Experiment set6IT048 for Phaeobacter inhibens DSM 17395

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casamino acids carbon source

Group: carbon source
Media: DinoMM_noCarbon_HighNutrient + casamino acids (2 mg/ml), pH=7
Culturing: Phaeo_ML1, tube, Aerobic, at 25 (C), shaken=200 rpm
Growth: about 5.5 generations
By: Adam on marchapr14
Media components: 20 g/L Sea salts, 0.3 g/L Ammonium Sulfate, 0.1 g/L Potassium phosphate monobasic, 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 14 genes in this experiment

For carbon source casamino acids in Phaeobacter inhibens DSM 17395

For carbon source casamino acids across organisms

SEED Subsystems

Subsystem #Specific
NAD and NADP cofactor biosynthesis global 2
NAD regulation 2
Aromatic amino acid interconversions with aryl acids 1
Ketoisovalerate oxidoreductase 1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate 1
Ton and Tol transport systems 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
acetate and ATP formation from acetyl-CoA III 1 1 1
acetate conversion to acetyl-CoA 1 1 1
ethanol degradation IV 3 3 2
ethanol degradation II 3 3 2
ethanol degradation III 3 2 2
NAD de novo biosynthesis I 6 6 2
superpathway of acetate utilization and formation 3 3 1
hypotaurine degradation 3 3 1
NAD de novo biosynthesis III 6 5 2
NAD de novo biosynthesis IV (anaerobic) 6 5 2
L-isoleucine biosynthesis V 3 2 1
histamine degradation 3 1 1
NAD biosynthesis from 2-amino-3-carboxymuconate semialdehyde 4 4 1
phytol degradation 4 3 1
L-tryptophan degradation X (mammalian, via tryptamine) 4 2 1
chitin deacetylation 4 2 1
fatty acid α-oxidation I (plants) 4 2 1
putrescine degradation III 4 1 1
nicotine biosynthesis 9 3 2
octane oxidation 5 3 1
sphingosine and sphingosine-1-phosphate metabolism 10 4 2
mitochondrial NADPH production (yeast) 5 2 1
dopamine degradation 5 1 1
3-methyl-branched fatty acid α-oxidation 6 3 1
superpathway of nicotine biosynthesis 12 4 2
superpathway of bitter acids biosynthesis 18 3 3
lupulone and humulone biosynthesis 6 1 1
colupulone and cohumulone biosynthesis 6 1 1
alkane oxidation 6 1 1
adlupulone and adhumulone biosynthesis 6 1 1
noradrenaline and adrenaline degradation 13 4 2
serotonin degradation 7 3 1
ceramide degradation by α-oxidation 7 2 1
limonene degradation IV (anaerobic) 7 1 1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast) 8 4 1
ceramide and sphingolipid recycling and degradation (yeast) 16 4 2
aromatic biogenic amine degradation (bacteria) 8 1 1
reductive glycine pathway of autotrophic CO2 fixation 9 6 1
NAD de novo biosynthesis II (from tryptophan) 9 6 1
cis-geranyl-CoA degradation 9 2 1
aspartate superpathway 25 23 2
superpathway of NAD biosynthesis in eukaryotes 14 8 1