Experiment set12IT006 for Pseudomonas putida KT2440

Beta-alanine carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + Beta-alanine (10 mM) + Dimethyl Sulfoxide (1 vol%)
Culturing: Putida_ML5_JBEI, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C), shaken=700rpm
By: Matthew Incha on 12-Feb-19
Media components: 40 mM 3-(N-morpholino)propanesulfonic acid, 4 mM Tricine, 1.32 mM Potassium phosphate dibasic, 0.01 mM Iron (II) sulfate heptahydrate, 9.5 mM Ammonium chloride, 0.276 mM Aluminum potassium sulfate dodecahydrate, 0.0005 mM Calcium chloride, 0.525 mM Magnesium chloride hexahydrate, 50 mM Sodium Chloride, 3e-09 M Ammonium heptamolybdate tetrahydrate, 4e-07 M Boric Acid, 3e-08 M Cobalt chloride hexahydrate, 1e-08 M Copper (II) sulfate pentahydrate, 8e-08 M Manganese (II) chloride tetrahydrate, 1e-08 M Zinc sulfate heptahydrate

Specific Phenotypes

For 18 genes in this experiment

For carbon source Beta-alanine in Pseudomonas putida KT2440

For carbon source Beta-alanine across organisms

SEED Subsystems

Subsystem	#Specific
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	4
Polyamine Metabolism	4
Pyruvate Alanine Serine Interconversions	2
Respiratory dehydrogenases 1	2
Arginine and Ornithine Degradation	1
Branched-Chain Amino Acid Biosynthesis	1
DNA-binding regulatory proteins, strays	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glycine and Serine Utilization	1
Glycine cleavage system	1
Isobutyryl-CoA to Propionyl-CoA Module	1
Photorespiration (oxidative C2 cycle)	1
Proline, 4-hydroxyproline uptake and utilization	1
Ribosome biogenesis bacterial	1
Valine degradation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Valine, leucine and isoleucine degradation
• Arginine and proline metabolism
• Propanoate metabolism
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Glutamate metabolism
• Alanine and aspartate metabolism
• Glycine, serine and threonine metabolism
• Phenylalanine metabolism
• Tryptophan metabolism
• beta-Alanine metabolism
• Aminosugars metabolism
• Lipopolysaccharide biosynthesis
• Inositol phosphate metabolism
• Ether lipid metabolism
• Sphingolipid metabolism
• Thiamine metabolism
• Riboflavin metabolism
• Nicotinate and nicotinamide metabolism
• Nitrogen metabolism
• Biosynthesis of siderophore group nonribosomal peptides

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
β-alanine degradation II	2	2	2
L-proline degradation I	3	3	2
L-alanine degradation I	2	2	1
β-alanine degradation I	2	1	1
glycine biosynthesis II	3	3	1
glycine cleavage	3	3	1
L-arginine degradation I (arginase pathway)	3	2	1
ethene biosynthesis II (microbes)	4	1	1
acrylate degradation I	5	3	1
propanoyl-CoA degradation II	5	3	1
β-alanine biosynthesis II	6	5	1
(5R)-carbapenem carboxylate biosynthesis	6	1	1
L-Nδ-acetylornithine biosynthesis	7	5	1
myo-inositol degradation I	7	1	1
2,4-dinitrotoluene degradation	7	1	1
L-citrulline biosynthesis	8	7	1
L-valine degradation I	8	6	1
superpathway of coenzyme A biosynthesis II (plants)	10	9	1
myo-, chiro- and scyllo-inositol degradation	10	1	1
superpathway of L-citrulline metabolism	12	9	1