Experiment set2IT073 for Pseudomonas fluorescens GW456-L13

L-Phenylalanine carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + L-Phenylalanine (20 mM), pH=7
Culturing: pseudo13_ML2, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
By: Mark on 3/10/2015
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 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 13 genes in this experiment

For carbon source L-Phenylalanine in Pseudomonas fluorescens GW456-L13

For carbon source L-Phenylalanine across organisms

SEED Subsystems

Subsystem	#Specific
Aromatic amino acid degradation	3
Homogentisate pathway of aromatic compound degradation	2
Chorismate: Intermediate for synthesis of PAPA antibiotics, PABA, anthranilate, 3-hydroxyanthranilate and more.	1
Chorismate Synthesis	1
Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate)	1
Folate Biosynthesis	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
HMG CoA Synthesis	1
Leucine Degradation and HMG-CoA Metabolism	1
Plastoquinone Biosynthesis	1
Polyhydroxybutyrate metabolism	1
Pterin biosynthesis	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
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Biosynthesis of phenylpropanoids
• Novobiocin biosynthesis
• Styrene degradation
• Butanoate metabolism
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of plant hormones
• Ubiquinone and menaquinone biosynthesis
• Glutamate metabolism
• Alanine and aspartate metabolism
• Methionine metabolism
• Cysteine metabolism
• Lysine biosynthesis
• Arginine and proline metabolism
• Benzoate degradation via hydroxylation
• Carbon fixation in photosynthetic organisms
• Folate biosynthesis
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-tyrosine biosynthesis IV	1	1	1
adenosine nucleotides degradation III	1	1	1
L-aspartate biosynthesis	1	1	1
L-phenylalanine degradation I (aerobic)	1	1	1
L-aspartate degradation I	1	1	1
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
L-tyrosine degradation I	5	5	3
L-phenylalanine biosynthesis III (cytosolic, plants)	2	2	1
4-aminobenzoate biosynthesis I	2	2	1
L-glutamate degradation II	2	2	1
3-oxoadipate degradation	2	2	1
3-dehydroquinate biosynthesis I	2	2	1
L-tryptophan degradation IV (via indole-3-lactate)	2	1	1
4-aminobenzoate biosynthesis II	2	1	1
malate/L-aspartate shuttle pathway	2	1	1
L-tyrosine degradation II	2	1	1
atromentin biosynthesis	2	1	1
superpathway of plastoquinol biosynthesis	5	2	2
L-phenylalanine biosynthesis I	3	3	1
L-tyrosine biosynthesis I	3	3	1
L-asparagine degradation III (mammalian)	3	2	1
L-phenylalanine degradation V	3	2	1
L-phenylalanine degradation II (anaerobic)	3	2	1
plastoquinol-9 biosynthesis I	3	1	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
(R)-cysteate degradation	3	1	1
sulfolactate degradation III	3	1	1
indole-3-acetate biosynthesis VI (bacteria)	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
L-tryptophan degradation VIII (to tryptophol)	4	1	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	5	2
superpathway of L-phenylalanine biosynthesis	10	10	2
superpathway of L-tyrosine biosynthesis	10	10	2
trans-4-hydroxy-L-proline degradation I	5	3	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
L-tryptophan degradation XIII (reductive Stickland reaction)	5	1	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	6	2
superpathway of aromatic amino acid biosynthesis	18	18	3
superpathway of L-threonine biosynthesis	6	6	1
catechol degradation III (ortho-cleavage pathway)	6	6	1
TCA cycle VIII (Chlamydia)	6	4	1
superpathway of sulfolactate degradation	6	2	1
coenzyme M biosynthesis II	6	1	1
chorismate biosynthesis I	7	7	1
superpathway of salicylate degradation	7	6	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	2
4-methylcatechol degradation (ortho cleavage)	7	4	1
anaerobic energy metabolism (invertebrates, cytosol)	7	4	1
L-glutamate degradation XI (reductive Stickland reaction)	7	3	1
vitamin E biosynthesis (tocopherols)	7	1	1
2-deoxy-D-ribose degradation II	8	3	1
aromatic compounds degradation via β-ketoadipate	9	9	1
superpathway of L-methionine biosynthesis (transsulfuration)	9	7	1
superpathway of tetrahydrofolate biosynthesis	10	8	1
L-glutamate degradation V (via hydroxyglutarate)	10	6	1
rosmarinic acid biosynthesis I	10	2	1
toluene degradation III (aerobic) (via p-cresol)	11	7	1
superpathway of candicidin biosynthesis	11	4	1
tropane alkaloids biosynthesis	11	1	1
(S)-reticuline biosynthesis I	11	1	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	12	1
superpathway of tetrahydrofolate biosynthesis and salvage	12	10	1
indole-3-acetate biosynthesis II	12	4	1
superpathway of L-tryptophan biosynthesis	13	13	1
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of rosmarinic acid biosynthesis	14	3	1
superpathway of chorismate metabolism	59	42	4
superpathway of hyoscyamine (atropine) and scopolamine biosynthesis	16	3	1
superpathway of anaerobic energy metabolism (invertebrates)	17	9	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	1
mandelate degradation to acetyl-CoA	18	10	1
aspartate superpathway	25	22	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	4	1
superpathway of aerobic toluene degradation	30	13	1
superpathway of aromatic compound degradation via 3-oxoadipate	35	21	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	20	1