Experiment set3H11 for Dinoroseobacter shibae DFL-12

Trisodium citrate dihydrate carbon source

Group: carbon source
Media: DinoMM_noCarbon_HighNutrient + Trisodium citrate dihydrate (20 mM)
Culturing: Dino_ML3, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 6.8 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 6 genes in this experiment

For carbon source Trisodium citrate dihydrate in Dinoroseobacter shibae DFL-12

For carbon source Trisodium citrate dihydrate across organisms

SEED Subsystems

Subsystem	#Specific
Lipid A modifications	1
Propionate-CoA to Succinate Module	1
TCA Cycle	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Citrate cycle (TCA cycle)
• Glyoxylate and dicarboxylate metabolism
• Reductive carboxylate cycle (CO2 fixation)
• 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
glyoxylate cycle	6	6	2
partial TCA cycle (obligate autotrophs)	8	6	2
nitrogen remobilization from senescing leaves	8	6	2
TCA cycle II (plants and fungi)	9	8	2
TCA cycle V (2-oxoglutarate synthase)	9	8	2
TCA cycle IV (2-oxoglutarate decarboxylase)	9	8	2
TCA cycle VII (acetate-producers)	9	6	2
TCA cycle VI (Helicobacter)	9	6	2
TCA cycle I (prokaryotic)	10	9	2
TCA cycle III (animals)	10	9	2
reductive TCA cycle I	11	7	2
superpathway of glyoxylate bypass and TCA	12	11	2
reductive TCA cycle II	12	6	2
superpathway of glyoxylate cycle and fatty acid degradation	14	12	2
mixed acid fermentation	16	10	2
methylaspartate cycle	19	14	2
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	19	2
ethene biosynthesis V (engineered)	25	17	2
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	22	2