Experiment set9IT058 for Paraburkholderia graminis OAS925

Acetylated xylan 10 g/L carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + Acetylated xylan (10 g/L)
Culturing: Burkholderia_OAS925_ML2, tube, Aerobic, at 30 (C), shaken=200 rpm
By: Marta Torres on 4-Jul-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 24 genes in this experiment

For carbon source Acetylated xylan in Paraburkholderia graminis OAS925

For carbon source Acetylated xylan across organisms

SEED Subsystems

Subsystem	#Specific
Heat shock dnaK gene cluster extended	2
Alkanesulfonate assimilation	1
Glutathione: Non-redox reactions	1
Glycerol and Glycerol-3-phosphate Uptake and Utilization	1
Glycerol fermenation to 1,3-propanediol	1
Hfl operon	1
Methylglyoxal Metabolism	1
Oxidative stress	1
Phosphate metabolism	1
Photorespiration (oxidative C2 cycle)	1
Proline, 4-hydroxyproline uptake and utilization	1
Protein degradation	1
Ribosome biogenesis bacterial	1
Stringent Response, (p)ppGpp metabolism	1
Transport of Manganese	1
Type III secretion systems, extended	1
Universal GTPases	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Tryptophan metabolism
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of alkaloids derived from shikimate pathway
• Ubiquinone and menaquinone biosynthesis
• Purine metabolism
• Puromycin biosynthesis
• Pyrimidine metabolism
• Histidine metabolism
• Tyrosine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Benzoxazinone biosynthesis
• Glutathione metabolism
• Nucleotide sugars metabolism
• alpha-Linolenic acid metabolism
• Pyruvate metabolism
• Naphthalene and anthracene degradation
• Trinitrotoluene degradation
• Methane metabolism
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Biosynthesis of phenylpropanoids
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
superoxide radicals degradation	2	2	1
pseudouridine degradation	2	1	1
methanol oxidation to formaldehyde IV	2	1	1
ethanol degradation IV	3	3	1
methylglyoxal degradation VIII	3	3	1
ppGpp metabolism	6	5	2
methylglyoxal degradation I	3	2	1
reactive oxygen species degradation	4	4	1
L-tryptophan biosynthesis	6	6	1
superpathway of methylglyoxal degradation	8	4	1
superpathway of L-tryptophan biosynthesis	13	13	1
superpathway of aromatic amino acid biosynthesis	18	18	1
superpathway of chorismate metabolism	59	42	1