Experiment set3IT018 for Cupriavidus basilensis FW507-4G11

L-Phenylalanine nitrogen source

Group: nitrogen source
Media: RCH2_defined_noNitrogen + L-Phenylalanine (20 mM), pH=7
Culturing: cupriavidus_4G11_ML11, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
By: Jayashree on 3/3/2015
Media components: 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 20 mM Sodium D,L-Lactate, 30 mM PIPES sesquisodium salt, 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 3 genes in this experiment

For nitrogen source L-Phenylalanine in Cupriavidus basilensis FW507-4G11

For nitrogen source L-Phenylalanine across organisms

SEED Subsystems

Subsystem	#Specific
Homogentisate pathway of aromatic compound degradation	2
Aromatic amino acid degradation	1
Pterin biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Tyrosine metabolism
• Phenylalanine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Methionine metabolism
• Lysine biosynthesis
• Novobiocin biosynthesis
• Styrene degradation
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-phenylalanine degradation I (aerobic)	1	1	1
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
L-tyrosine biosynthesis IV	1	1	1
L-phenylalanine biosynthesis III (cytosolic, plants)	2	2	1
atromentin biosynthesis	2	1	1
L-tyrosine degradation II	2	1	1
L-tyrosine degradation I	5	5	2
L-tyrosine biosynthesis I	3	3	1
L-phenylalanine biosynthesis I	3	3	1
L-phenylalanine degradation II (anaerobic)	3	2	1
L-phenylalanine degradation V	3	2	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
L-tyrosine degradation III	4	2	1
L-phenylalanine degradation III	4	2	1
superpathway of plastoquinol biosynthesis	5	2	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
superpathway of aromatic amino acid biosynthesis	18	18	2
L-phenylalanine degradation IV (mammalian, via side chain)	9	6	1
superpathway of L-phenylalanine biosynthesis	10	10	1
superpathway of L-tyrosine biosynthesis	10	10	1
rosmarinic acid biosynthesis I	10	2	1
(S)-reticuline biosynthesis I	11	3	1
tropane alkaloids biosynthesis	11	1	1
superpathway of rosmarinic acid biosynthesis	14	2	1
superpathway of hyoscyamine (atropine) and scopolamine biosynthesis	16	3	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	7	1
superpathway of chorismate metabolism	59	45	2