Experiment set57IT046 for Escherichia coli BW25113

Ying_sugar7 rep A; time point 3

Group: carbon source
Media: SDM_noCarbon + 1X Ying_sugar7
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_sugar7 1x includes: 366 uM Sucrose, 366 uM D-Glucose, 366 uM D-Trehalose dihydrate, 366 uM m-Inositol, 366 uM D-Xylose, 366 uM D-Mannitol, 366 uM N-Acetyl-D-Glucosamine

Specific Phenotypes

For 14 genes in this experiment

For carbon source Ying_sugar7 in Escherichia coli BW25113

For carbon source Ying_sugar7 across organisms

SEED Subsystems

Subsystem	#Specific
tRNA processing	2
Arginine Biosynthesis extended	1
Arginine and Ornithine Degradation	1
Entner-Doudoroff Pathway	1
Glycolate, glyoxylate interconversions	1
Glycolysis and Gluconeogenesis	1
Glycolysis and Gluconeogenesis, including Archaeal enzymes	1
Heat shock dnaK gene cluster extended	1
Lysine Biosynthesis DAP Pathway	1
Photorespiration (oxidative C2 cycle)	1
Ribosomal protein S12p Asp methylthiotransferase	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:

• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Lysine biosynthesis
• Arginine and proline metabolism
• Glycolysis / Gluconeogenesis
• Urea cycle and metabolism of amino groups
• Puromycin biosynthesis
• Glutamate metabolism
• Alanine and aspartate metabolism
• Valine, leucine and isoleucine biosynthesis
• Tryptophan metabolism
• Lipopolysaccharide biosynthesis
• Glyoxylate and dicarboxylate metabolism
• Carbon fixation in photosynthetic organisms
• Biosynthesis of siderophore group nonribosomal peptides
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from histidine and purine
• 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
L-alanine biosynthesis II	1	1	1
L-alanine degradation III	1	1	1
superpathway of L-alanine biosynthesis	4	4	2
L-alanine degradation V (oxidative Stickland reaction)	2	2	1
glycolate and glyoxylate degradation II	2	2	1
L-alanine biosynthesis I	2	2	1
pyruvate fermentation to acetate and alanine	3	2	1
L-alanine degradation II (to D-lactate)	3	2	1
glycolate and glyoxylate degradation III	3	1	1
glycolate and glyoxylate degradation I	4	4	1
tRNA processing	10	10	2
L-arginine degradation II (AST pathway)	5	5	1
L-ornithine biosynthesis I	5	5	1
photorespiration II	10	6	2
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	8	2
L-alanine degradation VI (reductive Stickland reaction)	6	2	1
superpathway of glycol metabolism and degradation	7	7	1
anaerobic energy metabolism (invertebrates, cytosol)	7	5	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	2
L-arginine biosynthesis I (via L-ornithine)	9	9	1
L-lysine biosynthesis I	9	9	1
L-arginine biosynthesis III (via N-acetyl-L-citrulline)	9	8	1
Entner-Doudoroff pathway III (semi-phosphorylative)	9	6	1
photorespiration III	9	5	1
superpathway of L-alanine fermentation (Stickland reaction)	9	5	1
photorespiration I	9	5	1
L-lysine degradation V	9	2	1
Rubisco shunt	10	9	1
L-arginine biosynthesis II (acetyl cycle)	10	9	1
glycolysis IV	10	8	1
glycolysis V (Pyrococcus)	10	7	1
glycolysis III (from glucose)	11	11	1
glycolysis II (from fructose 6-phosphate)	11	11	1
glycolysis VI (from fructose)	11	8	1
homolactic fermentation	12	12	1
gluconeogenesis I	13	13	1
glycolysis I (from glucose 6-phosphate)	13	13	1
Bifidobacterium shunt	15	13	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
superpathway of arginine and polyamine biosynthesis	17	16	1
superpathway of anaerobic energy metabolism (invertebrates)	17	12	1
superpathway of hexitol degradation (bacteria)	18	18	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	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
aspartate superpathway	25	24	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
superpathway of L-lysine degradation	43	14	1