Experiment set22IT058 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 9 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	4
Aromatic amino acid degradation	3
Central meta-cleavage pathway of aromatic compound degradation	1
Lysine Biosynthesis DAP Pathway	1
Molybdenum cofactor biosynthesis	1
Riboflavin, FMN and FAD metabolism	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Tyrosine metabolism
• Glutamate metabolism
• Lysine biosynthesis
• Butanoate metabolism
• Riboflavin metabolism
• Urea cycle and metabolism of amino groups
• Geraniol degradation
• Arginine and proline metabolism
• Tryptophan metabolism
• alpha-Linolenic acid metabolism
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Limonene and pinene degradation

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
4-aminobutanoate degradation I	2	2	1
4-aminobutanoate degradation III	2	2	1
superpathway of 4-aminobutanoate degradation	3	3	1
4-aminobutanoate degradation IV	3	1	1
N-methylpyrrolidone degradation	3	1	1
4-hydroxyphenylacetate degradation	8	6	2
GABA shunt II	4	3	1
GABA shunt I	4	2	1
flavin biosynthesis I (bacteria and plants)	9	8	2
flavin biosynthesis III (fungi)	9	7	2
L-lysine degradation IV	5	5	1
6-hydroxymethyl-dihydropterin diphosphate biosynthesis III (Chlamydia)	5	3	1
L-lysine degradation X	6	5	1
L-lysine degradation III	6	2	1
L-lysine degradation I	7	4	1
toxoflavin biosynthesis	7	3	1
L-lysine biosynthesis I	9	9	1
flavin biosynthesis II (archaea)	10	5	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, L-threonine and L-methionine biosynthesis I	18	16	1
aspartate superpathway	25	22	1
superpathway of L-lysine degradation	43	17	1