Experiment set5H36 for Phaeobacter inhibens DSM 17395

m-Inositol carbon source

Group: carbon source
Media: DinoMM_noCarbon_HighNutrient + m-Inositol (20 mM), pH=7
Culturing: Phaeo_ML1, tube, Aerobic, at 25 (C), shaken=200 rpm
Growth: about 5.4 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 12 genes in this experiment

For carbon source m-Inositol in Phaeobacter inhibens DSM 17395

For carbon source m-Inositol across organisms

SEED Subsystems

Subsystem	#Specific
Inositol catabolism	10
Isobutyryl-CoA to Propionyl-CoA Module	1
Valine degradation	1

Metabolic Maps

Color code by fitness: see overview map or list of maps.

Maps containing gene(s) with specific phenotypes:

• Inositol phosphate metabolism
• Glycolysis / Gluconeogenesis
• Pentose phosphate pathway
• Pentose and glucuronate interconversions
• Fructose and mannose metabolism
• Galactose metabolism
• Ascorbate and aldarate metabolism
• Valine, leucine and isoleucine degradation
• 1,1,1-Trichloro-2,2-bis(4-chlorophenyl)ethane (DDT) degradation
• Phenylalanine metabolism
• Benzoate degradation via hydroxylation
• Streptomycin biosynthesis
• Biphenyl degradation
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• Ethylbenzene degradation
• Carbon fixation in photosynthetic organisms
• Nicotinate and nicotinamide metabolism
• Limonene and pinene degradation
• Caprolactam degradation
• Biosynthesis of ansamycins
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
myo-inositol degradation I	7	7	7
myo-, chiro- and scyllo-inositol degradation	10	7	7
β-alanine degradation I	2	1	1
β-alanine degradation II	2	1	1
sedoheptulose bisphosphate bypass	2	1	1
propanoyl-CoA degradation II	5	3	1
sucrose degradation V (sucrose α-glucosidase)	5	2	1
myo-inositol degradation II	5	1	1
pentose phosphate pathway (non-oxidative branch) II	6	5	1
Calvin-Benson-Bassham cycle	13	10	2
2,4-dinitrotoluene degradation	7	1	1
L-valine degradation I	8	5	1
oxygenic photosynthesis	17	11	2
sucrose biosynthesis I (from photosynthesis)	9	7	1
formaldehyde assimilation II (assimilatory RuMP Cycle)	9	6	1
1,3-propanediol biosynthesis (engineered)	9	4	1
glycolysis IV	10	7	1
glycolysis V (Pyrococcus)	10	7	1
glycolysis II (from fructose 6-phosphate)	11	9	1
glycolysis III (from glucose)	11	9	1
glycolysis VI (from fructose)	11	7	1
formaldehyde assimilation III (dihydroxyacetone cycle)	12	10	1
homolactic fermentation	12	9	1
gluconeogenesis III	12	9	1
ethene biosynthesis V (engineered)	25	17	2
gluconeogenesis I	13	12	1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	20	2
glycolysis I (from glucose 6-phosphate)	13	10	1
1-butanol autotrophic biosynthesis (engineered)	27	19	2
superpathway of glycolysis and the Entner-Doudoroff pathway	17	14	1
superpathway of hexitol degradation (bacteria)	18	11	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	8	1
streptomycin biosynthesis	18	2	1
superpathway of anaerobic sucrose degradation	19	14	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	14	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	17	1
superpathway of N-acetylneuraminate degradation	22	15	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	20	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	21	1