Experiment set1IT052 for Variovorax sp. OAS795

L-Arabinose carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + L-Arabinose (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 15 genes in this experiment

For carbon source L-Arabinose in Variovorax sp. OAS795

For carbon source L-Arabinose across organisms

SEED Subsystems

Subsystem	#Specific
4-Hydroxyphenylacetic acid catabolic pathway	5
Aromatic amino acid degradation	5
Central meta-cleavage pathway of aromatic compound degradation	3
L-Arabinose utilization	3
Benzoate transport and degradation cluster	1
Fermentations: Mixed acid	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Xylose utilization	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Tyrosine metabolism
• Ascorbate and aldarate metabolism
• Benzoate degradation via hydroxylation
• Nucleotide sugars metabolism
• 1- and 2-Methylnaphthalene degradation
• Butanoate metabolism
• Glycolysis / Gluconeogenesis
• Fatty acid biosynthesis
• Fatty acid metabolism
• Glutamate metabolism
• Glycine, serine and threonine metabolism
• Valine, leucine and isoleucine biosynthesis
• Phenylalanine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Aminosugars metabolism
• alpha-Linolenic acid metabolism
• 2,4-Dichlorobenzoate degradation
• Benzoate degradation via CoA ligation
• 3-Chloroacrylic acid degradation
• Pantothenate and CoA biosynthesis
• Retinol metabolism
• Porphyrin and chlorophyll metabolism
• Limonene and pinene degradation
• Metabolism of xenobiotics by cytochrome P450
• Drug metabolism - cytochrome P450
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide backbone
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
acetaldehyde biosynthesis I	1	1	1
ethanol degradation I	2	2	1
4-aminobutanoate degradation III	2	2	1
pyruvate fermentation to ethanol II	2	1	1
pyruvate fermentation to isobutanol (engineered)	5	4	2
L-lyxonate degradation	3	3	1
D-galactarate degradation II	3	3	1
ethanol degradation II	3	3	1
D-glucarate degradation II	3	3	1
L-arabinose degradation III	6	5	2
L-valine degradation II	3	2	1
L-isoleucine degradation II	3	2	1
L-leucine degradation III	3	2	1
pyruvate fermentation to ethanol III	3	2	1
pyruvate fermentation to ethanol I	3	2	1
L-methionine degradation III	3	1	1
L-valine biosynthesis	4	4	1
3,4-dichlorobenzoate degradation	4	3	1
phytol degradation	4	3	1
4-hydroxyphenylacetate degradation	8	5	2
L-phenylalanine degradation III	4	2	1
L-tyrosine degradation III	4	2	1
cytidine-5'-diphosphate-glycerol biosynthesis	4	1	1
salidroside biosynthesis	4	1	1
trans-4-hydroxy-L-proline degradation II	4	1	1
ethanolamine utilization	5	5	1
D-glucuronate degradation II	5	4	1
acetylene degradation (anaerobic)	5	4	1
(S)-propane-1,2-diol degradation	5	3	1
D-galacturonate degradation II	5	3	1
D-xylose degradation V	5	2	1
cinnamate and 3-hydroxycinnamate degradation to 2-hydroxypentadienoate	5	2	1
3-phenylpropanoate and 3-(3-hydroxyphenyl)propanoate degradation to 2-hydroxypentadienoate	5	2	1
D-xylose degradation III	5	2	1
phenylethanol biosynthesis	5	1	1
cyclohexanol degradation	5	1	1
L-arabinose degradation V	6	4	1
L-isoleucine biosynthesis IV	6	4	1
D-arabinose degradation III	6	3	1
3-chlorobenzoate degradation II (via protocatechuate)	6	3	1
noradrenaline and adrenaline degradation	13	4	2
L-isoleucine biosynthesis I (from threonine)	7	7	1
3-methylbutanol biosynthesis (engineered)	7	6	1
L-isoleucine biosynthesis III	7	4	1
nylon-6 oligomer degradation	7	4	1
serotonin degradation	7	3	1
L-isoleucine biosynthesis II	8	6	1
L-arabinose degradation IV	8	5	1
protocatechuate degradation I (meta-cleavage pathway)	8	5	1
3-phenylpropanoate and 3-(3-hydroxyphenyl)propanoate degradation	8	5	1
butanol and isobutanol biosynthesis (engineered)	8	3	1
superpathway of branched chain amino acid biosynthesis	17	17	2
superpathway of fermentation (Chlamydomonas reinhardtii)	9	5	1
superpathway of vanillin and vanillate degradation	10	6	1
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	5	1
L-tryptophan degradation V (side chain pathway)	13	1	1
superpathway of pentose and pentitol degradation	42	15	3
mixed acid fermentation	16	12	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	8	1
heterolactic fermentation	18	15	1
superpathway of L-threonine metabolism	18	15	1
superpathway of anaerobic sucrose degradation	19	16	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	15	1
superpathway of N-acetylneuraminate degradation	22	15	1
superpathway of microbial D-galacturonate and D-glucuronate degradation	31	13	1