Experiment set5H19 for Shewanella oneidensis MR-1

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L-Phenylalanine nitrogen source

Group: nitrogen source
Media: ShewMM_noNitrogen + L-Phenylalanine (10 mM), pH=7
Culturing: MR1_ML3, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 4.0 generations
By: Adam on 8/21/2013
Media components: 1.75 g/L Sodium Chloride, 0.61 g/L Magnesium chloride hexahydrate, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 20 mM Sodium D,L-Lactate, 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 40 genes in this experiment

For nitrogen source L-Phenylalanine in Shewanella oneidensis MR-1

For nitrogen source L-Phenylalanine across organisms

SEED Subsystems

Subsystem #Specific
Glycogen metabolism 3
Aromatic amino acid degradation 2
Homogentisate pathway of aromatic compound degradation 2
Serine-glyoxylate cycle 2
Allantoin Utilization 1
Arginine Deiminase Pathway 1
Arginine and Ornithine Degradation 1
Catechol branch of beta-ketoadipate pathway 1
Copper homeostasis 1
D-Galacturonate and D-Glucuronate Utilization 1
D-galactarate, D-glucarate and D-glycerate catabolism 1
Folate Biosynthesis 1
Glutathione: Non-redox reactions 1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria 1
Glycine and Serine Utilization 1
Isobutyryl-CoA to Propionyl-CoA Module 1
Isoleucine degradation 1
Leucine Degradation and HMG-CoA Metabolism 1
Mannose-sensitive hemagglutinin type 4 pilus 1
Photorespiration (oxidative C2 cycle) 1
Plastoquinone Biosynthesis 1
Polyamine Metabolism 1
Protocatechuate branch of beta-ketoadipate pathway 1
Pterin biosynthesis 1
Queuosine-Archaeosine Biosynthesis 1
Tocopherol Biosynthesis 1
Trehalose Biosynthesis 1
Valine degradation 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-tyrosine biosynthesis IV 1 1 1
L-phenylalanine degradation I (aerobic) 1 1 1
glycogen biosynthesis I (from ADP-D-Glucose) 4 4 3
L-tyrosine degradation I 5 5 3
2-O-α-mannosyl-D-glycerate degradation 2 1 1
adipate degradation 5 4 2
starch biosynthesis 10 6 4
adipate biosynthesis 5 3 2
(8E,10E)-dodeca-8,10-dienol biosynthesis 11 6 4
L-phenylalanine degradation V 3 3 1
benzoyl-CoA biosynthesis 3 3 1
L-isoleucine degradation I 6 5 2
propanoate fermentation to 2-methylbutanoate 6 4 2
ketolysis 3 2 1
gentisate degradation I 3 1 1
acrylate degradation II 3 1 1
plastoquinol-9 biosynthesis I 3 1 1
benzoyl-CoA degradation I (aerobic) 7 2 2
queuosine biosynthesis I (de novo) 4 4 1
glycolate and glyoxylate degradation I 4 3 1
tetrahydromonapterin biosynthesis 4 2 1
D-galactarate degradation I 4 2 1
D-glucarate degradation I 4 2 1
4-hydroxy-2-nonenal detoxification 4 1 1
glycogen biosynthesis II (from UDP-D-Glucose) 4 1 1
phenylacetate degradation I (aerobic) 9 2 2
2-methyl-branched fatty acid β-oxidation 14 11 3
(R)- and (S)-3-hydroxybutanoate biosynthesis (engineered) 5 5 1
fatty acid β-oxidation II (plant peroxisome) 5 3 1
fatty acid β-oxidation IV (unsaturated, even number) 5 3 1
glutaryl-CoA degradation 5 3 1
glucosylglycerol biosynthesis 5 3 1
queuosine biosynthesis III (queuosine salvage) 5 3 1
propanoyl-CoA degradation II 5 3 1
3-phenylpropanoate degradation 10 4 2
superpathway of D-glucarate and D-galactarate degradation 5 2 1
superpathway of plastoquinol biosynthesis 5 2 1
acrylate degradation I 5 2 1
pentachlorophenol degradation 10 3 2
benzoate biosynthesis III (CoA-dependent, non-β-oxidative) 5 1 1
pyruvate fermentation to hexanol (engineered) 11 7 2
superpathway of phenylethylamine degradation 11 3 2
oleate β-oxidation 35 32 6
fatty acid salvage 6 6 1
pyruvate fermentation to butanol II (engineered) 6 5 1
β-alanine biosynthesis II 6 4 1
methyl ketone biosynthesis (engineered) 6 3 1
6-gingerol analog biosynthesis (engineered) 6 2 1
5-nitroanthranilate degradation 6 2 1
fatty acid β-oxidation I (generic) 7 6 1
superpathway of glycol metabolism and degradation 7 5 1
fatty acid β-oxidation VI (mammalian peroxisome) 7 3 1
pyruvate fermentation to butanoate 7 3 1
vitamin E biosynthesis (tocopherols) 7 1 1
Spodoptera littoralis pheromone biosynthesis 22 4 3
L-valine degradation I 8 7 1
2-deoxy-D-ribose degradation II 8 4 1
pyruvate fermentation to butanol I 8 4 1
glutathione-mediated detoxification I 8 3 1
2-methylpropene degradation 8 2 1
glycogen biosynthesis III (from α-maltose 1-phosphate) 8 2 1
photorespiration III 9 7 1
photorespiration I 9 7 1
TCA cycle VI (Helicobacter) 9 7 1
valproate β-oxidation 9 6 1
superpathway of Clostridium acetobutylicum acidogenic fermentation 9 5 1
Entner-Doudoroff pathway II (non-phosphorylative) 9 5 1
3-hydroxypropanoate/4-hydroxybutanate cycle 18 7 2
benzoate biosynthesis I (CoA-dependent, β-oxidative) 9 3 1
L-phenylalanine degradation IV (mammalian, via side chain) 9 3 1
gliotoxin biosynthesis 9 2 1
glutathione-mediated detoxification II 9 1 1
photorespiration II 10 8 1
superpathway of coenzyme A biosynthesis II (plants) 10 8 1
L-glutamate degradation V (via hydroxyglutarate) 10 5 1
methyl tert-butyl ether degradation 10 2 1
L-glutamate degradation VII (to butanoate) 12 4 1
indole glucosinolate activation (intact plant cell) 12 3 1
camalexin biosynthesis 12 2 1
formaldehyde assimilation I (serine pathway) 13 8 1
superpathway of Clostridium acetobutylicum solventogenic fermentation 13 6 1
3-hydroxypropanoate cycle 13 4 1
glyoxylate assimilation 13 3 1
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase) 13 2 1
superpathway of glyoxylate cycle and fatty acid degradation 14 11 1
docosahexaenoate biosynthesis III (6-desaturase, mammals) 14 2 1
L-tryptophan degradation III (eukaryotic) 15 3 1
glycerol degradation to butanol 16 10 1
crotonate fermentation (to acetate and cyclohexane carboxylate) 16 3 1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation 17 8 1
benzoate fermentation (to acetate and cyclohexane carboxylate) 17 3 1
superpathway of the 3-hydroxypropanoate cycle 18 4 1
toluene degradation VI (anaerobic) 18 3 1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered) 26 21 1
platensimycin biosynthesis 26 6 1
1-butanol autotrophic biosynthesis (engineered) 27 21 1
superpathway of microbial D-galacturonate and D-glucuronate degradation 31 6 1