Experiment set25S55 for Pseudomonas fluorescens SBW25-INTG

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 22 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
Potassium homeostasis	2
Alginate metabolism	1
Arginine and Ornithine Degradation	1
Bacterial RNA-metabolizing Zn-dependent hydrolases	1
Conserved gene cluster associated with Met-tRNA formyltransferase	1
Folate Biosynthesis	1
Fructose utilization	1
Glutathione-regulated potassium-efflux system and associated functions	1
HMG CoA Synthesis	1
Homogentisate pathway of aromatic compound degradation	1
Leucine Degradation and HMG-CoA Metabolism	1
Lysine degradation	1
Pentose phosphate pathway	1
Polyamine Metabolism	1
Pyruvate Alanine Serine Interconversions	1
Salicylate and gentisate catabolism	1
Serine-glyoxylate cycle	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Lysine biosynthesis
• Arginine and proline metabolism
• Alanine and aspartate metabolism
• Valine, leucine and isoleucine degradation
• Lysine degradation
• beta-Alanine metabolism
• Propanoate metabolism
• Pentose phosphate pathway
• Fructose and mannose metabolism
• Urea cycle and metabolism of amino groups
• Glutamate metabolism
• Methionine metabolism
• Tyrosine metabolism
• Aminophosphonate metabolism
• Nucleotide sugars metabolism
• Styrene degradation
• Butanoate metabolism
• Caprolactam degradation
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
β-alanine degradation II	2	2	1
4-aminobutanoate degradation III	2	2	1
putrescine degradation V	2	2	1
4-aminobutanoate degradation I	2	2	1
4-aminobutanoate degradation II	2	2	1
L-ornithine biosynthesis II	3	3	1
L-proline biosynthesis III (from L-ornithine)	3	3	1
superpathway of 4-aminobutanoate degradation	3	3	1
L-arginine degradation I (arginase pathway)	3	3	1
L-arginine degradation VI (arginase 2 pathway)	4	4	1
GABA shunt II	4	3	1
GABA shunt I	4	2	1
L-tyrosine degradation I	5	5	1
L-ornithine biosynthesis I	5	5	1
L-arginine degradation XIII (reductive Stickland reaction)	5	5	1
L-lysine degradation IV	5	5	1
pentose phosphate pathway (non-oxidative branch) I	5	5	1
L-arginine degradation II (AST pathway)	5	5	1
β-alanine biosynthesis II	6	5	1
L-leucine degradation I	6	5	1
L-lysine degradation X	6	5	1
L-lysine degradation III	6	2	1
L-Nδ-acetylornithine biosynthesis	7	6	1
L-lysine degradation I	7	4	1
4-aminobutanoate degradation V	7	3	1
alginate degradation	7	2	1
pentose phosphate pathway	8	8	1
L-citrulline biosynthesis	8	8	1
L-arginine biosynthesis I (via L-ornithine)	9	9	1
L-lysine biosynthesis I	9	9	1
L-arginine biosynthesis III (via N-acetyl-L-citrulline)	9	8	1
formaldehyde assimilation II (assimilatory RuMP Cycle)	9	6	1
L-arginine biosynthesis II (acetyl cycle)	10	10	1
superpathway of coenzyme A biosynthesis II (plants)	10	9	1
Rubisco shunt	10	8	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	7	1
formaldehyde assimilation III (dihydroxyacetone cycle)	12	10	1
superpathway of L-citrulline metabolism	12	10	1
superpathway of L-arginine and L-ornithine degradation	13	9	1
Bifidobacterium shunt	15	12	1
superpathway of glucose and xylose degradation	17	16	1
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
superpathway of L-lysine degradation	43	17	1