Experiment set2IT093 for Cupriavidus basilensis FW507-4G11

L-Tryptophan nitrogen source

Group: nitrogen source
Media: RCH2_defined_noNitrogen + L-Tryptophan (12.5 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 5 genes in this experiment

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

For nitrogen source L-Tryptophan across organisms

SEED Subsystems

Subsystem	#Specific
NAD and NADP cofactor biosynthesis global	2
Aromatic amino acid degradation	1
Folate Biosynthesis	1
One-carbon metabolism by tetrahydropterines	1
Serine-glyoxylate cycle	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Tryptophan metabolism
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• C21-Steroid hormone metabolism
• Glycine, serine and threonine metabolism
• Bisphenol A degradation
• Nucleotide sugars metabolism
• Polyketide sugar unit biosynthesis
• Aminosugars metabolism
• Linoleic acid metabolism
• Tetrachloroethene degradation
• Carbazole degradation
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• One carbon pool by folate
• Retinol metabolism
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide products
• Biosynthesis of alkaloids derived from shikimate pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-tryptophan degradation I (via anthranilate)	3	3	2
anthranilate degradation II (aerobic)	2	2	1
L-tryptophan degradation to 2-amino-3-carboxymuconate semialdehyde	5	4	2
3-hydroxy-4-methyl-anthranilate biosynthesis II	5	3	2
NAD de novo biosynthesis II (from tryptophan)	9	8	2
L-tryptophan degradation IX	12	11	2
L-tryptophan degradation XII (Geobacillus)	12	11	2
3-hydroxy-4-methyl-anthranilate biosynthesis I	6	2	1
superpathway of NAD biosynthesis in eukaryotes	14	11	2
L-tryptophan degradation III (eukaryotic)	15	10	2
L-tryptophan degradation XI (mammalian, via kynurenine)	23	11	3
folate transformations III (E. coli)	9	9	1
benzoyl-CoA degradation III (anaerobic)	9	6	1
folate transformations II (plants)	11	10	1
folate transformations I	13	9	1
superpathway of aromatic compound degradation via 3-oxoadipate	35	25	2
superpathway of aromatic compound degradation via 2-hydroxypentadienoate	42	21	2