Experiment set27IT065 for Pseudomonas putida KT2440

L-Phenylalanine nitrogen source

Group: nitrogen source
Media: MOPS minimal media_Glucose_noNitrogen + L-Phenylalanine (10 mM)
Culturing: Putida_ML5_JBEI, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=200 rpm
By: Mitchell Thompson on 11/8/20
Media components: 10 mM D-Glucose, 40 mM 3-(N-morpholino)propanesulfonic acid, 4 mM Tricine, 1.32 mM Potassium phosphate dibasic, 0.01 mM Iron (II) sulfate heptahydrate, 0.276 mM Aluminum potassium sulfate dodecahydrate, 0.0005 mM Calcium chloride, 0.525 mM Magnesium chloride hexahydrate, 50 mM Sodium Chloride, 3e-09 M Ammonium heptamolybdate tetrahydrate, 4e-07 M Boric Acid, 3e-08 M Cobalt chloride hexahydrate, 1e-08 M Copper (II) sulfate pentahydrate, 8e-08 M Manganese (II) chloride tetrahydrate, 1e-08 M Zinc sulfate heptahydrate

Specific Phenotypes

For 12 genes in this experiment

For nitrogen source L-Phenylalanine in Pseudomonas putida KT2440

For nitrogen source L-Phenylalanine across organisms

SEED Subsystems

Subsystem	#Specific
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	4
Aromatic amino acid degradation	3
Chorismate: Intermediate for synthesis of PAPA antibiotics, PABA, anthranilate, 3-hydroxyanthranilate and more.	2
Folate Biosynthesis	2
Chorismate Synthesis	1
Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate)	1
Homogentisate pathway of aromatic compound degradation	1
Plastoquinone Biosynthesis	1
Pterin 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:

• Biosynthesis of phenylpropanoids
• Purine metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Folate biosynthesis
• Ubiquinone and menaquinone biosynthesis
• Pyrimidine metabolism
• Glutathione metabolism
• Styrene degradation
• Nicotinate and nicotinamide metabolism
• Metabolism of xenobiotics by cytochrome P450
• Drug metabolism - cytochrome P450
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
4-aminobenzoate biosynthesis I	2	2	2
L-tyrosine biosynthesis IV	1	1	1
L-phenylalanine degradation I (aerobic)	1	1	1
L-glutamine degradation I	1	1	1
L-glutamate biosynthesis I	2	2	1
3-dehydroquinate biosynthesis I	2	2	1
polyphosphate metabolism	2	2	1
4-aminobenzoate biosynthesis II	2	1	1
L-tyrosine degradation I	5	5	2
L-phenylalanine degradation V	3	3	1
ammonia assimilation cycle III	3	3	1
NAD salvage pathway III (to nicotinamide riboside)	3	2	1
gentisate degradation I	3	1	1
plastoquinol-9 biosynthesis I	3	1	1
UTP and CTP dephosphorylation I	7	5	2
purine nucleotides degradation II (aerobic)	11	11	3
inosine 5'-phosphate degradation	4	4	1
guanosine nucleotides degradation II	4	4	1
L-asparagine biosynthesis III (tRNA-dependent)	4	4	1
guanosine nucleotides degradation III	4	4	1
adenosine nucleotides degradation I	8	7	2
purine nucleotides degradation I (plants)	12	10	3
guanosine nucleotides degradation I	4	3	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	3	1
4-hydroxy-2-nonenal detoxification	4	1	1
adenosine nucleotides degradation II	5	5	1
superpathway of tetrahydrofolate biosynthesis	10	8	2
pentachlorophenol degradation	10	4	2
superpathway of plastoquinol biosynthesis	5	2	1
superpathway of candicidin biosynthesis	11	4	2
superpathway of tetrahydrofolate biosynthesis and salvage	12	10	2
superpathway of guanosine nucleotides degradation (plants)	6	5	1
superpathway of purines degradation in plants	18	13	3
5-nitroanthranilate degradation	6	2	1
chorismate biosynthesis I	7	7	1
L-glutamate and L-glutamine biosynthesis	7	6	1
ureide biosynthesis	7	6	1
vitamin E biosynthesis (tocopherols)	7	1	1
L-citrulline biosynthesis	8	7	1
glutathione-mediated detoxification I	8	3	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	6	1
gliotoxin biosynthesis	9	2	1
tunicamycin biosynthesis	9	2	1
glutathione-mediated detoxification II	9	1	1
chloramphenicol biosynthesis	9	1	1
superpathway of L-tyrosine biosynthesis	10	10	1
superpathway of L-phenylalanine biosynthesis	10	10	1
3-phenylpropanoate degradation	10	4	1
NAD salvage (plants)	11	4	1
superpathway of L-citrulline metabolism	12	9	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	3