Experiment set5IT094 for Escherichia coli BW25113

M63 no sulfur + 5 mM L-cys

Group: sulfur source
Media: M63_no_sulfur + L-Cysteine (5 mM)
Culturing: Keio_ML9, tube, Aerobic, at 37 (C), shaken=200 rpm
By: Hans on 5/11/2015
Media components: 64 mM Potassium phosphate monobasic, 33 mM Ammonium chloride, 1 mM Magnesium chloride hexahydrate, 0.3 mM Thiamine HCl, 2 g/L D-Glucose, Sulfur free mineral mix (0.03 g/L Magnesium chloride hexahydrate, 0.015 g/L Nitrilotriacetic acid disodium salt, 0.01 g/L Sodium Chloride, 0.005 g/L Manganese (II) chloride tetrahydrate, 0.001 g/L Cobalt chloride hexahydrate, 0.0013 g/L Zinc chloride, 0.001 g/L Calcium chloride dihydrate, 0.001 g/L Iron (II) chloride tetrahydrate, 0.00025 g/L Nickel (II) chloride hexahydrate, 0.0002 g/L Potassium aluminum chloride, 0.0001 g/L copper (II) chloride dihydrate, 0.0001 g/L Boric Acid, 0.0001 g/L Sodium Molybdate Dihydrate, 0.003 mg/L Sodium selenite pentahydrate, 0.0025 mg/L Sodium tungstate dihydrate)

Specific Phenotypes

For 3 genes in this experiment

For sulfur source L-Cysteine in Escherichia coli BW25113

For sulfur source L-Cysteine across organisms

SEED Subsystems

Subsystem	#Specific
Arginine Biosynthesis extended	1
Heat shock dnaK gene cluster extended	1
Lysine Biosynthesis DAP Pathway	1
ZZ gjo need homes	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Purine metabolism
• Lysine biosynthesis
• Arginine and proline metabolism
• Urea cycle and metabolism of amino groups
• Lipopolysaccharide biosynthesis
• Thiamine metabolism
• Folate biosynthesis
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
UTP and CTP dephosphorylation I	7	5	2
L-arginine degradation II (AST pathway)	5	5	1
L-ornithine biosynthesis I	5	5	1
pyrimidine deoxyribonucleotides de novo biosynthesis IV	7	6	1
pyrimidine deoxyribonucleotides biosynthesis from CTP	8	6	1
L-lysine biosynthesis I	9	9	1
L-arginine biosynthesis I (via L-ornithine)	9	9	1
pyrimidine deoxyribonucleotides de novo biosynthesis I	9	9	1
L-arginine biosynthesis III (via N-acetyl-L-citrulline)	9	8	1
pyrimidine deoxyribonucleotides de novo biosynthesis III	9	8	1
L-arginine biosynthesis II (acetyl cycle)	10	9	1
superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis (E. coli)	14	14	1
superpathway of arginine and polyamine biosynthesis	17	16	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	18	1
superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis	18	18	1
aspartate superpathway	25	24	1