Experiment set22IT059 for Pseudomonas fluorescens SBW25-INTG

4-hydroxyphenylacetic acid 2 mM carbon source

Group: carbon source
Media: MME_noNitrogen_noCarbon + 4-hydroxyphenylacetic acid (2 mM) + Ammonium chloride (10 mM), pH=7
Culturing: PseudoSBW25_INTG_ML3, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
By: Joshua Elmore on 8-Mar-22
Media components: 9.1 mM Potassium phosphate dibasic trihydrate, 20 mM 3-(N-morpholino)propanesulfonic acid, 4.3 mM Sodium 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 10 genes in this experiment

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

For carbon source 4-hydroxyphenylacetic acid across organisms

SEED Subsystems

Subsystem	#Specific
4-Hydroxyphenylacetic acid catabolic pathway	5
Aromatic amino acid degradation	4
Central meta-cleavage pathway of aromatic compound degradation	3
Aromatic Amin Catabolism	1
Benzoate transport and degradation cluster	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Tyrosine metabolism
• Butanoate metabolism
• Glutamate metabolism
• Nucleotide sugars metabolism
• 1- and 2-Methylnaphthalene degradation
• Limonene and pinene degradation
• Fatty acid biosynthesis
• Urea cycle and metabolism of amino groups
• Geraniol degradation
• Lysine biosynthesis
• Arginine and proline metabolism
• Benzoate degradation via hydroxylation
• Tryptophan metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Aminosugars metabolism
• alpha-Linolenic acid metabolism
• Naphthalene and anthracene degradation
• Benzoate degradation via CoA ligation
• Porphyrin and chlorophyll metabolism
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide backbone

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
4-aminobutanoate degradation III	2	2	1
4-aminobutanoate degradation I	2	2	1
4-hydroxyphenylacetate degradation	8	6	3
superpathway of 4-aminobutanoate degradation	3	3	1
N-methylpyrrolidone degradation	3	1	1
4-aminobutanoate degradation IV	3	1	1
GABA shunt II	4	3	1
GABA shunt I	4	2	1
L-lysine degradation IV	5	5	1
L-lysine degradation X	6	5	1
L-lysine degradation III	6	2	1
L-lysine degradation I	7	4	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	7	1
superpathway of L-arginine and L-ornithine degradation	13	9	1
superpathway of L-lysine degradation	43	17	1