Experiment set6IT037 for Paraburkholderia bryophila 376MFSha3.1

3-Hydroxypropionate carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + 3-Hydroxypropionate (10 mM) + Dimethyl Sulfoxide (1 vol%)
Culturing: Burk376_ML3, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C), shaken=700rpm
By: RobinH_and_TrentonO on 13-Feb-19
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 6 genes in this experiment

For carbon source 3-Hydroxypropionate in Paraburkholderia bryophila 376MFSha3.1

For carbon source 3-Hydroxypropionate across organisms

SEED Subsystems

Subsystem	#Specific
Branched-Chain Amino Acid Biosynthesis	1
Choline and Betaine Uptake and Betaine Biosynthesis	1
Isobutyryl-CoA to Propionyl-CoA Module	1
Leucine Biosynthesis	1
Photorespiration (oxidative C2 cycle)	1
Valine degradation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pyruvate metabolism
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Glycine, serine and threonine metabolism
• Valine, leucine and isoleucine degradation
• Valine, leucine and isoleucine biosynthesis
• Aminosugars metabolism
• Lipopolysaccharide biosynthesis
• Inositol phosphate metabolism
• Ether lipid metabolism
• Sphingolipid metabolism
• Glyoxylate and dicarboxylate metabolism
• Propanoate metabolism
• Thiamine metabolism
• Riboflavin metabolism
• Nicotinate and nicotinamide metabolism
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
β-alanine degradation II	2	2	1
choline degradation I	2	2	1
glycine betaine biosynthesis II (Gram-positive bacteria)	2	2	1
glycolate and glyoxylate degradation II	2	2	1
glycine betaine biosynthesis I (Gram-negative bacteria)	2	2	1
β-alanine degradation I	2	1	1
choline-O-sulfate degradation	3	3	1
chitin deacetylation	4	3	1
propanoyl-CoA degradation II	5	2	1
acrylate degradation I	5	2	1
glyoxylate cycle	6	6	1
L-leucine biosynthesis	6	6	1
myo-inositol degradation I	7	6	1
3-methylbutanol biosynthesis (engineered)	7	6	1
superpathway of glycol metabolism and degradation	7	5	1
D-xylose degradation IV	7	4	1
2,4-dinitrotoluene degradation	7	1	1
L-arabinose degradation IV	8	6	1
L-valine degradation I	8	5	1
myo-, chiro- and scyllo-inositol degradation	10	6	1
superpathway of glyoxylate bypass and TCA	12	9	1
superpathway of glyoxylate cycle and fatty acid degradation	14	10	1
crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA cycle (engineered)	14	3	1
superpathway of branched chain amino acid biosynthesis	17	17	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	21	1
superpathway of pentose and pentitol degradation	42	21	1