Experiment set1IT058 for Variovorax sp. OAS795

D-Glucuronic Acid carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + D-Glucuronic Acid (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 19 genes in this experiment

For carbon source D-Glucuronic Acid in Variovorax sp. OAS795

For carbon source D-Glucuronic Acid across organisms

SEED Subsystems

Subsystem	#Specific
Aromatic amino acid degradation	2
Branched-Chain Amino Acid Biosynthesis	1
D-Galacturonate and D-Glucuronate Utilization	1
D-galactarate, D-glucarate and D-glycerate catabolism	1
Glycolate, glyoxylate interconversions	1
Homogentisate pathway of aromatic compound degradation	1
Lacto-N-Biose I and Galacto-N-Biose Metabolic Pathway	1
Lactose and Galactose Uptake and Utilization	1
N-linked Glycosylation in Bacteria	1
Plastoquinone Biosynthesis	1
Rhamnose containing glycans	1
Tocopherol Biosynthesis	1
linker unit-arabinogalactan synthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glyoxylate and dicarboxylate metabolism
• Ascorbate and aldarate metabolism
• Glycine, serine and threonine metabolism
• Nucleotide sugars metabolism
• Pentose phosphate pathway
• Fructose and mannose metabolism
• Galactose metabolism
• Ubiquinone and menaquinone biosynthesis
• C21-Steroid hormone metabolism
• Urea cycle and metabolism of amino groups
• Valine, leucine and isoleucine biosynthesis
• Arginine and proline metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Bisphenol A degradation
• beta-Alanine metabolism
• Polyketide sugar unit biosynthesis
• Aminosugars metabolism
• Linoleic acid metabolism
• Pyruvate metabolism
• Tetrachloroethene degradation
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• Pantothenate and CoA biosynthesis
• 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
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
UDP-α-D-galactose biosynthesis	1	1	1
UDP-N-acetyl-D-galactosamine biosynthesis I	1	1	1
D-glucuronate degradation III	2	2	1
putrescine degradation V	2	1	1
UDP-α-D-galactofuranose biosynthesis	2	1	1
D-galacturonate degradation III	2	1	1
putrescine degradation I	2	1	1
D-glucuronate degradation II	5	4	2
D-galacturonate degradation II	5	3	2
D-galactarate degradation II	3	3	1
D-glucarate degradation II	3	3	1
putrescine degradation IV	3	2	1
D-galactose detoxification	3	1	1
plastoquinol-9 biosynthesis I	3	1	1
L-valine biosynthesis	4	4	1
L-serine biosynthesis II	4	3	1
D-erythronate degradation II	4	2	1
L-threonate degradation	4	2	1
L-tyrosine degradation I	5	5	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
D-galactose degradation I (Leloir pathway)	5	3	1
D-xylose degradation VI	5	3	1
superpathway of plastoquinol biosynthesis	5	2	1
L-isoleucine biosynthesis IV	6	4	1
L-lysine degradation X	6	4	1
D-arabinose degradation IV	6	4	1
superpathway of UDP-glucose-derived O-antigen building blocks biosynthesis	6	4	1
L-arabinose degradation V	6	4	1
L-isoleucine biosynthesis I (from threonine)	7	7	1
UDP-N-acetyl-D-galactosamine biosynthesis II	7	4	1
L-isoleucine biosynthesis III	7	4	1
D-xylose degradation IV	7	3	1
L-rhamnose degradation III	7	3	1
L-lysine degradation I	7	3	1
stachyose degradation	7	2	1
vitamin E biosynthesis (tocopherols)	7	1	1
L-isoleucine biosynthesis II	8	6	1
L-arabinose degradation IV	8	5	1
superpathway of ornithine degradation	8	4	1
L-fucose degradation III	8	4	1
ketogluconate metabolism	8	4	1
superpathway of branched chain amino acid biosynthesis	17	17	2
L-phenylalanine degradation IV (mammalian, via side chain)	9	4	1
UDP-sugars interconversion	9	3	1
teichuronic acid biosynthesis (B. subtilis 168)	9	2	1
superpathway of microbial D-galacturonate and D-glucuronate degradation	31	13	3
colanic acid building blocks biosynthesis	11	11	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	7	1
superpathway of L-isoleucine biosynthesis I	13	13	1
formaldehyde assimilation I (serine pathway)	13	9	1
superpathway of L-arginine and L-ornithine degradation	13	9	1
superpathway of L-threonine metabolism	18	15	1
mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	18	1	1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	33	12	1
superpathway of pentose and pentitol degradation	42	15	1
superpathway of L-lysine degradation	43	10	1