Experiment set17IT029 for Pseudomonas stutzeri RCH2

LB with Choline Lysine 20 mM

Group: stress
Media: LB + Choline Lysine (20 mM)
Culturing: psRCH2_ML7c, 48 well microplate; Tecan Infinite F200, Aerobic, at 28 (C), shaken=orbital
By: Kelly on 4/17/2014
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride
Growth plate: 884 F1,F2

Specific Phenotypes

For 20 genes in this experiment

For stress Choline Lysine in Pseudomonas stutzeri RCH2

For stress Choline Lysine across organisms

SEED Subsystems

Subsystem	#Specific
Coenzyme A Biosynthesis	2
Sodium Hydrogen Antiporter	2
ATP-dependent RNA helicases, bacterial	1
Acid resistance mechanisms	1
Arginine and Ornithine Degradation	1
Biogenesis of c-type cytochromes	1
Choline and Betaine Uptake and Betaine Biosynthesis	1
Cobalt-zinc-cadmium resistance	1
Periplasmic disulfide interchange	1
Polyamine Metabolism	1
Ribosome biogenesis bacterial	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Urea cycle and metabolism of amino groups
• Glycine, serine and threonine metabolism
• Arginine and proline metabolism
• Pantothenate and CoA biosynthesis
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• C21-Steroid hormone metabolism
• Pyrimidine metabolism
• Alanine and aspartate metabolism
• Bisphenol A degradation
• beta-Alanine metabolism
• Glutathione metabolism
• Nucleotide sugars metabolism
• Polyketide sugar unit biosynthesis
• Aminosugars metabolism
• Linoleic acid metabolism
• Tetrachloroethene degradation
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• Retinol metabolism
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide products
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
cadaverine biosynthesis	1	1	1
β-alanine biosynthesis III	1	1	1
arginine dependent acid resistance	1	1	1
glycine betaine biosynthesis I (Gram-negative bacteria)	2	2	1
choline degradation I	2	2	1
glycine betaine biosynthesis II (Gram-positive bacteria)	2	2	1
superpathway of putrescine biosynthesis	4	2	2
putrescine biosynthesis III	2	1	1
putrescine biosynthesis I	2	1	1
L-arginine degradation III (arginine decarboxylase/agmatinase pathway)	2	1	1
pseudouridine degradation	2	1	1
superpathway of polyamine biosynthesis I	8	5	3
L-arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway)	3	3	1
putrescine biosynthesis II	3	3	1
choline-O-sulfate degradation	3	2	1
aminopropylcadaverine biosynthesis	3	2	1
phosphopantothenate biosynthesis I	4	4	1
superpathway of polyamine biosynthesis II	8	5	2
phosphopantothenate biosynthesis III (archaea)	4	2	1
spermidine biosynthesis III	4	1	1
superpathway of coenzyme A biosynthesis I (bacteria)	9	9	2
desferrioxamine E biosynthesis	5	1	1
bisucaberin biosynthesis	5	1	1
desferrioxamine B biosynthesis	5	1	1
lupanine biosynthesis	5	1	1
superpathway of arginine and polyamine biosynthesis	17	14	3
L-lysine degradation X	6	5	1
superpathway of L-arginine and L-ornithine degradation	13	8	2
L-lysine degradation I	7	4	1
superpathway of ornithine degradation	8	6	1
superpathway of coenzyme A biosynthesis II (plants)	10	9	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	6	1
superpathway of hyoscyamine (atropine) and scopolamine biosynthesis	16	3	1
superpathway of L-lysine degradation	43	11	1