glycolate, glyoxylate interconversions 1
Lactose and Galactose Uptake and Utilization 1
Mannitol Utilization 1
Methionine Biosynthesis 1
Methionine Degradation 1
Multidrug Resistance Efflux Pumps 1
Photorespiration (oxidative C2 cycle) 1
Purine conversions 1
Pyruvate Alanine Serine Interconversions 1
Ribosome biogenesis bacterial 1
Staphylococcal pathogenicity islands SaPI 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
L-alanine biosynthesis II 1 1 1
alanine racemization 1 1 1
L-alanine degradation III 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 purine deoxyribonucleosides degradation 7 7 4
adenine and adenosine salvage III 4 4 2
superpathway of L-alanine biosynthesis 4 4 2
adenine and adenosine salvage I 2 2 1
xanthine and xanthosine salvage 2 2 1
L-alanine degradation I 2 2 1
L-alanine biosynthesis I 2 2 1
L-cysteine biosynthesis I 2 2 1
glutathione degradation (DUG pathway) 2 2 1
pyrimidine ribonucleosides degradation 2 2 1
UDP-α-D-glucose biosynthesis 2 2 1
L-alanine degradation V (oxidative Stickland reaction) 2 2 1
guanine and guanosine salvage I 2 2 1
superpathway of pyrimidine deoxyribonucleosides degradation 6 6 2
superpathway of guanine and guanosine salvage 3 3 1
adenine and adenosine salvage V 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
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
L-cysteine biosynthesis VII (from S-sulfo-L-cysteine) 4 3 1
adenosine nucleotides degradation II 5 5 1
superpathway of pyrimidine ribonucleosides degradation 5 4 1
sucrose degradation II (sucrose synthase) 5 4 1
seleno-amino acid biosynthesis (plants) 5 3 1
C4 photosynthetic carbon assimilation cycle, NAD-ME type 11 8 2
γ-glutamyl cycle 6 5 1
superpathway of UDP-glucose-derived O-antigen building blocks biosynthesis 6 5 1
nucleoside and nucleotide degradation (halobacteria) 6 3 1
L-alanine degradation VI (reductive Stickland reaction) 6 2 1
hydrogen sulfide biosynthesis II (mammalian) 6 1 1
fluoroacetate and fluorothreonine biosynthesis 6 1 1
stachyose degradation 7 7 1
superpathway of purine nucleotide salvage 14 13 2
ureide biosynthesis 7 5 1
C4 photosynthetic carbon assimilation cycle, PEPCK type 14 9 2
sucrose biosynthesis II 8 6 1
superpathway of anaerobic energy metabolism (invertebrates) 17 12 2
superpathway of sulfate assimilation and cysteine biosynthesis 9 9 1
sucrose biosynthesis I (from photosynthesis) 9 7 1
superpathway of L-alanine fermentation (Stickland reaction) 9 5 1
photorespiration I 9 5 1
photorespiration III 9 5 1
ansatrienin biosynthesis 9 1 1
photorespiration II 10 6 1
colanic acid building blocks biosynthesis 11 11 1
salinosporamide A biosynthesis 15 3 1
cyclosporin A biosynthesis 15 2 1
arsenic detoxification (mammals) 17 8 1
type I lipoteichoic acid biosynthesis (S. aureus) 17 5 1
superpathway of anaerobic sucrose degradation 19 17 1
superpathway of seleno-compound metabolism 19 6 1
Methanobacterium thermoautotrophicum biosynthetic metabolism 56 22 1