Experiment set3IT019 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
Branched-Chain Amino Acid Biosynthesis	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:

• Tryptophan metabolism
• Carbazole degradation
• Benzoate degradation via CoA ligation
• Acridone alkaloid biosynthesis
• Biosynthesis of alkaloids derived from shikimate pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
anthranilate degradation II (aerobic)	2	2	2
L-tryptophan degradation I (via anthranilate)	3	3	2
anthranilate degradation III (anaerobic)	2	1	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
4-hydroxy-2(1H)-quinolone biosynthesis	5	3	1
aurachin RE biosynthesis	5	1	1
L-tryptophan degradation XII (Geobacillus)	12	11	2
L-tryptophan degradation IX	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
2-heptyl-3-hydroxy-4(1H)-quinolone biosynthesis	8	1	1
superpathway of quinolone and alkylquinolone biosynthesis	10	3	1
aurachin A, B, C and D biosynthesis	11	3	1
superpathway of aromatic compound degradation via 3-oxoadipate	35	25	2
superpathway of aromatic compound degradation via 2-hydroxypentadienoate	42	21	2
anaerobic aromatic compound degradation (Thauera aromatica)	27	7	1