Experiment set2IT045 for Variovorax sp. OAS795

Sodium butyrate carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + Sodium butyrate (4 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 25 genes in this experiment

For carbon source Sodium butyrate in Variovorax sp. OAS795

For carbon source Sodium butyrate across organisms

SEED Subsystems

Subsystem	#Specific
Trehalose Biosynthesis	2
ABC transporter dipeptide (TC 3.A.1.5.2)	1
Campylobacter Iron Metabolism	1
Entner-Doudoroff Pathway	1
Glutaredoxins	1
Glycolysis and Gluconeogenesis	1
Glycolysis and Gluconeogenesis, including Archaeal enzymes	1
Iron acquisition in Vibrio	1
NAD and NADP cofactor biosynthesis global	1
NAD regulation	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
TCA Cycle	1
Transport of Iron	1
cAMP signaling in bacteria	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glycolysis / Gluconeogenesis
• Citrate cycle (TCA cycle)
• Nicotinate and nicotinamide metabolism
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones
• Glutamate metabolism
• Starch and sucrose metabolism
• Pyruvate metabolism
• Nitrogen metabolism
• Biosynthesis of phenylpropanoids

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
trehalose biosynthesis IV	1	1	1
NAD salvage pathway II (PNC IV cycle)	5	4	2
NAD de novo biosynthesis I	6	6	2
trehalose biosynthesis V	3	3	1
NAD de novo biosynthesis IV (anaerobic)	6	5	2
NAD de novo biosynthesis III	6	5	2
anaerobic energy metabolism (invertebrates, cytosol)	7	7	2
NAD salvage pathway I (PNC VI cycle)	7	6	2
NAD biosynthesis from 2-amino-3-carboxymuconate semialdehyde	4	4	1
NAD salvage pathway V (PNC V cycle)	5	4	1
nicotinate degradation I	6	4	1
picolinate degradation	7	6	1
nitrogen remobilization from senescing leaves	8	7	1
glycogen biosynthesis III (from α-maltose 1-phosphate)	8	4	1
superpathway of anaerobic energy metabolism (invertebrates)	17	13	2
TCA cycle II (plants and fungi)	9	9	1
NAD de novo biosynthesis II (from tryptophan)	9	7	1
Entner-Doudoroff pathway III (semi-phosphorylative)	9	6	1
Rubisco shunt	10	10	1
TCA cycle III (animals)	10	9	1
glycolysis IV	10	8	1
glycolysis V (Pyrococcus)	10	7	1
photorespiration II	10	6	1
nicotine degradation III (VPP pathway)	10	4	1
glycolysis III (from glucose)	11	11	1
glycolysis II (from fructose 6-phosphate)	11	11	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	20	2
glycolysis VI (from fructose)	11	8	1
NAD salvage (plants)	11	6	1
nicotine degradation II (pyrrolidine pathway)	11	5	1
gluconeogenesis III	12	11	1
homolactic fermentation	12	11	1
aspartate superpathway	25	24	2
glycolysis I (from glucose 6-phosphate)	13	12	1
gluconeogenesis I	13	11	1
superpathway of NAD biosynthesis in eukaryotes	14	9	1
Bifidobacterium shunt	15	14	1
glycerol degradation to butanol	16	10	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	16	1
superpathway of glucose and xylose degradation	17	14	1
superpathway of hexitol degradation (bacteria)	18	13	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	12	1
superpathway of nicotinate degradation	18	8	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
ethene biosynthesis V (engineered)	25	19	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	24	1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	21	1
1-butanol autotrophic biosynthesis (engineered)	27	20	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	24	1