Experiment set12H12 for Pseudomonas stutzeri RCH2

L-Proline carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + L-Proline (20 mM), pH=7.2
Culturing: psRCH2_ML7c, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 5.9 generations
By: Kelly on 2/25/2014
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)

Specific Phenotypes

For 12 genes in this experiment

For carbon source L-Proline in Pseudomonas stutzeri RCH2

For carbon source L-Proline across organisms

SEED Subsystems

Subsystem	#Specific
Arginine and Ornithine Degradation	1
Flagellar motility	1
Flagellum	1
HMG CoA Synthesis	1
Leucine Degradation and HMG-CoA Metabolism	1
Proline, 4-hydroxyproline uptake and utilization	1
Respiratory dehydrogenases 1	1
Restriction-Modification System	1
Ribosome biogenesis bacterial	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
• Glutamate metabolism
• Valine, leucine and isoleucine degradation
• Tryptophan metabolism
• Biosynthesis of siderophore group nonribosomal peptides

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-proline degradation I	3	3	2
proline to cytochrome bo oxidase electron transfer	2	1	1
L-arginine degradation I (arginase pathway)	3	2	1
ethene biosynthesis II (microbes)	4	1	1
L-leucine degradation I	6	5	1
(5R)-carbapenem carboxylate biosynthesis	6	1	1
L-Nδ-acetylornithine biosynthesis	7	5	1
L-citrulline biosynthesis	8	7	1
superpathway of L-citrulline metabolism	12	9	1