Experiment set8IT055 for Phaeobacter inhibens DSM 17395

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L-Phenylalanine nitrogen source

Group: nitrogen source
Media: DinoMM_noNitrogen_HighNutrient_SucroseC + L-Phenylalanine (5 mM), pH=7.2
Culturing: Phaeo_ML1, tube, Aerobic, at 25 (C), shaken=200 rpm
Growth: about 5.7 generations
By: Mark on 1/20/2015
Media components: 20 g/L Sea salts, 0.1 g/L Potassium phosphate monobasic, 20 mM Sucrose, 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 6 genes in this experiment

For nitrogen source L-Phenylalanine in Phaeobacter inhibens DSM 17395

For nitrogen source L-Phenylalanine across organisms

SEED Subsystems

Subsystem #Specific
Acetyl-CoA fermentation to Butyrate 2
Butanol Biosynthesis 2
Isoleucine degradation 2
Polyhydroxybutyrate metabolism 2
Valine degradation 2
n-Phenylalkanoic acid degradation 2
Aromatic amino acid interconversions with aryl acids 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
fatty acid β-oxidation III (unsaturated, odd number) 1 1 1
benzoyl-CoA biosynthesis 3 3 2
fatty acid β-oxidation IV (unsaturated, even number) 5 3 3
fatty acid β-oxidation I (generic) 7 5 4
oleate β-oxidation (thioesterase-dependent, yeast) 2 2 1
oleate β-oxidation 35 30 16
adipate degradation 5 5 2
adipate biosynthesis 5 4 2
glutaryl-CoA degradation 5 3 2
fatty acid β-oxidation II (plant peroxisome) 5 3 2
fatty acid β-oxidation V (unsaturated, odd number, di-isomerase-dependent) 5 2 2
pyruvate fermentation to hexanol (engineered) 11 7 4
(8E,10E)-dodeca-8,10-dienol biosynthesis 11 5 4
2-methyl-branched fatty acid β-oxidation 14 10 5
fatty acid salvage 6 6 2
hypotaurine degradation 3 3 1
ethanol degradation II 3 3 1
ethanol degradation IV 3 3 1
valproate β-oxidation 9 6 3
phenylacetate degradation I (aerobic) 9 6 3
L-isoleucine degradation I 6 4 2
pyruvate fermentation to butanol II (engineered) 6 4 2
ethanol degradation III 3 2 1
methyl ketone biosynthesis (engineered) 6 3 2
propanoate fermentation to 2-methylbutanoate 6 3 2
oleate β-oxidation (reductase-dependent, yeast) 3 1 1
histamine degradation 3 1 1
pyruvate fermentation to butanoate 7 3 2
fatty acid β-oxidation VI (mammalian peroxisome) 7 3 2
benzoyl-CoA degradation I (aerobic) 7 3 2
superpathway of phenylethylamine degradation 11 6 3
phytol degradation 4 3 1
L-valine degradation I 8 5 2
L-tryptophan degradation X (mammalian, via tryptamine) 4 2 1
fatty acid α-oxidation I (plants) 4 2 1
pyruvate fermentation to butanol I 8 3 2
putrescine degradation III 4 1 1
oleate β-oxidation (isomerase-dependent, yeast) 4 1 1
superpathway of Clostridium acetobutylicum acidogenic fermentation 9 5 2
benzoate biosynthesis I (CoA-dependent, β-oxidative) 9 3 2
(R)- and (S)-3-hydroxybutanoate biosynthesis (engineered) 5 5 1
octane oxidation 5 3 1
sphingosine and sphingosine-1-phosphate metabolism 10 4 2
9-cis, 11-trans-octadecadienoyl-CoA degradation (isomerase-dependent, yeast) 10 4 2
3-phenylpropanoate degradation 10 4 2
L-glutamate degradation V (via hydroxyglutarate) 10 4 2
4-hydroxybenzoate biosynthesis III (plants) 5 2 1
mitochondrial NADPH production (yeast) 5 2 1
benzoate biosynthesis III (CoA-dependent, non-β-oxidative) 5 1 1
dopamine degradation 5 1 1
3-methyl-branched fatty acid α-oxidation 6 3 1
L-glutamate degradation VII (to butanoate) 12 4 2
6-gingerol analog biosynthesis (engineered) 6 2 1
alkane oxidation 6 1 1
superpathway of Clostridium acetobutylicum solventogenic fermentation 13 5 2
noradrenaline and adrenaline degradation 13 4 2
superpathway of glyoxylate cycle and fatty acid degradation 14 10 2
serotonin degradation 7 3 1
ceramide degradation by α-oxidation 7 2 1
limonene degradation IV (anaerobic) 7 1 1
Spodoptera littoralis pheromone biosynthesis 22 3 3
L-tryptophan degradation III (eukaryotic) 15 5 2
glycerol degradation to butanol 16 9 2
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast) 8 4 1
ceramide and sphingolipid recycling and degradation (yeast) 16 4 2
crotonate fermentation (to acetate and cyclohexane carboxylate) 16 4 2
2-methylpropene degradation 8 2 1
aromatic biogenic amine degradation (bacteria) 8 1 1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation 17 7 2
benzoate fermentation (to acetate and cyclohexane carboxylate) 17 4 2
3-hydroxypropanoate/4-hydroxybutanate cycle 18 11 2
toluene degradation VI (anaerobic) 18 4 2
methyl tert-butyl ether degradation 10 2 1
gallate degradation III (anaerobic) 11 3 1
10-trans-heptadecenoyl-CoA degradation (reductase-dependent, yeast) 12 2 1
10-cis-heptadecenoyl-CoA degradation (yeast) 12 2 1
androstenedione degradation I (aerobic) 25 6 2
platensimycin biosynthesis 26 6 2
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase) 13 2 1
1-butanol autotrophic biosynthesis (engineered) 27 19 2
androstenedione degradation II (anaerobic) 27 4 2
superpathway of testosterone and androsterone degradation 28 6 2
superpathway of cholesterol degradation I (cholesterol oxidase) 42 8 3
docosahexaenoate biosynthesis III (6-desaturase, mammals) 14 2 1
superpathway of cholesterol degradation II (cholesterol dehydrogenase) 47 9 3
cholesterol degradation to androstenedione I (cholesterol oxidase) 17 2 1
cholesterol degradation to androstenedione II (cholesterol dehydrogenase) 22 3 1
superpathway of cholesterol degradation III (oxidase) 49 5 2
photosynthetic 3-hydroxybutanoate biosynthesis (engineered) 26 20 1