Experiment set3H38 for Dinoroseobacter shibae DFL-12

Sodium propionate carbon source

Group: carbon source
Media: DinoMM_noCarbon_HighNutrient + Sodium propionate (20 mM)
Culturing: Dino_ML3, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 5.7 generations
By: Adam on 2/27/2014
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 7 genes in this experiment

For carbon source Sodium propionate in Dinoroseobacter shibae DFL-12

For carbon source Sodium propionate across organisms

SEED Subsystems

Subsystem	#Specific
Propionyl-CoA to Succinyl-CoA Module	3
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	2
Methionine Degradation	1
Serine-glyoxylate cycle	1
TCA Cycle	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Valine, leucine and isoleucine degradation
• Glycolysis / Gluconeogenesis
• Citrate cycle (TCA cycle)
• Pyruvate metabolism
• Propanoate metabolism
• 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
• Glycine, serine and threonine metabolism
• Valine, leucine and isoleucine biosynthesis
• Butanoate metabolism

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
pyruvate decarboxylation to acetyl CoA I	3	3	2
propanoyl CoA degradation I	3	3	2
2-oxobutanoate degradation I	4	3	2
2-oxoglutarate decarboxylation to succinyl-CoA	3	3	1
glycine cleavage	3	3	1
2-oxoisovalerate decarboxylation to isobutanoyl-CoA	3	3	1
glycine biosynthesis II	3	3	1
pyruvate fermentation to acetate II	3	3	1
pyruvate fermentation to acetate V	3	2	1
anaerobic energy metabolism (invertebrates, mitochondrial)	10	6	3
pyruvate fermentation to acetate and (S)-lactate I	4	3	1
3,3'-disulfanediyldipropannoate degradation	4	2	1
superpathway of anaerobic energy metabolism (invertebrates)	17	10	3
3-hydroxypropanoate cycle	13	9	2
pyruvate fermentation to propanoate I	7	4	1
superpathway of L-methionine salvage and degradation	16	10	2
superpathway of the 3-hydroxypropanoate cycle	18	12	2
3-hydroxypropanoate/4-hydroxybutanate cycle	18	11	2
methylaspartate cycle	19	14	2
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	19	2
ethylmalonyl-CoA pathway	11	8	1
L-glutamate degradation VIII (to propanoate)	11	4	1
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	7	1
crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA cycle (engineered)	14	7	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	22	1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	18	1
1-butanol autotrophic biosynthesis (engineered)	27	19	1
mycolate biosynthesis	205	21	1
superpathway of mycolate biosynthesis	239	22	1