Experiment set25S57 for Pseudomonas fluorescens SBW25-INTG

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4-Aminobutyric acid carbon source

Group: carbon source
Media: MME_noCarbon + 4-Aminobutyric acid (10 mM), pH=7
Culturing: PseudoSBW25_INTG_ML3, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C), shaken=1200 rpm
By: Andrew Frank on 1/31/23
Media components: 9.1 mM Potassium phosphate dibasic trihydrate, 20 mM 3-(N-morpholino)propanesulfonic acid, 4.3 mM Sodium Chloride, 10 mM Ammonium chloride, 0.41 mM Magnesium Sulfate Heptahydrate, 0.07 mM Calcium chloride dihydrate, MME Trace Minerals (0.5 mg/L EDTA tetrasodium tetrahydrate salt, 2 mg/L Ferric chloride, 0.05 mg/L Boric Acid, 0.05 mg/L Zinc chloride, 0.03 mg/L copper (II) chloride dihydrate, 0.05 mg/L Manganese (II) chloride tetrahydrate, 0.05 mg/L Diammonium molybdate, 0.05 mg/L Cobalt chloride hexahydrate, 0.05 mg/L Nickel (II) chloride hexahydrate)

Specific Phenotypes

For 33 genes in this experiment

For carbon source 4-Aminobutyric acid in Pseudomonas fluorescens SBW25-INTG

For carbon source 4-Aminobutyric acid across organisms

SEED Subsystems

Subsystem #Specific
ABC transporter branched-chain amino acid (TC 3.A.1.4.1) 4
Arginine and Ornithine Degradation 2
Copper homeostasis 2
HMG CoA Synthesis 2
Leucine Degradation and HMG-CoA Metabolism 2
Lysine degradation 2
Polyamine Metabolism 2
Potassium homeostasis 2
Pyruvate Alanine Serine Interconversions 2
Serine-glyoxylate cycle 2
Bacterial RNA-metabolizing Zn-dependent hydrolases 1
Biogenesis of c-type cytochromes 1
Conserved gene cluster associated with Met-tRNA formyltransferase 1
DNA-binding regulatory proteins, strays 1
Entner-Doudoroff Pathway 1
Glutathione-regulated potassium-efflux system and associated functions 1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria 1
Homogentisate pathway of aromatic compound degradation 1
Methylcitrate cycle 1
Methylglyoxal Metabolism 1
Propionate-CoA to Succinate Module 1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate 1
Salicylate and gentisate catabolism 1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway #Steps #Present #Specific
putrescine degradation V 2 2 2
indole-3-acetate biosynthesis III (bacteria) 2 2 1
4-aminobutanoate degradation I 2 2 1
β-alanine degradation II 2 2 1
phenylethylamine degradation I 2 2 1
4-aminobutanoate degradation III 2 2 1
4-aminobutanoate degradation II 2 2 1
putrescine degradation I 2 1 1
phenylethylamine degradation II 2 1 1
phenylethanol degradation 2 1 1
ethylene glycol degradation 2 1 1
L-lysine degradation IV 5 5 2
superpathway of 4-aminobutanoate degradation 3 3 1
ethanol degradation IV 3 3 1
L-ornithine biosynthesis II 3 3 1
ethanol degradation II 3 3 1
putrescine biosynthesis II 3 3 1
L-arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway) 3 3 1
L-proline biosynthesis III (from L-ornithine) 3 3 1
L-arginine degradation I (arginase pathway) 3 3 1
L-leucine degradation I 6 5 2
L-lysine degradation X 6 5 2
putrescine degradation IV 3 2 1
ethanol degradation III 3 2 1
L-phenylalanine degradation II (anaerobic) 3 2 1
hypotaurine degradation 3 2 1
styrene degradation 3 1 1
histamine degradation 3 1 1
L-lysine degradation I 7 4 2
L-arginine degradation VI (arginase 2 pathway) 4 4 1
queuosine biosynthesis I (de novo) 4 4 1
GABA shunt II 4 3 1
putrescine degradation III 4 3 1
phytol degradation 4 3 1
L-tryptophan degradation X (mammalian, via tryptamine) 4 2 1
GABA shunt I 4 2 1
D-arabinose degradation II 4 2 1
fatty acid α-oxidation I (plants) 4 2 1
L-arginine degradation II (AST pathway) 5 5 1
L-arginine degradation XIII (reductive Stickland reaction) 5 5 1
L-tyrosine degradation I 5 5 1
2-methylcitrate cycle I 5 5 1
L-ornithine biosynthesis I 5 5 1
octane oxidation 5 4 1
mitochondrial NADPH production (yeast) 5 4 1
sphingosine and sphingosine-1-phosphate metabolism 10 4 2
dopamine degradation 5 2 1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation 11 7 2
β-alanine biosynthesis II 6 5 1
2-methylcitrate cycle II 6 5 1
3-methyl-branched fatty acid α-oxidation 6 3 1
L-lysine degradation III 6 2 1
alkane oxidation 6 1 1
superpathway of L-arginine and L-ornithine degradation 13 9 2
noradrenaline and adrenaline degradation 13 8 2
L-Nδ-acetylornithine biosynthesis 7 6 1
superpathway of glycol metabolism and degradation 7 5 1
serotonin degradation 7 4 1
4-aminobutanoate degradation V 7 3 1
ceramide degradation by α-oxidation 7 2 1
limonene degradation IV (anaerobic) 7 1 1
L-citrulline biosynthesis 8 8 1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast) 8 7 1
superpathway of polyamine biosynthesis II 8 6 1
superpathway of ornithine degradation 8 4 1
aromatic biogenic amine degradation (bacteria) 8 4 1
ceramide and sphingolipid recycling and degradation (yeast) 16 4 2
L-lysine biosynthesis I 9 9 1
L-arginine biosynthesis I (via L-ornithine) 9 9 1
L-arginine biosynthesis III (via N-acetyl-L-citrulline) 9 8 1
Entner-Doudoroff pathway II (non-phosphorylative) 9 6 1
L-phenylalanine degradation IV (mammalian, via side chain) 9 5 1
L-arginine biosynthesis II (acetyl cycle) 10 10 1
superpathway of coenzyme A biosynthesis II (plants) 10 9 1
superpathway of phenylethylamine degradation 11 6 1
superpathway of L-citrulline metabolism 12 10 1
superpathway of L-lysine degradation 43 17 3
superpathway of arginine and polyamine biosynthesis 17 15 1
nicotine degradation I (pyridine pathway) 17 5 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I 18 16 1
aspartate superpathway 25 22 1
anaerobic aromatic compound degradation (Thauera aromatica) 27 4 1
superpathway of pentose and pentitol degradation 42 16 1