Experiment set2H21 for Phaeobacter inhibens DSM 17395

marine broth with Fusidic acid sodium salt 0.0002 mg/ml

Group: stress
Media: marine_broth_2216 + Fusidic acid sodium salt (2e-04 mg/ml)
Culturing: Phaeo_ML1, 48 well microplate; Tecan Infinite F200, Aerobic, at 25 (C), shaken=orbital
By: Jordan on 8/1/2013
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: 614 E5,E6

Specific Phenotypes

For 5 genes in this experiment

For stress Fusidic acid sodium salt in Phaeobacter inhibens DSM 17395

For stress Fusidic acid sodium salt across organisms

SEED Subsystems

Subsystem	#Specific
Heat shock dnaK gene cluster extended	1
Isobutyryl-CoA to Propionyl-CoA Module	1
Valine 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
• Tryptophan metabolism
• beta-Alanine metabolism
• Propanoate metabolism
• Fatty acid elongation in mitochondria
• Fatty acid metabolism
• Ubiquinone and menaquinone biosynthesis
• Geraniol degradation
• Lysine degradation
• Histidine metabolism
• Tyrosine metabolism
• Benzoxazinone biosynthesis
• alpha-Linolenic acid metabolism
• Naphthalene and anthracene degradation
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• Porphyrin and chlorophyll metabolism
• Limonene and pinene degradation
• Carotenoid biosynthesis - General
• Caprolactam degradation
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
benzoyl-CoA biosynthesis	3	3	1
2-methyl-branched fatty acid β-oxidation	14	10	3
adipate degradation	5	5	1
adipate biosynthesis	5	4	1
fatty acid β-oxidation II (plant peroxisome)	5	3	1
fatty acid β-oxidation IV (unsaturated, even number)	5	3	1
propanoyl-CoA degradation II	5	3	1
acrylate degradation I	5	2	1
benzoate biosynthesis III (CoA-dependent, non-β-oxidative)	5	1	1
(8E,10E)-dodeca-8,10-dienol biosynthesis	11	5	2
β-alanine biosynthesis II	6	4	1
methyl ketone biosynthesis (engineered)	6	3	1
fatty acid β-oxidation I (generic)	7	5	1
benzoyl-CoA degradation I (aerobic)	7	3	1
fatty acid β-oxidation VI (mammalian peroxisome)	7	3	1
L-valine degradation I	8	5	1
phenylacetate degradation I (aerobic)	9	6	1
valproate β-oxidation	9	6	1
benzoate biosynthesis I (CoA-dependent, β-oxidative)	9	3	1
superpathway of coenzyme A biosynthesis II (plants)	10	8	1
3-phenylpropanoate degradation	10	4	1
superpathway of phenylethylamine degradation	11	6	1
Spodoptera littoralis pheromone biosynthesis	22	3	2
oleate β-oxidation	35	30	3
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase)	13	2	1
superpathway of glyoxylate cycle and fatty acid degradation	14	10	1
docosahexaenoate biosynthesis III (6-desaturase, mammals)	14	2	1
platensimycin biosynthesis	26	6	1