Experiment set2IT073 for Burkholderia phytofirmans PsJN

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Xylitol carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + Xylitol (20 mM), pH=7
Culturing: BFirm_ML3, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
Growth: about 3.8 generations
By: Mark on 6/2/2015
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)
Growth plate: BFirm_carbon_plate1 D1

Specific Phenotypes

For 14 genes in this experiment

For carbon source Xylitol in Burkholderia phytofirmans PsJN

For carbon source Xylitol across organisms

SEED Subsystems

Subsystem #Specific
Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization 2
Ammonia assimilation 1
Bacterial Chemotaxis 1
Capsular heptose biosynthesis 1
Colanic acid biosynthesis 1
TCA 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
xylitol degradation I 2 2 2
D-xylose degradation I 2 2 1
D-arabinitol degradation I 2 2 1
D-mannose degradation II 2 1 1
ribitol degradation I 2 1 1
GDP-D-rhamnose biosynthesis 2 1 1
D-mannose degradation I 2 1 1
GDP-D-perosamine biosynthesis 2 1 1
GDP-6-deoxy-D-talose biosynthesis 2 1 1
D-sorbitol degradation I 3 3 1
GDP-L-fucose biosynthesis I (from GDP-D-mannose) 3 3 1
L-arabinose degradation II 3 3 1
β-1,4-D-mannosyl-N-acetyl-D-glucosamine degradation 3 2 1
GDP-N-acetyl-α-D-perosamine biosynthesis 3 1 1
erythritol degradation II 3 1 1
GDP-mycosamine biosynthesis 3 1 1
GDP-N-formyl-α-D-perosamine biosynthesis 3 1 1
mannitol biosynthesis 3 1 1
GDP-mannose biosynthesis 4 4 1
mannitol degradation II 4 2 1
L-threitol degradation 4 1 1
cytosolic NADPH production (yeast) 5 4 1
GDP-L-colitose biosynthesis 5 3 1
1,5-anhydrofructose degradation 5 2 1
colanic acid building blocks biosynthesis 11 11 2
superpathway of GDP-mannose-derived O-antigen building blocks biosynthesis 14 9 2
β-(1,4)-mannan degradation 7 2 1
partial TCA cycle (obligate autotrophs) 8 7 1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast) 8 6 1
nitrogen remobilization from senescing leaves 8 6 1
TCA cycle V (2-oxoglutarate synthase) 9 8 1
TCA cycle IV (2-oxoglutarate decarboxylase) 9 7 1
TCA cycle VII (acetate-producers) 9 7 1
TCA cycle VI (Helicobacter) 9 6 1
TCA cycle I (prokaryotic) 10 8 1
superpathway of pentose and pentitol degradation 42 22 4
reductive TCA cycle I 11 6 1
superpathway of candicidin biosynthesis 11 4 1
superpathway of glyoxylate bypass and TCA 12 10 1
mixed acid fermentation 16 13 1
superpathway of glucose and xylose degradation 17 16 1
methylaspartate cycle 19 11 1
ethene biosynthesis V (engineered) 25 18 1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass 26 22 1