Experiment set57IT015 for Escherichia coli BW25113

Ying_Nucleobase14 rep C; time point 1

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 14 genes in this experiment

For carbon source Ying_Nucleobase14 in Escherichia coli BW25113

For carbon source Ying_Nucleobase14 across organisms

SEED Subsystems

Subsystem	#Specific
Alanine biosynthesis	1
Arginine and Ornithine Degradation	1
CytR regulation	1
DNA-binding regulatory proteins, strays	1
Deoxyribose and Deoxynucleoside Catabolism	1
Pyruvate Alanine Serine Interconversions	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Alanine and aspartate metabolism
• Pentose phosphate pathway
• Purine metabolism
• Pyrimidine metabolism
• Glutamate metabolism
• Valine, leucine and isoleucine biosynthesis
• D-Alanine metabolism
• Carbon fixation in photosynthetic organisms
• Drug metabolism - other enzymes
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

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
superpathway of L-alanine biosynthesis	4	4	2
pyrimidine ribonucleosides degradation	2	2	1
L-alanine degradation V (oxidative Stickland reaction)	2	2	1
L-alanine biosynthesis I	2	2	1
L-alanine degradation I	2	2	1
superpathway of pyrimidine deoxyribonucleosides degradation	6	6	2
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
anaerobic energy metabolism (invertebrates, cytosol)	7	5	2
superpathway of pyrimidine ribonucleosides degradation	5	4	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	8	2
purine ribonucleosides degradation	6	6	1
L-alanine degradation VI (reductive Stickland reaction)	6	2	1
superpathway of purine deoxyribonucleosides degradation	7	7	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	2
superpathway of anaerobic energy metabolism (invertebrates)	17	12	2
superpathway of L-alanine fermentation (Stickland reaction)	9	5	1
ansatrienin biosynthesis	9	1	1
nucleoside and nucleotide degradation (archaea)	10	4	1
cyclosporin A biosynthesis	15	2	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	22	1