Experiment set5IT086 for Pseudomonas fluorescens FW300-N2C3

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L-Phenylalanine nitrogen source

Group: nitrogen source
Media: RCH2_defined_Glucose_noNitrogen + L-Phenylalanine (5 mM), pH=7
Culturing: pseudo5_N2-C3_1_ML2, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
By: Mark on 12/17/2014
Media components: 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 20 mM D-Glucose, 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 11 genes in this experiment

For nitrogen source L-Phenylalanine in Pseudomonas fluorescens FW300-N2C3

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
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis 1
Homogentisate pathway of aromatic compound degradation 1
NAD and NADP cofactor biosynthesis global 1
NAD regulation 1
Plastoquinone Biosynthesis 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:

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway #Steps #Present #Specific
L-phenylalanine degradation I (aerobic) 1 1 1
3-(4-hydroxyphenyl)pyruvate biosynthesis 1 1 1
L-aspartate biosynthesis 1 1 1
L-tyrosine biosynthesis IV 1 1 1
L-aspartate degradation I 1 1 1
L-tyrosine degradation I 5 5 3
L-glutamate degradation II 2 2 1
L-phenylalanine biosynthesis III (cytosolic, plants) 2 2 1
malate/L-aspartate shuttle pathway 2 1 1
atromentin biosynthesis 2 1 1
L-tryptophan degradation IV (via indole-3-lactate) 2 1 1
L-tyrosine degradation II 2 1 1
superpathway of plastoquinol biosynthesis 5 2 2
L-tyrosine biosynthesis I 3 3 1
L-phenylalanine 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
gentisate degradation I 3 2 1
(R)-cysteate degradation 3 1 1
plastoquinol-9 biosynthesis I 3 1 1
indole-3-acetate biosynthesis VI (bacteria) 3 1 1
L-tyrosine degradation IV (to 4-methylphenol) 3 1 1
sulfolactate degradation III 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
4-hydroxy-2-nonenal detoxification 4 1 1
L-phenylalanine degradation IV (mammalian, via side chain) 9 4 2
NAD salvage pathway II (PNC IV cycle) 5 3 1
trans-4-hydroxy-L-proline degradation I 5 3 1
pentachlorophenol degradation 10 3 2
L-phenylalanine degradation VI (reductive Stickland reaction) 5 1 1
L-tryptophan degradation XIII (reductive Stickland reaction) 5 1 1
4-hydroxybenzoate biosynthesis I (eukaryotes) 5 1 1
L-tyrosine degradation V (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
NAD de novo biosynthesis IV (anaerobic) 6 5 1
NAD de novo biosynthesis I 6 5 1
NAD de novo biosynthesis III 6 4 1
TCA cycle VIII (Chlamydia) 6 4 1
5-nitroanthranilate degradation 6 3 1
superpathway of sulfolactate degradation 6 2 1
coenzyme M biosynthesis II 6 1 1
NAD salvage pathway I (PNC VI cycle) 7 5 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
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 5 1
rosmarinic acid biosynthesis I 10 3 1
(S)-reticuline biosynthesis I 11 1 1
tropane alkaloids biosynthesis 11 1 1
superpathway of L-methionine biosynthesis (by sulfhydrylation) 12 12 1
indole-3-acetate biosynthesis II 12 5 1
indole glucosinolate activation (intact plant cell) 12 3 1
camalexin biosynthesis 12 2 1
aspartate superpathway 25 22 2
superpathway of L-isoleucine biosynthesis I 13 13 1
superpathway of rosmarinic acid biosynthesis 14 4 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
anaerobic aromatic compound degradation (Thauera aromatica) 27 3 1
superpathway of chorismate metabolism 59 44 2
Methanobacterium thermoautotrophicum biosynthetic metabolism 56 21 1