Experiment set1IT077 for Variovorax sp. OAS795

D,L-Malic Acid carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + D,L-Malic 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 21 genes in this experiment

For carbon source D,L-Malic Acid in Variovorax sp. OAS795

For carbon source D,L-Malic Acid across organisms

SEED Subsystems

Subsystem	#Specific
Cobalt-zinc-cadmium resistance	1
DNA repair, UvrABC system	1
Folate Biosynthesis	1
Multidrug Resistance Efflux Pumps	1
Orphan regulatory proteins	1
Proteolysis in bacteria, ATP-dependent	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
Soluble cytochromes and functionally related electron carriers	1
TCA Cycle	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Citrate cycle (TCA cycle)
• Glyoxylate and dicarboxylate metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones
• Butanoate metabolism
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
cis-cyclopropane fatty acid (CFA) biosynthesis	1	1	1
D-malate degradation	1	1	1
sterculate biosynthesis	2	1	1
partial TCA cycle (obligate autotrophs)	8	7	3
TCA cycle V (2-oxoglutarate synthase)	9	9	3
TCA cycle II (plants and fungi)	9	9	3
glyoxylate cycle	6	6	2
dTMP de novo biosynthesis (mitochondrial)	3	3	1
tetrahydrofolate biosynthesis I	3	3	1
TCA cycle IV (2-oxoglutarate decarboxylase)	9	8	3
TCA cycle VI (Helicobacter)	9	7	3
TCA cycle VII (acetate-producers)	9	7	3
TCA cycle I (prokaryotic)	10	9	3
TCA cycle III (animals)	10	9	3
reductive TCA cycle I	11	8	3
superpathway of glyoxylate bypass and TCA	12	11	3
nitrogen remobilization from senescing leaves	8	7	2
gentisate degradation II	4	3	1
reductive TCA cycle II	12	7	3
L-threonate degradation	4	2	1
D-erythronate degradation II	4	2	1
superpathway of glyoxylate cycle and fatty acid degradation	14	11	3
mixed acid fermentation	16	12	3
TCA cycle VIII (Chlamydia)	6	6	1
methylgallate degradation	6	3	1
methylaspartate cycle	19	12	3
incomplete reductive TCA cycle	7	5	1
pyruvate fermentation to propanoate I	7	4	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	20	3
protocatechuate degradation I (meta-cleavage pathway)	8	5	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	24	3
folate transformations III (E. coli)	9	7	1
superpathway of tetrahydrofolate biosynthesis	10	8	1
anaerobic energy metabolism (invertebrates, mitochondrial)	10	6	1
superpathway of vanillin and vanillate degradation	10	6	1
folate transformations II (plants)	11	8	1
L-glutamate degradation VIII (to propanoate)	11	4	1
superpathway of tetrahydrofolate biosynthesis and salvage	12	10	1
syringate degradation	12	4	1
ethene biosynthesis V (engineered)	25	19	2
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	7	1
superpathway of anaerobic energy metabolism (invertebrates)	17	13	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	24	1
superpathway of chorismate metabolism	59	40	1
mycolate biosynthesis	205	26	3
superpathway of mycolate biosynthesis	239	27	3