Experiment set57IT049 for Escherichia coli BW25113

Ying_Nucleobase14 rep A; 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 43 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	4
Purine conversions	2
2-phosphoglycolate salvage	1
Adenosyl nucleosidases	1
Alanine biosynthesis	1
Arginine and Ornithine Degradation	1
Cinnamic Acid Degradation	1
Curli production	1
CytR regulation	1
D-Galacturonate and D-Glucuronate Utilization	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
Nitric oxide synthase	1
Oxidative stress	1
Photorespiration (oxidative C2 cycle)	1
Pyruvate Alanine Serine Interconversions	1
Ribosome biogenesis bacterial	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:

• Purine metabolism
• Pentose phosphate pathway
• Pyrimidine metabolism
• Alanine and aspartate metabolism
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine
• Glycolysis / Gluconeogenesis
• Pentose and glucuronate interconversions
• Galactose metabolism
• Fatty acid biosynthesis
• Glutamate metabolism
• Valine, leucine and isoleucine biosynthesis
• Lysine degradation
• Histidine metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Tryptophan metabolism
• D-Alanine metabolism
• Glutathione metabolism
• Starch and sucrose metabolism
• Nucleotide sugars metabolism
• Lipopolysaccharide biosynthesis
• Glycerophospholipid metabolism
• Ether lipid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• 1- and 2-Methylnaphthalene degradation
• Glyoxylate and dicarboxylate metabolism
• Benzoate degradation via CoA ligation
• Ethylbenzene degradation
• Butanoate metabolism
• Carbon fixation in photosynthetic organisms
• Nicotinate and nicotinamide metabolism
• Limonene and pinene degradation
• Diterpenoid biosynthesis
• Carotenoid biosynthesis - General
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Drug metabolism - other enzymes
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of siderophore group nonribosomal peptides
• Biosynthesis of type II polyketide backbone
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• 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
guanine and guanosine salvage I	2	2	2
adenine and adenosine salvage I	2	2	2
L-alanine biosynthesis II	1	1	1
L-alanine degradation III	1	1	1
alanine racemization	1	1	1
purine ribonucleosides degradation	6	6	5
purine deoxyribonucleosides degradation I	4	4	3
superpathway of purine deoxyribonucleosides degradation	7	7	5
superpathway of guanine and guanosine salvage	3	3	2
purine deoxyribonucleosides degradation II	3	3	2
2-deoxy-α-D-ribose 1-phosphate degradation	3	3	2
superpathway of pyrimidine deoxyribonucleosides degradation	6	6	3
superpathway of L-alanine biosynthesis	4	4	2
adenine and adenosine salvage III	4	4	2
adenine and adenosine salvage II	2	2	1
xanthine and xanthosine salvage	2	2	1
UDP-α-D-glucose biosynthesis	2	2	1
L-alanine degradation I	2	2	1
guanine and guanosine salvage II	2	2	1
superoxide radicals degradation	2	2	1
L-alanine degradation V (oxidative Stickland reaction)	2	2	1
pyrimidine ribonucleosides degradation	2	2	1
L-alanine biosynthesis I	2	2	1
glutathione degradation (DUG pathway)	2	2	1
2-deoxy-D-ribose degradation I	3	3	1
adenine and adenosine salvage V	3	3	1
pyrimidine deoxyribonucleosides degradation	3	3	1
adenine salvage	3	3	1
pyruvate fermentation to acetate and alanine	3	2	1
L-alanine degradation II (to D-lactate)	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
guanosine nucleotides degradation III	4	4	1
reactive oxygen species degradation	4	4	1
inosine 5'-phosphate degradation	4	4	1
adenosine nucleotides degradation II	5	5	1
sucrose degradation II (sucrose synthase)	5	4	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
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
fluoroacetate and fluorothreonine biosynthesis	6	1	1
stachyose degradation	7	7	1
ethene biosynthesis III (microbes)	7	6	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
sucrose biosynthesis II	8	6	1
superpathway of anaerobic energy metabolism (invertebrates)	17	12	2
sucrose biosynthesis I (from photosynthesis)	9	7	1
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
superpathway of anaerobic sucrose degradation	19	17	2
Rubisco shunt	10	9	1
glycolysis IV	10	8	1
glycolysis V (Pyrococcus)	10	7	1
glycolysis III (from glucose)	11	11	1
colanic acid building blocks biosynthesis	11	11	1
glycolysis II (from fructose 6-phosphate)	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
type I lipoteichoic acid biosynthesis (S. aureus)	17	5	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 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