Experiment set9IT030 for Paraburkholderia graminis OAS925

Azelaic acid 20 mM carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + Azelaic acid (20 mM)
Culturing: Burkholderia_OAS925_ML2, tube, Aerobic, at 30 (C), shaken=200 rpm
By: Marta Torres on 29-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 19 genes in this experiment

For carbon source Azelaic acid in Paraburkholderia graminis OAS925

For carbon source Azelaic acid across organisms

SEED Subsystems

Subsystem	#Specific
Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria	2
Chorismate Synthesis	1
Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate)	1
Folate Biosynthesis	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Menaquinone and Phylloquinone Biosynthesis	1
Phosphate metabolism	1
Photorespiration (oxidative C2 cycle)	1
Polyhydroxybutyrate metabolism	1
Queuosine-Archaeosine Biosynthesis	1
Quinate degradation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Fatty acid metabolism
• Glycerophospholipid metabolism
• Ascorbate and aldarate metabolism
• Ubiquinone and menaquinone biosynthesis
• Purine metabolism
• Lysine degradation
• Tryptophan metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Aminophosphonate metabolism
• High-mannose type N-glycan biosynthesis
• Nucleotide sugars metabolism
• Lipopolysaccharide biosynthesis
• Sphingolipid metabolism
• Pyruvate metabolism
• 2,4-Dichlorobenzoate degradation
• Glyoxylate and dicarboxylate metabolism
• Benzoate degradation via CoA ligation
• Folate biosynthesis
• Retinol metabolism
• Alkaloid biosynthesis II
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
glycolate and glyoxylate degradation II	2	2	1
cardiolipin biosynthesis II	3	3	1
gallate biosynthesis	3	2	1
quinate degradation I	3	1	1
quinate degradation II	3	1	1
cardiolipin and phosphatidylethanolamine biosynthesis (Xanthomonas)	4	3	1
chitin deacetylation	4	2	1
chorismate biosynthesis from 3-dehydroquinate	5	5	1
6-hydroxymethyl-dihydropterin diphosphate biosynthesis I	5	4	1
glyoxylate cycle	6	6	1
chorismate biosynthesis I	7	7	1
superpathway of glycol metabolism and degradation	7	5	1
D-xylose degradation IV	7	4	1
2-carboxy-1,4-naphthoquinol biosynthesis	7	1	1
L-arabinose degradation IV	8	6	1
benzoyl-CoA degradation III (anaerobic)	9	4	1
superpathway of demethylmenaquinol-8 biosynthesis I	9	2	1
superpathway of demethylmenaquinol-9 biosynthesis	9	1	1
superpathway of demethylmenaquinol-6 biosynthesis I	9	1	1
superpathway of L-phenylalanine biosynthesis	10	10	1
superpathway of L-tyrosine biosynthesis	10	10	1
superpathway of tetrahydrofolate biosynthesis	10	9	1
superpathway of menaquinol-8 biosynthesis I	10	3	1
superpathway of menaquinol-9 biosynthesis	10	2	1
superpathway of menaquinol-12 biosynthesis	10	2	1
superpathway of menaquinol-7 biosynthesis	10	2	1
superpathway of menaquinol-10 biosynthesis	10	2	1
superpathway of menaquinol-6 biosynthesis	10	2	1
superpathway of menaquinol-11 biosynthesis	10	2	1
superpathway of menaquinol-13 biosynthesis	10	2	1
superpathway of tetrahydrofolate biosynthesis and salvage	12	11	1
superpathway of glyoxylate bypass and TCA	12	10	1
chorismate biosynthesis II (archaea)	12	8	1
superpathway of L-tryptophan biosynthesis	13	13	1
superpathway of cardiolipin biosynthesis (bacteria)	13	9	1
superpathway of glyoxylate cycle and fatty acid degradation	14	11	1
crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA cycle (engineered)	14	2	1
superpathway of phylloquinol biosynthesis	15	2	1
superpathway of aromatic amino acid biosynthesis	18	18	1
superpathway of chorismate metabolism	59	42	3
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	22	1
superpathway of aromatic compound degradation via 3-oxoadipate	35	19	1
superpathway of pentose and pentitol degradation	42	21	1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate	42	13	1