Experiment set4IT037 for Dinoroseobacter shibae DFL-12

marine broth with Benzethonium chloride 0.008 mM

Group: stress
Media: marine_broth_2216 + Benzethonium chloride (0.008 mM)
Culturing: Dino_ML3, 48 well microplate; Tecan Infinite F200, Aerobic, at 25 (C), shaken=orbital
By: Adam on 2/27/2014
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: 826 E7,E8

Specific Phenotypes

For 23 genes in this experiment

For stress Benzethonium chloride in Dinoroseobacter shibae DFL-12

For stress Benzethonium chloride across organisms

SEED Subsystems

Subsystem	#Specific
Valine degradation	2
Widespread colonization island	2
Acetyl-CoA fermentation to Butyrate	1
Biogenesis of c-type cytochromes	1
Butanol Biosynthesis	1
Control of cell elongation - division cycle in Bacilli	1
Copper homeostasis: copper tolerance	1
DNA Repair Base Excision	1
Isobutyryl-CoA to Propionyl-CoA Module	1
Isoleucine degradation	1
Methionine Biosynthesis	1
Methionine Degradation	1
Multidrug Resistance Efflux Pumps	1
Periplasmic disulfide interchange	1
Phosphate metabolism	1
Photosystem II-type photosynthetic reaction center	1
Polyhydroxybutyrate metabolism	1
Propionate-CoA to Succinate Module	1
TCA Cycle	1
n-Phenylalkanoic acid degradation	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
• Lysine degradation
• beta-Alanine metabolism
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• Butanoate metabolism
• Limonene and pinene degradation
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of plant hormones
• Citrate cycle (TCA cycle)
• Fatty acid biosynthesis
• Fatty acid elongation in mitochondria
• Fatty acid metabolism
• Geraniol degradation
• Histidine metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Tryptophan metabolism
• Lipopolysaccharide biosynthesis
• Glycerophospholipid metabolism
• Ether lipid metabolism
• alpha-Linolenic acid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• 1- and 2-Methylnaphthalene degradation
• Glyoxylate and dicarboxylate metabolism
• Ethylbenzene degradation
• Reductive carboxylate cycle (CO2 fixation)
• Diterpenoid biosynthesis
• Carotenoid biosynthesis - General
• Caprolactam degradation
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of type II polyketide backbone
• Biosynthesis of phenylpropanoids
• 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

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
10,13-epoxy-11-methyl-octadecadienoate biosynthesis	2	2	1
glyoxylate cycle	6	6	2
benzoyl-CoA biosynthesis	3	3	1
nitrogen remobilization from senescing leaves	8	6	2
partial TCA cycle (obligate autotrophs)	8	6	2
L-valine degradation I	8	5	2
TCA cycle V (2-oxoglutarate synthase)	9	8	2
TCA cycle II (plants and fungi)	9	8	2
TCA cycle IV (2-oxoglutarate decarboxylase)	9	8	2
phenylacetate degradation I (aerobic)	9	6	2
TCA cycle VI (Helicobacter)	9	6	2
TCA cycle VII (acetate-producers)	9	6	2
superpathway of glyoxylate cycle and fatty acid degradation	14	12	3
2-methyl-branched fatty acid β-oxidation	14	10	3
adipate degradation	5	5	1
TCA cycle I (prokaryotic)	10	9	2
TCA cycle III (animals)	10	9	2
adipate biosynthesis	5	4	1
fatty acid β-oxidation IV (unsaturated, even number)	5	4	1
glutaryl-CoA degradation	5	3	1
propanoyl-CoA degradation II	5	3	1
fatty acid β-oxidation II (plant peroxisome)	5	3	1
acrylate degradation I	5	2	1
benzoate biosynthesis III (CoA-dependent, non-β-oxidative)	5	2	1
reductive TCA cycle I	11	7	2
pyruvate fermentation to hexanol (engineered)	11	7	2
superpathway of phenylethylamine degradation	11	6	2
(8E,10E)-dodeca-8,10-dienol biosynthesis	11	5	2
oleate β-oxidation	35	28	6
superpathway of glyoxylate bypass and TCA	12	11	2
fatty acid salvage	6	5	1
L-isoleucine degradation I	6	4	1
pyruvate fermentation to butanol II (engineered)	6	4	1
β-alanine biosynthesis II	6	4	1
reductive TCA cycle II	12	6	2
propanoate fermentation to 2-methylbutanoate	6	3	1
methyl ketone biosynthesis (engineered)	6	3	1
fatty acid β-oxidation I (generic)	7	5	1
fatty acid β-oxidation VI (mammalian peroxisome)	7	4	1
pyruvate fermentation to butanoate	7	4	1
benzoyl-CoA degradation I (aerobic)	7	3	1
mixed acid fermentation	16	10	2
pyruvate fermentation to butanol I	8	3	1
superpathway of Clostridium acetobutylicum acidogenic fermentation	9	6	1
valproate β-oxidation	9	5	1
benzoate biosynthesis I (CoA-dependent, β-oxidative)	9	4	1
methylaspartate cycle	19	14	2
superpathway of coenzyme A biosynthesis II (plants)	10	8	1
3-phenylpropanoate degradation	10	4	1
L-glutamate degradation V (via hydroxyglutarate)	10	4	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	19	2
gallate degradation III (anaerobic)	11	5	1
Spodoptera littoralis pheromone biosynthesis	22	3	2
L-glutamate degradation VII (to butanoate)	12	5	1
ethene biosynthesis V (engineered)	25	17	2
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	22	2
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	5	1
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase)	13	2	1
docosahexaenoate biosynthesis III (6-desaturase, mammals)	14	2	1
L-tryptophan degradation III (eukaryotic)	15	4	1
glycerol degradation to butanol	16	10	1
crotonate fermentation (to acetate and cyclohexane carboxylate)	16	3	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	8	1
benzoate fermentation (to acetate and cyclohexane carboxylate)	17	3	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	11	1
toluene degradation VI (anaerobic)	18	3	1
platensimycin biosynthesis	26	6	1
1-butanol autotrophic biosynthesis (engineered)	27	19	1