Experiment set3IT084 for Pseudomonas fluorescens GW456-L13

L-Tryptophan nitrogen source

Group: nitrogen source
Media: RCH2_defined_Glucose_noNitrogen + L-Tryptophan (12.5 mM), pH=7
Culturing: pseudo13_ML2, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=500 rpm
By: Mark on 1/21/2016
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 4 genes in this experiment

For nitrogen source L-Tryptophan in Pseudomonas fluorescens GW456-L13

For nitrogen source L-Tryptophan across organisms

SEED Subsystems

Subsystem	#Specific
NAD and NADP cofactor biosynthesis global	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:

• Benzoate degradation via hydroxylation
• Tryptophan metabolism
• Styrene degradation
• Butanoate metabolism

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
3-oxoadipate degradation	2	2	1
L-tryptophan degradation I (via anthranilate)	3	3	1
3-hydroxy-4-methyl-anthranilate biosynthesis II	5	3	1
L-tryptophan degradation to 2-amino-3-carboxymuconate semialdehyde	5	3	1
catechol degradation III (ortho-cleavage pathway)	6	6	1
superpathway of salicylate degradation	7	6	1
4-methylcatechol degradation (ortho cleavage)	7	4	1
L-glutamate degradation XI (reductive Stickland reaction)	7	3	1
aromatic compounds degradation via β-ketoadipate	9	9	1
NAD de novo biosynthesis II (from tryptophan)	9	6	1
L-glutamate degradation V (via hydroxyglutarate)	10	6	1
toluene degradation III (aerobic) (via p-cresol)	11	7	1
L-tryptophan degradation XI (mammalian, via kynurenine)	23	8	2
L-tryptophan degradation XII (Geobacillus)	12	7	1
L-tryptophan degradation IX	12	7	1
superpathway of NAD biosynthesis in eukaryotes	14	9	1
L-tryptophan degradation III (eukaryotic)	15	7	1
superpathway of aromatic compound degradation via 3-oxoadipate	35	21	2
mandelate degradation to acetyl-CoA	18	10	1
superpathway of aerobic toluene degradation	30	13	1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate	42	15	1