Experiment set6IT006 for Marinobacter adhaerens HP15

Glycerol

Group: carbon source
Media: DinoMM_noCarbon_HighNutrient + Glycerol (20 mM), pH=7
Culturing: Marino_ML2, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 4.4 generations
By: Adam on 3/4/2014
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 1 genes in this experiment

For carbon source Glycerol in Marinobacter adhaerens HP15

For carbon source Glycerol across organisms

SEED Subsystems

Subsystem	#Specific
Calvin-Benson cycle	1
Entner-Doudoroff Pathway	1
Glycolysis and Gluconeogenesis	1
Pyridoxin (Vitamin B6) Biosynthesis	1
Redox-dependent regulation of nucleus processes	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glycolysis / Gluconeogenesis
• Urea cycle and metabolism of amino groups
• Geraniol degradation
• Lysine biosynthesis
• Arginine and proline metabolism
• Tryptophan metabolism
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Limonene and pinene degradation
• 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
pyridoxal 5'-phosphate biosynthesis I	7	7	1
Entner-Doudoroff pathway I	9	8	1
sucrose biosynthesis I (from photosynthesis)	9	6	1
glycolysis IV	10	9	1
glycolysis III (from glucose)	11	10	1
glycolysis II (from fructose 6-phosphate)	11	9	1
glycolysis VI (from fructose)	11	7	1
homolactic fermentation	12	11	1
formaldehyde assimilation III (dihydroxyacetone cycle)	12	9	1
superpathway of pyridoxal 5'-phosphate biosynthesis and salvage	12	8	1
gluconeogenesis III	12	7	1
gluconeogenesis I	13	10	1
glycolysis I (from glucose 6-phosphate)	13	10	1
Bifidobacterium shunt	15	15	1
glycerol degradation to butanol	16	10	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	14	1
superpathway of glucose and xylose degradation	17	13	1
heterolactic fermentation	18	14	1
superpathway of hexitol degradation (bacteria)	18	12	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	15	1
superpathway of anaerobic sucrose degradation	19	14	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	18	1
superpathway of N-acetylneuraminate degradation	22	13	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	21	1