Experiment set1IT044 for Pseudomonas simiae WCS417

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L-Arabinose carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + L-Arabinose (20 mM), pH=7
Culturing: fluoroDangl_ML3, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
By: Mark on 2/18/2015
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 10 genes in this experiment

For carbon source L-Arabinose in Pseudomonas simiae WCS417

For carbon source L-Arabinose across organisms

SEED Subsystems

Subsystem #Specific
L-Arabinose utilization 5
D-Galacturonate and D-Glucuronate Utilization 1
Glycolysis and Gluconeogenesis 1
Glycolysis and Gluconeogenesis, including Archaeal enzymes 1
Nitrate and nitrite ammonification 1
Polyamine Metabolism 1
Proline, 4-hydroxyproline uptake and utilization 1
Pyruvate metabolism I: anaplerotic reactions, PEP 1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway #Steps #Present #Specific
L-arabinose degradation III 6 5 4
L-lyxonate degradation 3 2 2
pyruvate fermentation to acetate VIII 2 1 1
D-galactarate degradation II 3 3 1
D-glucarate degradation II 3 3 1
L-arabinose degradation V 6 3 2
L-carnitine degradation II 3 1 1
trans-4-hydroxy-L-proline degradation II 4 4 1
L-valine biosynthesis 4 4 1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast) 8 7 2
1,2-dichloroethane degradation 4 3 1
L-arabinose degradation IV 8 5 2
pyruvate fermentation to isobutanol (engineered) 5 4 1
mitochondrial NADPH production (yeast) 5 4 1
cytosolic NADPH production (yeast) 5 4 1
D-glucuronate degradation II 5 4 1
D-galacturonate degradation II 5 3 1
D-xylose degradation III 5 1 1
D-xylose degradation V 5 1 1
L-isoleucine biosynthesis IV 6 4 1
D-arabinose degradation III 6 2 1
L-isoleucine biosynthesis I (from threonine) 7 7 1
L-isoleucine biosynthesis III 7 4 1
L-isoleucine biosynthesis II 8 5 1
superpathway of pentose and pentitol degradation 42 16 5
superpathway of branched chain amino acid biosynthesis 17 17 2
glycolysis V (Pyrococcus) 10 7 1
glycolysis II (from fructose 6-phosphate) 11 9 1
superpathway of L-isoleucine biosynthesis I 13 13 1
gluconeogenesis I 13 11 1
glycolysis I (from glucose 6-phosphate) 13 10 1
superpathway of glycolysis and the Entner-Doudoroff pathway 17 14 1
superpathway of L-threonine metabolism 18 12 1
superpathway of hexitol degradation (bacteria) 18 12 1
gluconeogenesis II (Methanobacterium thermoautotrophicum) 18 9 1
hexitol fermentation to lactate, formate, ethanol and acetate 19 14 1
superpathway of anaerobic sucrose degradation 19 14 1
superpathway of N-acetylneuraminate degradation 22 15 1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass 26 22 1
superpathway of microbial D-galacturonate and D-glucuronate degradation 31 13 1
Methanobacterium thermoautotrophicum biosynthetic metabolism 56 20 1