Experiment set57IT048 for Escherichia coli BW25113

Ying_sugar7 rep C; 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 15 genes in this experiment

For carbon source Ying_sugar7 in Escherichia coli BW25113

For carbon source Ying_sugar7 across organisms

SEED Subsystems

Subsystem	#Specific
Arginine and Ornithine Degradation	1
Curli production	1
Heat shock dnaK gene cluster extended	1
Ribosome biogenesis bacterial	1
tRNA processing	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Purine metabolism
• Glutamate metabolism
• Alanine and aspartate metabolism
• Valine, leucine and isoleucine biosynthesis
• Tryptophan metabolism
• Carbon fixation in photosynthetic organisms
• Biosynthesis of siderophore group nonribosomal peptides
• 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
L-alanine degradation III	1	1	1
superpathway of L-alanine biosynthesis	4	4	2
polyphosphate metabolism	2	2	1
L-alanine biosynthesis I	2	2	1
L-alanine degradation V (oxidative Stickland reaction)	2	2	1
molybdenum cofactor biosynthesis	3	3	1
pyruvate fermentation to acetate and alanine	3	2	1
L-alanine degradation II (to D-lactate)	3	2	1
tRNA processing	10	10	2
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	8	2
ppGpp metabolism	6	6	1
L-alanine degradation VI (reductive Stickland reaction)	6	2	1
anaerobic energy metabolism (invertebrates, cytosol)	7	5	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	2
superpathway of L-alanine fermentation (Stickland reaction)	9	5	1
superpathway of anaerobic energy metabolism (invertebrates)	17	12	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	22	1