Experiment set10H5 for Pseudomonas stutzeri RCH2

D-Fructose carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + D-Fructose (20 mM), pH=7.2
Culturing: psRCH2_ML7c, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 5.2 generations
By: Kelly on 2/24/2014
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 14 genes in this experiment

For carbon source D-Fructose in Pseudomonas stutzeri RCH2

For carbon source D-Fructose across organisms

SEED Subsystems

Subsystem	#Specific
Fructose utilization	4
ATP-dependent RNA helicases, bacterial	1
Fructose and Mannose Inducible PTS	1
Maltose and Maltodextrin Utilization	1
Mannitol Utilization	1
N-linked Glycosylation in Bacteria	1
Ribosome activity modulation	1
Transcription initiation, bacterial sigma factors	1
Trehalose Uptake and Utilization	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Fructose and mannose metabolism
• Nucleotide sugars metabolism
• Glycolysis / Gluconeogenesis
• Pentose phosphate pathway
• Galactose metabolism
• Ascorbate and aldarate metabolism
• Fatty acid biosynthesis
• Tyrosine metabolism
• Benzoate degradation via hydroxylation
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Starch and sucrose metabolism
• Aminosugars metabolism
• Lipopolysaccharide biosynthesis
• 1- and 2-Methylnaphthalene degradation
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• Nicotinate and nicotinamide metabolism
• Porphyrin and chlorophyll metabolism
• Limonene and pinene degradation
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide backbone

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
fructose degradation	1	1	1
UDP-N-acetyl-β-L-fucosamine biosynthesis	4	1	1
UDP-N-acetyl-β-L-quinovosamine biosynthesis	4	1	1
D-galactosamine and N-acetyl-D-galactosamine degradation	4	1	1
galactitol degradation	5	2	1
N-acetyl-D-galactosamine degradation	5	1	1
lactose degradation I	5	1	1
CMP-pseudaminate biosynthesis	6	6	1
CMP-diacetamido-8-epilegionaminic acid biosynthesis	7	1	1
superpathway of hexitol degradation (bacteria)	18	13	1
superpathway of UDP-N-acetylglucosamine-derived O-antigen building blocks biosynthesis	24	9	1