Experiment set7IT051 for Phaeobacter inhibens DSM 17395

marine broth with D-Cycloserine 0.0625 mg/ml

Group: stress
Media: marine_broth_2216 + D-Cycloserine (0.0625 mg/ml)
Culturing: Phaeo_ML1, 48 well microplate; Tecan Infinite F200, Aerobic, at 25 (C), shaken=orbital
By: Adam on marchapr14
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: 897 E1,E2

Specific Phenotypes

For 10 genes in this experiment

For stress D-Cycloserine in Phaeobacter inhibens DSM 17395

For stress D-Cycloserine across organisms

SEED Subsystems

Subsystem	#Specific
DNA repair, UvrABC system	3
DNA repair, bacterial RecFOR pathway	3
Arginine and Ornithine Degradation	2
Calvin-Benson cycle	1
DNA-replication	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
• 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	6	1
Entner-Doudoroff pathway I	9	8	1
sucrose biosynthesis I (from photosynthesis)	9	7	1
glycolysis IV	10	7	1
glycolysis III (from glucose)	11	9	1
glycolysis II (from fructose 6-phosphate)	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
superpathway of pyridoxal 5'-phosphate biosynthesis and salvage	12	7	1
gluconeogenesis I	13	12	1
glycolysis I (from glucose 6-phosphate)	13	10	1
Bifidobacterium shunt	15	12	1
glycerol degradation to butanol	16	9	1
superpathway of glucose and xylose degradation	17	14	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	14	1
heterolactic fermentation	18	13	1
superpathway of hexitol degradation (bacteria)	18	11	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