Experiment set5IT021 for Pseudomonas fluorescens FW300-N2E3

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L-Tryptophan nitrogen source

Group: nitrogen source
Media: RCH2_defined_Glucose_noNitrogen + L-Tryptophan (5 mM), pH=7
Culturing: pseudo3_N2E3_ML2, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
By: Mark on 12/17/2015
Media components: 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 20 mM D-Glucose, 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 12 genes in this experiment

For nitrogen source L-Tryptophan in Pseudomonas fluorescens FW300-N2E3

For nitrogen source L-Tryptophan across organisms

SEED Subsystems

Subsystem #Specific
Aromatic amino acid degradation 4
Benzoate degradation 3
NAD and NADP cofactor biosynthesis global 3
Branched-Chain Amino Acid Biosynthesis 2
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis 2
Catechol branch of beta-ketoadipate pathway 1
Chloroaromatic degradation pathway 1
Protocatechuate branch of beta-ketoadipate pathway 1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway #Steps #Present #Specific
L-tryptophan degradation I (via anthranilate) 3 3 3
anthranilate degradation I (aerobic) 1 1 1
L-tryptophan degradation to 2-amino-3-carboxymuconate semialdehyde 5 3 3
3-hydroxy-4-methyl-anthranilate biosynthesis II 5 3 3
benzoate degradation I (aerobic) 2 2 1
NAD de novo biosynthesis II (from tryptophan) 9 6 3
3-hydroxy-4-methyl-anthranilate biosynthesis I 6 2 2
2-nitrobenzoate degradation II 3 1 1
catechol degradation to β-ketoadipate 4 4 1
protocatechuate degradation II (ortho-cleavage pathway) 4 4 1
L-tryptophan degradation XII (Geobacillus) 12 4 3
L-tryptophan degradation IX 12 4 3
superpathway of NAD biosynthesis in eukaryotes 14 9 3
L-tryptophan degradation III (eukaryotic) 15 6 3
L-tryptophan degradation XI (mammalian, via kynurenine) 23 7 4
superpathway of aromatic compound degradation via 3-oxoadipate 35 18 6
catechol degradation III (ortho-cleavage pathway) 6 6 1
superpathway of salicylate degradation 7 6 1
4-methylcatechol degradation (ortho cleavage) 7 4 1
3-hydroxyquinaldate biosynthesis 8 2 1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate 42 11 5
aromatic compounds degradation via β-ketoadipate 9 9 1
mandelate degradation to acetyl-CoA 18 9 2
quinoxaline-2-carboxylate biosynthesis 10 4 1
meta cleavage pathway of aromatic compounds 10 4 1
toluene degradation III (aerobic) (via p-cresol) 11 7 1
toluene degradation IV (aerobic) (via catechol) 13 4 1
superpathway of aerobic toluene degradation 30 11 2