Experiment set1H25 for Pseudomonas stutzeri RCH2

L-Proline carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + L-Proline (20 mM), pH=7.2
Culturing: psRCH2_ML7, 48 well microplate; Tecan Infinite F200, Aerobic, at 30 (C), shaken=orbital
By: Kelly on 6/18/2013
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 30 mM PIPES sesquisodium salt, Wolfe's mineral mix (0.03 g/L Magnesium Sulfate Heptahydrate, 0.015 g/L Nitrilotriacetic acid, 0.01 g/L Sodium Chloride, 0.005 g/L Manganese (II) sulfate monohydrate, 0.001 g/L Cobalt chloride hexahydrate, 0.001 g/L Zinc sulfate heptahydrate, 0.001 g/L Calcium chloride dihydrate, 0.001 g/L Iron (II) sulfate heptahydrate, 0.00025 g/L Nickel (II) chloride hexahydrate, 0.0002 g/L Aluminum potassium sulfate dodecahydrate, 0.0001 g/L Copper (II) sulfate pentahydrate, 0.0001 g/L Boric Acid, 0.0001 g/L Sodium Molybdate Dihydrate, 0.003 mg/L Sodium selenite pentahydrate), Wolfe's vitamin mix (0.1 mg/L Pyridoxine HCl, 0.05 mg/L 4-Aminobenzoic acid, 0.05 mg/L Lipoic acid, 0.05 mg/L Nicotinic Acid, 0.05 mg/L Riboflavin, 0.05 mg/L Thiamine HCl, 0.05 mg/L calcium pantothenate, 0.02 mg/L biotin, 0.02 mg/L Folic Acid, 0.001 mg/L Cyanocobalamin)
Growth plate: 550 A7,A8

Specific Phenotypes

For 14 genes in this experiment

For carbon source L-Proline in Pseudomonas stutzeri RCH2

For carbon source L-Proline across organisms

SEED Subsystems

Subsystem	#Specific
Phosphate metabolism	2
Respiratory dehydrogenases 1	2
Arginine and Ornithine Degradation	1
Carboxysome	1
HMG CoA Synthesis	1
Leucine Degradation and HMG-CoA Metabolism	1
Proline, 4-hydroxyproline uptake and utilization	1
Restriction-Modification System	1
Serine-glyoxylate cycle	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Arginine and proline metabolism
• Oxidative phosphorylation
• Glutamate metabolism
• Valine, leucine and isoleucine degradation
• Nicotinate and nicotinamide metabolism

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-proline degradation I	3	3	2
NADH to cytochrome bd oxidase electron transfer II	2	2	1
NADH to cytochrome bd oxidase electron transfer I	2	2	1
NADH to nitrate electron transfer	2	2	1
NADH to cytochrome bo oxidase electron transfer II	2	1	1
proline to cytochrome bo oxidase electron transfer	2	1	1
NADH to cytochrome aa3 oxidase electron transfer	2	1	1
nitrate reduction VIIIb (dissimilatory)	2	1	1
NADH to cytochrome bo oxidase electron transfer I	2	1	1
aerobic respiration III (alternative oxidase pathway)	3	3	1
L-arginine degradation I (arginase pathway)	3	2	1
NAD(P)/NADPH interconversion	6	3	2
aerobic respiration II (cytochrome c) (yeast)	4	3	1
aerobic respiration I (cytochrome c)	4	3	1
ethene biosynthesis II (microbes)	4	1	1
mitochondrial NADPH production (yeast)	5	3	1
L-leucine degradation I	6	5	1
Fe(II) oxidation	6	3	1
(5R)-carbapenem carboxylate biosynthesis	6	1	1
L-Nδ-acetylornithine biosynthesis	7	5	1
L-citrulline biosynthesis	8	7	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	5	1
superpathway of L-citrulline metabolism	12	9	1