Experiment set47S233 for Pseudomonas putida KT2440

mixed carbon sources Trisodium citrate dihydrate 10 mM and L-Meta-tyrosine 10 mM

Group: mixed carbon source
Media: MME_noCarbon + Trisodium citrate dihydrate (10 mM) + L-Meta-tyrosine (10 mM)
Culturing: Putida_ML5_PNNL, 96 deep well, Aerobic, at 30 (C), shaken=1200 rpm
By: Andrew Frank on 11/17/23
Media components: 9.1 mM Potassium phosphate dibasic trihydrate, 20 mM 3-(N-morpholino)propanesulfonic acid, 4.3 mM Sodium Chloride, 10 mM Ammonium chloride, 0.41 mM Magnesium Sulfate Heptahydrate, 0.07 mM Calcium chloride dihydrate, MME Trace Minerals (0.5 mg/L EDTA tetrasodium tetrahydrate salt, 2 mg/L Ferric chloride, 0.05 mg/L Boric Acid, 0.05 mg/L Zinc chloride, 0.03 mg/L copper (II) chloride dihydrate, 0.05 mg/L Manganese (II) chloride tetrahydrate, 0.05 mg/L Diammonium molybdate, 0.05 mg/L Cobalt chloride hexahydrate, 0.05 mg/L Nickel (II) chloride hexahydrate)

Specific Phenotypes

For 9 genes in this experiment

For mixed carbon source Trisodium citrate dihydrate in Pseudomonas putida KT2440

For mixed carbon source Trisodium citrate dihydrate across organisms

SEED Subsystems

Subsystem	#Specific
Aromatic amino acid degradation	2
Catechol branch of beta-ketoadipate pathway	1
Chloroaromatic degradation pathway	1
Chorismate Synthesis	1
Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate)	1
Copper homeostasis	1
Homogentisate pathway of aromatic compound degradation	1
Protocatechuate branch of beta-ketoadipate pathway	1
Pterin biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Phenylalanine, tyrosine and tryptophan biosynthesis
• Geraniol degradation
• Tyrosine metabolism
• Phenylalanine metabolism
• Benzoate degradation via hydroxylation
• 1- and 2-Methylnaphthalene degradation
• Styrene degradation
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-tyrosine biosynthesis IV	1	1	1
L-phenylalanine degradation I (aerobic)	1	1	1
3-dehydroquinate biosynthesis I	2	2	1
3-oxoadipate degradation	2	2	1
L-phenylalanine degradation V	3	3	1
L-tyrosine degradation I	5	5	1
catechol degradation III (ortho-cleavage pathway)	6	6	1
chorismate biosynthesis I	7	7	1
superpathway of salicylate degradation	7	7	1
4-methylcatechol degradation (ortho cleavage)	7	5	1
aromatic compounds degradation via β-ketoadipate	9	9	1
superpathway of L-tyrosine biosynthesis	10	10	1
superpathway of L-phenylalanine biosynthesis	10	10	1
toluene degradation III (aerobic) (via p-cresol)	11	7	1
superpathway of L-tryptophan biosynthesis	13	13	1
superpathway of aromatic amino acid biosynthesis	18	18	1
mandelate degradation to acetyl-CoA	18	11	1
superpathway of aerobic toluene degradation	30	13	1
superpathway of aromatic compound degradation via 3-oxoadipate	35	19	1
superpathway of chorismate metabolism	59	42	1