Experiment set3IT064 for Sphingomonas koreensis DSMZ 15582

Compare to:

D-Xylose carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + D-Xylose (20 mM)
Culturing: korea_ML2, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 3.3 generations
By: Jordan on 10/21/2014
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 6 genes in this experiment

For carbon source D-Xylose in Sphingomonas koreensis DSMZ 15582

For carbon source D-Xylose across organisms

SEED Subsystems

Subsystem #Specific
Xylose utilization 2
Branched-Chain Amino Acid Biosynthesis 1
D-Galacturonate and D-Glucuronate Utilization 1
Gentisare degradation 1
Ketoisovalerate oxidoreductase 1
Proline, 4-hydroxyproline uptake and utilization 1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate 1
Salicylate and gentisate catabolism 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
D-xylose degradation V 5 5 5
acetate and ATP formation from acetyl-CoA III 1 1 1
acetate conversion to acetyl-CoA 1 1 1
D-xylose degradation III 5 4 4
pyruvate fermentation to acetate VIII 2 1 1
D-xylose degradation VI 5 4 2
ethanol degradation IV 3 3 1
ethanol degradation II 3 3 1
superpathway of acetate utilization and formation 3 3 1
L-isoleucine biosynthesis IV 6 4 2
ethanol degradation III 3 2 1
L-isoleucine biosynthesis V 3 2 1
D-arabinose degradation III 6 3 2
D-galactarate degradation II 3 1 1
L-carnitine degradation II 3 1 1
D-glucarate degradation II 3 1 1
L-lyxonate degradation 3 1 1
D-xylose degradation IV 7 4 2
L-valine biosynthesis 4 4 1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast) 8 7 2
chitin deacetylation 4 2 1
1,2-dichloroethane degradation 4 1 1
trans-4-hydroxy-L-proline degradation II 4 1 1
D-xylose degradation to ethylene glycol (engineered) 4 1 1
mitochondrial NADPH production (yeast) 5 4 1
pyruvate fermentation to isobutanol (engineered) 5 4 1
cytosolic NADPH production (yeast) 5 4 1
D-glucuronate degradation II 5 2 1
2-methylcitrate cycle I 5 1 1
D-galacturonate degradation II 5 1 1
β-alanine biosynthesis II 6 4 1
L-arabinose degradation III 6 2 1
superpathway of bitter acids biosynthesis 18 3 3
lupulone and humulone biosynthesis 6 1 1
2-methylcitrate cycle II 6 1 1
adlupulone and adhumulone biosynthesis 6 1 1
colupulone and cohumulone biosynthesis 6 1 1
L-isoleucine biosynthesis I (from threonine) 7 7 1
L-isoleucine biosynthesis III 7 4 1
superpathway of pentose and pentitol degradation 42 12 6
L-isoleucine biosynthesis II 8 4 1
superpathway of branched chain amino acid biosynthesis 17 17 2
reductive glycine pathway of autotrophic CO2 fixation 9 5 1
cis-geranyl-CoA degradation 9 1 1
superpathway of coenzyme A biosynthesis II (plants) 10 8 1
superpathway of L-isoleucine biosynthesis I 13 13 1
superpathway of L-threonine metabolism 18 14 1
superpathway of microbial D-galacturonate and D-glucuronate degradation 31 12 1