Experiment set4H13 for Marinobacter adhaerens HP15

marine broth with Cholin acetate 153.15 mM

Group: stress
Media: marine_broth_2216 + Cholin acetate (153.15 mM)
Culturing: Marino_ML2, 48 well microplate; Tecan Infinite F200, Aerobic, at 30 (C), shaken=orbital
By: Jordan on 10/23/2013
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: 760 D7,D8

Specific Phenotypes

For 22 genes in this experiment

For stress Cholin acetate in Marinobacter adhaerens HP15

For stress Cholin acetate across organisms

SEED Subsystems

Subsystem	#Specific
Polyamine Metabolism	4
Choline and Betaine Uptake and Betaine Biosynthesis	3
DNA-binding regulatory proteins, strays	1
Glutathione: Non-redox reactions	1
Methionine Biosynthesis	1
Methionine Degradation	1
Methylglyoxal Metabolism	1
Oxidative stress	1
Phosphate metabolism	1
Stringent Response, (p)ppGpp metabolism	1
Thioredoxin-disulfide reductase	1
Ubiquinone Biosynthesis	1

Metabolic Maps

Color code by fitness: see overview map or list of maps.

Maps containing gene(s) with specific phenotypes:

• Glycine, serine and threonine metabolism
• Biosynthesis of alkaloids derived from shikimate pathway
• Ubiquinone and menaquinone biosynthesis
• Purine metabolism
• Histidine metabolism
• Phenylalanine metabolism
• gamma-Hexachlorocyclohexane degradation
• Bisphenol A degradation
• Tryptophan metabolism
• Cyanoamino acid metabolism
• Pyruvate metabolism
• Toluene and xylene degradation
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• 1,4-Dichlorobenzene degradation
• Benzoate degradation via CoA ligation
• Styrene degradation
• Methane metabolism
• Indole and ipecac alkaloid biosynthesis
• Limonene and pinene degradation
• Brassinosteroid biosynthesis
• Carotenoid biosynthesis - General
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Isoflavonoid biosynthesis
• Alkaloid biosynthesis I
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
choline degradation I	2	2	2
glycine betaine biosynthesis I (Gram-negative bacteria)	2	2	2
glycine betaine biosynthesis II (Gram-positive bacteria)	2	2	2
choline-O-sulfate degradation	3	2	2
β-alanine biosynthesis IV	2	1	1
β-alanine biosynthesis I	2	1	1
ppGpp metabolism	6	6	2
methylglyoxal degradation I	3	2	1
glycine betaine biosynthesis III (plants)	3	2	1
methylglyoxal degradation VIII	3	2	1
dimethylsulfoniopropanoate biosynthesis I (Wollastonia)	3	1	1
choline degradation IV	4	2	1
dimethylsulfoniopropanoate biosynthesis II (Spartina)	4	1	1
superpathway of methylglyoxal degradation	8	4	1
secologanin and strictosidine biosynthesis	17	1	1