Experiment set7H32 for Pseudomonas stutzeri RCH2

RCH2 defined media with Nalidixic acid sodium salt 0.0005 mg/ml

Group: stress
Media: RCH2_defined_no_vitamin + Nalidixic acid sodium salt (5e-04 mg/ml), pH=7.2
Culturing: psRCH2_ML7, 48 well microplate; Tecan Infinite F200, Aerobic, at 30 (C), shaken=orbital
By: Adam on 8/13/2013
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 20 mM Sodium D,L-Lactate, 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)
Growth plate: 644 E1,E2

Specific Phenotypes

For 2 genes in this experiment

For stress Nalidixic acid sodium salt in Pseudomonas stutzeri RCH2

For stress Nalidixic acid sodium salt across organisms

SEED Subsystems

Subsystem	#Specific
Entner-Doudoroff Pathway	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Methylglyoxal Metabolism	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glycolysis / Gluconeogenesis
• Ascorbate and aldarate metabolism
• Fatty acid metabolism
• Urea cycle and metabolism of amino groups
• Valine, leucine and isoleucine degradation
• Lysine degradation
• Arginine and proline metabolism
• Histidine metabolism
• Tryptophan metabolism
• beta-Alanine metabolism
• Glycerolipid metabolism
• Pyruvate metabolism
• 1,2-Dichloroethane degradation
• Propanoate metabolism
• 3-Chloroacrylic acid degradation
• Butanoate metabolism
• Limonene and pinene degradation

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
putrescine degradation V	2	2	1
ethylene glycol degradation	2	1	1
phenylethylamine degradation II	2	1	1
putrescine degradation I	2	1	1
phenylethylamine degradation I	2	1	1
phenylethanol degradation	2	1	1
ethanol degradation IV	3	3	1
ethanol degradation II	3	3	1
ethanol degradation III	3	2	1
L-phenylalanine degradation II (anaerobic)	3	2	1
hypotaurine degradation	3	2	1
putrescine degradation IV	3	2	1
histamine degradation	3	1	1
styrene degradation	3	1	1
phytol degradation	4	3	1
fatty acid α-oxidation I (plants)	4	2	1
putrescine degradation III	4	1	1
D-arabinose degradation II	4	1	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	1	1
octane oxidation	5	3	1
mitochondrial NADPH production (yeast)	5	3	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
dopamine degradation	5	1	1
3-methyl-branched fatty acid α-oxidation	6	3	1
alkane oxidation	6	1	1
noradrenaline and adrenaline degradation	13	4	2
superpathway of glycol metabolism and degradation	7	5	1
serotonin degradation	7	3	1
ceramide degradation by α-oxidation	7	2	1
limonene degradation IV (anaerobic)	7	1	1
superpathway of ornithine degradation	8	6	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	5	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
aromatic biogenic amine degradation (bacteria)	8	1	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	5	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	3	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	6	1
superpathway of phenylethylamine degradation	11	4	1
superpathway of L-arginine and L-ornithine degradation	13	8	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	3	1
superpathway of pentose and pentitol degradation	42	7	1