Experiment set1IT048 for Serratia liquefaciens MT49

Cadmium acetate dihydrate 40 uM, aerobic

Group: stress
Media: DefinedMedia_AdamsLab_Glucose_YeastExtract + Cadmium acetate dihydrate (40 uM), pH=7
Culturing: MT049_ML3, hungate, Aerobic, at 24 (C), shaken=150 rpm
Growth: about 6.0 generations
By: Mike Thorgersen on 6/4/19
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 5 mM Sodium phosphate monobasic monohydrate, 2.5 g/L Sodium bicarbonate, 20 mM D-Glucose, 1 g/L Yeast Extract, 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)

Specific Phenotypes

For 6 genes in this experiment

For stress Cadmium acetate dihydrate in Serratia liquefaciens MT49

For stress Cadmium acetate dihydrate across organisms

SEED Subsystems

Subsystem	#Specific
Arginine Biosynthesis extended	2
Ammonia assimilation	1
Chorismate Synthesis	1
Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate)	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	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
• Urea cycle and metabolism of amino groups
• Arginine and proline metabolism
• Glutamate metabolism
• Lysine biosynthesis
• Nitrogen metabolism
• Geraniol degradation
• Tryptophan metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Limonene and pinene degradation
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-glutamate biosynthesis I	2	2	2
L-glutamate biosynthesis IV	1	1	1
L-glutamate biosynthesis III	1	1	1
L-glutamine degradation II	1	1	1
L-glutamine degradation I	1	1	1
ammonia assimilation cycle III	3	3	2
L-glutamate and L-glutamine biosynthesis	7	7	4
3-dehydroquinate biosynthesis I	2	2	1
ammonia assimilation cycle I	2	2	1
L-ornithine biosynthesis I	5	5	2
superpathway of ammonia assimilation (plants)	3	3	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	3	1
L-asparagine biosynthesis III (tRNA-dependent)	4	3	1
L-arginine biosynthesis I (via L-ornithine)	9	9	2
L-arginine biosynthesis III (via N-acetyl-L-citrulline)	9	8	2
L-arginine biosynthesis II (acetyl cycle)	10	9	2
chorismate biosynthesis I	7	7	1
L-citrulline biosynthesis	8	7	1
superpathway of arginine and polyamine biosynthesis	17	17	2
superpathway of L-phenylalanine biosynthesis	10	10	1
superpathway of L-tyrosine biosynthesis	10	10	1
superpathway of L-citrulline metabolism	12	9	1
superpathway of L-tryptophan biosynthesis	13	13	1
superpathway of aromatic amino acid biosynthesis	18	18	1
superpathway of chorismate metabolism	59	54	1