Experiment set6IT016 for Dinoroseobacter shibae DFL-12

marine broth with syringaldehyde 0.625 mM

Group: stress
Media: marine_broth_2216 + syringaldehyde (0.625 mM)
Culturing: Dino_ML3, 48 well microplate; Tecan Infinite F200, Aerobic, at 25 (C), shaken=orbital
By: Mark on 1/15/2015
Media components: 5 g/L Bacto Peptone, 1 g/L Yeast Extract, 0.1 g/L Ferric citrate, 19.45 g/L Sodium Chloride, 5.9 g/L Magnesium chloride hexahydrate, 3.24 g/L Magnesium sulfate, 1.8 g/L Calcium chloride, 0.55 g/L Potassium Chloride, 0.16 g/L Sodium bicarbonate, 0.08 g/L Potassium bromide, 34 mg/L Strontium chloride, 22 mg/L Boric Acid, 4 mg/L Sodium metasilicate, 2.4 mg/L sodium fluoride, 8 mg/L Disodium phosphate
Growth plate: redo2 D1,D2

Specific Phenotypes

For 1 genes in this experiment

For stress syringaldehyde in Dinoroseobacter shibae DFL-12

For stress syringaldehyde across organisms

SEED Subsystems

Subsystem	#Specific
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 VI (Helicobacter)	9	6	2
TCA cycle VII (acetate-producers)	9	6	2
TCA cycle III (animals)	10	9	2
TCA cycle I (prokaryotic)	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