Experiment set1IT006 for Variovorax sp. OAS795

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D-Xylose carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + D-Xylose (20 mM)
Culturing: Variovorax_OAS795_ML2, 96 deep-well microplate; 0.8 mL volume, Aerobic, at 30 (C), shaken=700 rpm
By: Marta on 10-Apr-21
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 7 genes in this experiment

For carbon source D-Xylose in Variovorax sp. OAS795

For carbon source D-Xylose across organisms

SEED Subsystems

Subsystem #Specific
L-Arabinose utilization 2
Aromatic amino acid degradation 1
Cysteine Biosynthesis 1
DNA-binding regulatory proteins, strays 1
Glycolate, glyoxylate interconversions 1
Photorespiration (oxidative C2 cycle) 1
Xylose utilization 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 V 6 4 3
methylglyoxal degradation VIII 3 3 1
L-arabinose degradation III 6 5 2
L-valine biosynthesis 4 4 1
L-arabinose degradation IV 8 5 2
methylglyoxal degradation VI 4 1 1
pyruvate fermentation to isobutanol (engineered) 5 4 1
D-xylose degradation VI 5 3 1
D-arabinose degradation IV 6 4 1
L-isoleucine biosynthesis IV 6 4 1
L-isoleucine biosynthesis I (from threonine) 7 7 1
L-isoleucine biosynthesis III 7 4 1
L-rhamnose degradation III 7 3 1
L-isoleucine biosynthesis II 8 6 1
L-fucose degradation III 8 4 1
superpathway of branched chain amino acid biosynthesis 17 17 2
superpathway of L-isoleucine biosynthesis I 13 13 1
superpathway of L-threonine metabolism 18 15 1
superpathway of pentose and pentitol degradation 42 15 2