Experiment set57IT033 for Escherichia coli BW25113

Ying_Nucleobase14 rep C; 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 23 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
2-phosphoglycolate salvage	1
Adenosyl nucleosidases	1
Alanine biosynthesis	1
Arginine and Ornithine Degradation	1
CytR regulation	1
Glycolate, glyoxylate interconversions	1
Multidrug Resistance Efflux Pumps	1
Nitric oxide synthase	1
Oxidative stress	1
Photorespiration (oxidative C2 cycle)	1
Purine conversions	1
Pyruvate Alanine Serine Interconversions	1
Ribosome biogenesis bacterial	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Purine metabolism
• Pyrimidine metabolism
• Alanine and aspartate metabolism
• Pentose phosphate pathway
• Glutamate metabolism
• Valine, leucine and isoleucine biosynthesis
• Tryptophan metabolism
• D-Alanine metabolism
• Glutathione metabolism
• Glyoxylate and dicarboxylate metabolism
• Carbon fixation in photosynthetic organisms
• Nicotinate and nicotinamide metabolism
• Drug metabolism - other enzymes
• Biosynthesis of siderophore group nonribosomal peptides
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
alanine racemization	1	1	1
L-alanine degradation III	1	1	1
L-alanine biosynthesis II	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
superpathway of L-alanine biosynthesis	4	4	2
adenine and adenosine salvage III	4	4	2
L-alanine degradation I	2	2	1
L-alanine biosynthesis I	2	2	1
adenine and adenosine salvage I	2	2	1
L-alanine degradation V (oxidative Stickland reaction)	2	2	1
superoxide radicals degradation	2	2	1
glutathione degradation (DUG pathway)	2	2	1
pyrimidine ribonucleosides degradation	2	2	1
guanine and guanosine salvage I	2	2	1
xanthine and xanthosine salvage	2	2	1
superpathway of pyrimidine deoxyribonucleosides degradation	6	6	2
adenine and adenosine salvage V	3	3	1
2-deoxy-α-D-ribose 1-phosphate degradation	3	3	1
pyrimidine deoxyribonucleosides degradation	3	3	1
superpathway of guanine and guanosine salvage	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
reactive oxygen species degradation	4	4	1
adenosine nucleotides degradation II	5	5	1
superpathway of pyrimidine ribonucleosides degradation	5	4	1
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
superpathway of purine nucleotide salvage	14	13	2
ethene biosynthesis III (microbes)	7	6	1
ureide biosynthesis	7	5	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	2
superpathway of anaerobic energy metabolism (invertebrates)	17	12	2
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
photorespiration II	10	6	1
salinosporamide A biosynthesis	15	3	1
cyclosporin A biosynthesis	15	2	1
arsenic detoxification (mammals)	17	8	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	22	1