Experiment set5S248 for Pseudomonas sp. RS175

L-Phenylalanine 5 mM carbon source

Group: carbon source
Media: MME_noCarbon + L-Phenylalanine (5 mM)
Culturing: Pseudomonas_RS175_ML2, 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 18 genes in this experiment

For carbon source L-Phenylalanine in Pseudomonas sp. RS175

For carbon source L-Phenylalanine across organisms

SEED Subsystems

Subsystem	#Specific
Aromatic amino acid degradation	3
Flagellum	3
Flagellar motility	2
Homogentisate pathway of aromatic compound degradation	2
Bacterial Chemotaxis	1
Bacterial RNA-metabolizing Zn-dependent hydrolases	1
Catechol branch of beta-ketoadipate pathway	1
Conserved gene cluster associated with Met-tRNA formyltransferase	1
DNA-replication	1
DNA Repair Base Excision	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Leucine Degradation and HMG-CoA Metabolism	1
Methionine Biosynthesis	1
Methionine Degradation	1
Plastoquinone Biosynthesis	1
Protocatechuate branch of beta-ketoadipate pathway	1
Ribosome biogenesis bacterial	1
Serine-glyoxylate cycle	1
Threonine and Homoserine 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:

• Tyrosine metabolism
• Phenylalanine metabolism
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• 1- and 2-Methylnaphthalene degradation
• Styrene degradation
• Butanoate metabolism
• Biosynthesis of phenylpropanoids
• Fatty acid biosynthesis
• Synthesis and degradation of ketone bodies
• Ubiquinone and menaquinone biosynthesis
• Purine metabolism
• Pyrimidine metabolism
• Glutamate metabolism
• Alanine and aspartate metabolism
• Methionine metabolism
• Cysteine metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Lysine biosynthesis
• Lysine degradation
• Arginine and proline metabolism
• Histidine metabolism
• Glutathione metabolism
• Lipopolysaccharide biosynthesis
• Glycerophospholipid metabolism
• Ether lipid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• Benzoate degradation via CoA ligation
• Ethylbenzene degradation
• Carbon fixation in photosynthetic organisms
• Limonene and pinene degradation
• Diterpenoid biosynthesis
• Carotenoid biosynthesis - General
• Anthocyanin biosynthesis
• Metabolism of xenobiotics by cytochrome P450
• Drug metabolism - cytochrome P450
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide backbone
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-aspartate biosynthesis	1	1	1
L-aspartate degradation I	1	1	1
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
L-tyrosine degradation I	5	5	4
L-phenylalanine biosynthesis III (cytosolic, plants)	2	2	1
L-glutamate degradation II	2	2	1
L-tryptophan degradation IV (via indole-3-lactate)	2	1	1
L-tyrosine degradation II	2	1	1
atromentin biosynthesis	2	1	1
malate/L-aspartate shuttle pathway	2	1	1
superpathway of plastoquinol biosynthesis	5	2	2
L-tyrosine biosynthesis I	3	3	1
ketolysis	3	3	1
L-phenylalanine biosynthesis I	3	3	1
sulfolactate degradation III	3	2	1
L-asparagine degradation III (mammalian)	3	2	1
L-phenylalanine degradation II (anaerobic)	3	2	1
(R)-cysteate degradation	3	1	1
indole-3-acetate biosynthesis VI (bacteria)	3	1	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
plastoquinol-9 biosynthesis I	3	1	1
superpathway of L-aspartate and L-asparagine biosynthesis	4	3	1
L-tyrosine degradation III	4	2	1
L-phenylalanine degradation III	4	2	1
4-hydroxy-2-nonenal detoxification	4	1	1
L-tryptophan degradation VIII (to tryptophol)	4	1	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	5	2
trans-4-hydroxy-L-proline degradation I	5	3	1
pentachlorophenol degradation	10	3	2
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
L-tryptophan degradation XIII (reductive Stickland reaction)	5	1	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	6	2
superpathway of L-threonine biosynthesis	6	6	1
TCA cycle VIII (Chlamydia)	6	4	1
superpathway of sulfolactate degradation	6	3	1
coenzyme M biosynthesis II	6	1	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	2
anaerobic energy metabolism (invertebrates, cytosol)	7	4	1
vitamin E biosynthesis (tocopherols)	7	1	1
glutathione-mediated detoxification I	8	3	1
superpathway of aromatic amino acid biosynthesis	18	18	2
superpathway of L-methionine biosynthesis (transsulfuration)	9	7	1
TCA cycle VI (Helicobacter)	9	7	1
gliotoxin biosynthesis	9	2	1
glutathione-mediated detoxification II	9	1	1
superpathway of L-tyrosine biosynthesis	10	10	1
superpathway of L-phenylalanine biosynthesis	10	10	1
rosmarinic acid biosynthesis I	10	2	1
tropane alkaloids biosynthesis	11	1	1
(S)-reticuline biosynthesis I	11	1	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	12	1
indole-3-acetate biosynthesis II	12	4	1
indole glucosinolate activation (intact plant cell)	12	3	1
camalexin biosynthesis	12	2	1
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of rosmarinic acid biosynthesis	14	2	1
superpathway of hyoscyamine (atropine) and scopolamine biosynthesis	16	3	1
superpathway of anaerobic energy metabolism (invertebrates)	17	8	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	1
aspartate superpathway	25	22	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	4	1
superpathway of chorismate metabolism	59	43	2
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	20	1