Experiment set5IT084 for Dinoroseobacter shibae DFL-12

marine broth with Benzalkonium Chloride 0.0005 mg/ml

Group: stress
Media: marine_broth_2216 + Benzalkonium Chloride (5e-04 mg/ml)
Culturing: Dino_ML3, 48 well microplate; Tecan Infinite F200, Aerobic, at 25 (C), shaken=orbital
By: Adam on 5/14/2014
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: 917 E3,E4

Specific Phenotypes

For 4 genes in this experiment

For stress Benzalkonium Chloride in Dinoroseobacter shibae DFL-12

For stress Benzalkonium Chloride across organisms

SEED Subsystems

Subsystem	#Specific
Acetyl-CoA fermentation to Butyrate	1
Butanol Biosynthesis	1
Isoleucine degradation	1
Polyhydroxybutyrate metabolism	1
Valine degradation	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:

• Oxidative phosphorylation
• Fatty acid elongation in mitochondria
• Fatty acid metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Lysine degradation
• Tryptophan metabolism
• beta-Alanine metabolism
• alpha-Linolenic acid metabolism
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• Butanoate metabolism
• Limonene and pinene degradation
• Caprolactam degradation
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
benzoyl-CoA biosynthesis	3	3	1
phenylacetate degradation I (aerobic)	9	6	2
2-methyl-branched fatty acid β-oxidation	14	10	3
adipate degradation	5	5	1
adipate biosynthesis	5	4	1
fatty acid β-oxidation IV (unsaturated, even number)	5	4	1
fatty acid β-oxidation II (plant peroxisome)	5	3	1
glutaryl-CoA degradation	5	3	1
benzoate biosynthesis III (CoA-dependent, non-β-oxidative)	5	2	1
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
fatty acid salvage	6	5	1
L-isoleucine degradation I	6	4	1
pyruvate fermentation to butanol II (engineered)	6	4	1
methyl ketone biosynthesis (engineered)	6	3	1
propanoate fermentation to 2-methylbutanoate	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
L-valine degradation I	8	5	1
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
3-phenylpropanoate degradation	10	4	1
L-glutamate degradation V (via hydroxyglutarate)	10	4	1
gallate degradation III (anaerobic)	11	5	1
Spodoptera littoralis pheromone biosynthesis	22	3	2
L-glutamate degradation VII (to butanoate)	12	5	1
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	5	1
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase)	13	2	1
superpathway of glyoxylate cycle and fatty acid degradation	14	12	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