Experiment set5IT093 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 4 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
Chorismate: Intermediate for synthesis of PAPA antibiotics, PABA, anthranilate, 3-hydroxyanthranilate and more.	1
Folate Biosynthesis	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:

• Lysine biosynthesis
• Arginine and proline metabolism
• Ubiquinone and menaquinone biosynthesis
• Urea cycle and metabolism of amino groups
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• Naphthalene and anthracene degradation
• Folate biosynthesis
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
4-aminobenzoate biosynthesis I	2	2	1
4-aminobenzoate biosynthesis II	2	1	1
5-(methoxycarbonylmethoxy)uridine biosynthesis	3	3	1
L-ornithine biosynthesis I	5	5	1
L-arginine degradation II (AST pathway)	5	5	1
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
superpathway of tetrahydrofolate biosynthesis	10	9	1
L-arginine biosynthesis II (acetyl cycle)	10	9	1
superpathway of candicidin biosynthesis	11	4	1
superpathway of tetrahydrofolate biosynthesis and salvage	12	11	1
superpathway of arginine and polyamine biosynthesis	17	16	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	18	1
aspartate superpathway	25	24	1
superpathway of chorismate metabolism	59	54	1