Experiment set47S226 for Pseudomonas putida KT2440

mixed carbon sources Trisodium citrate dihydrate 10 mM and 3-Chloro-L-tyrosine 10 mM

Group: mixed carbon source
Media: MME_noCarbon + Trisodium citrate dihydrate (10 mM) + 3-Chloro-L-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 10 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	1
Chorismate Synthesis	1
Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate)	1
Homogentisate pathway of aromatic compound degradation	1
Methionine Biosynthesis	1
Methionine Degradation	1
Plastoquinone Biosynthesis	1
Queuosine-Archaeosine Biosynthesis	1
Tocopherol Biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Ubiquinone and menaquinone biosynthesis
• Tyrosine metabolism
• Ascorbate and aldarate metabolism
• Phenylalanine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Glutathione metabolism
• Nucleotide sugars metabolism
• Glycosaminoglycan degradation
• Styrene degradation
• Metabolism of xenobiotics by cytochrome P450
• Drug metabolism - cytochrome P450
• 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
3-dehydroquinate biosynthesis I	2	2	1
L-tyrosine degradation I	5	5	2
plastoquinol-9 biosynthesis I	3	1	1
gentisate degradation I	3	1	1
4-hydroxy-2-nonenal detoxification	4	1	1
pentachlorophenol degradation	10	4	2
superpathway of plastoquinol biosynthesis	5	2	1
5-nitroanthranilate degradation	6	2	1
chorismate biosynthesis I	7	7	1
vitamin E biosynthesis (tocopherols)	7	1	1
glutathione-mediated detoxification I	8	3	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	6	1
gliotoxin biosynthesis	9	2	1
glutathione-mediated detoxification II	9	1	1
superpathway of L-phenylalanine biosynthesis	10	10	1
superpathway of L-tyrosine biosynthesis	10	10	1
3-phenylpropanoate degradation	10	4	1
indole glucosinolate activation (intact plant cell)	12	3	1
camalexin biosynthesis	12	2	1
superpathway of L-tryptophan biosynthesis	13	13	1
superpathway of aromatic amino acid biosynthesis	18	18	1
superpathway of chorismate metabolism	59	42	1