Experiment set2IT053 for Paraburkholderia graminis OAS925

D-Serine carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + D-Serine (20 mM)
Culturing: Burkholderia_OAS925_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 5 genes in this experiment

For carbon source D-Serine in Paraburkholderia graminis OAS925

For carbon source D-Serine across organisms

SEED Subsystems

Subsystem	#Specific
Branched-Chain Amino Acid Biosynthesis	1
Glycine and Serine Utilization	1
Glycolate, glyoxylate interconversions	1
Pyruvate Alanine Serine Interconversions	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glycine, serine and threonine metabolism
• Glyoxylate and dicarboxylate metabolism
• Pentose phosphate pathway
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• C21-Steroid hormone metabolism
• Cysteine metabolism
• Valine, leucine and isoleucine biosynthesis
• Bisphenol A degradation
• Nucleotide sugars metabolism
• Polyketide sugar unit biosynthesis
• Aminosugars metabolism
• Linoleic acid metabolism
• Pyruvate metabolism
• Tetrachloroethene degradation
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• Retinol metabolism
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide products
• Biosynthesis of alkaloids derived from shikimate pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
D-serine degradation	3	3	3
L-serine degradation	3	3	3
L-methionine degradation II	3	2	2
L-tryptophan degradation II (via pyruvate)	3	2	2
L-cysteine degradation II	3	2	2
L-threonine degradation I	6	5	3
L-threonine degradation V	2	1	1
L-isoleucine biosynthesis I (from threonine)	7	7	3
glycine betaine degradation III	7	6	3
felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis	5	2	2
glycine betaine degradation I	8	6	3
L-methionine biosynthesis II	6	4	2
glycine degradation	3	2	1
L-serine biosynthesis II	4	3	1
L-mimosine degradation	8	4	2
glutathione-mediated detoxification I	8	3	2
superpathway of L-isoleucine biosynthesis I	13	13	3
hypoglycin biosynthesis	14	4	3
glucose degradation (oxidative)	5	4	1
superpathway of branched chain amino acid biosynthesis	17	17	3
superpathway of L-threonine metabolism	18	14	3
D-xylose degradation IV	7	4	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	12	2
L-arabinose degradation IV	8	6	1
purine nucleobases degradation II (anaerobic)	24	16	3
ketogluconate metabolism	8	5	1
formaldehyde assimilation I (serine pathway)	13	9	1
cyclosporin A biosynthesis	15	2	1
superpathway of pentose and pentitol degradation	42	21	1