Experiment set22IT060 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 13 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	3
Aromatic amino acid degradation	2
Benzoate transport and degradation cluster	1
Central meta-cleavage pathway of aromatic compound degradation	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Lysine Biosynthesis DAP Pathway	1
Threonine and Homoserine Biosynthesis	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
• Butanoate metabolism
• Lysine biosynthesis
• Arginine and proline metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Nucleotide sugars metabolism
• 1- and 2-Methylnaphthalene degradation
• Limonene and pinene degradation
• Fatty acid biosynthesis
• Urea cycle and metabolism of amino groups
• Alanine and aspartate metabolism
• Cysteine metabolism
• Geraniol degradation
• Phenylalanine metabolism
• Benzoate degradation via hydroxylation
• Tryptophan metabolism
• Novobiocin biosynthesis
• Aminosugars metabolism
• alpha-Linolenic acid metabolism
• Naphthalene and anthracene degradation
• Benzoate degradation via CoA ligation
• Carbon fixation in photosynthetic organisms
• Porphyrin and chlorophyll metabolism
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide backbone
• Biosynthesis of phenylpropanoids
• 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
L-aspartate biosynthesis	1	1	1
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
L-aspartate degradation I	1	1	1
4-aminobutanoate degradation III	2	2	1
L-glutamate degradation II	2	2	1
4-aminobutanoate degradation I	2	2	1
L-tyrosine degradation II	2	1	1
L-tryptophan degradation IV (via indole-3-lactate)	2	1	1
atromentin biosynthesis	2	1	1
malate/L-aspartate shuttle pathway	2	1	1
L-phenylalanine biosynthesis I	3	3	1
L-tyrosine biosynthesis I	3	3	1
superpathway of 4-aminobutanoate degradation	3	3	1
L-asparagine degradation III (mammalian)	3	2	1
L-phenylalanine degradation II (anaerobic)	3	2	1
sulfolactate degradation III	3	1	1
N-methylpyrrolidone degradation	3	1	1
indole-3-acetate biosynthesis VI (bacteria)	3	1	1
4-aminobutanoate degradation IV	3	1	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
(R)-cysteate degradation	3	1	1
GABA shunt II	4	3	1
superpathway of L-aspartate and L-asparagine biosynthesis	4	3	1
L-tyrosine degradation III	4	2	1
L-phenylalanine degradation III	4	2	1
GABA shunt I	4	2	1
L-tryptophan degradation VIII (to tryptophol)	4	1	1
L-lysine degradation IV	5	5	1
L-tyrosine degradation I	5	5	1
trans-4-hydroxy-L-proline degradation I	5	3	1
superpathway of plastoquinol biosynthesis	5	2	1
L-tryptophan degradation XIII (reductive Stickland reaction)	5	1	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	6	2
superpathway of L-threonine biosynthesis	6	6	1
TCA cycle VIII (Chlamydia)	6	5	1
L-lysine degradation X	6	5	1
L-lysine degradation III	6	2	1
superpathway of sulfolactate degradation	6	2	1
coenzyme M biosynthesis II	6	1	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	2
L-lysine degradation I	7	4	1
anaerobic energy metabolism (invertebrates, cytosol)	7	4	1
4-hydroxyphenylacetate degradation	8	6	1
superpathway of aromatic amino acid biosynthesis	18	18	2
L-lysine biosynthesis I	9	9	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	2
superpathway of L-methionine biosynthesis (transsulfuration)	9	7	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	5	1
superpathway of L-phenylalanine biosynthesis	10	10	1
superpathway of L-tyrosine biosynthesis	10	10	1
rosmarinic acid biosynthesis I	10	1	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	7	1
(S)-reticuline biosynthesis I	11	1	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	12	1
indole-3-acetate biosynthesis II	12	5	1
aspartate superpathway	25	22	2
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of L-arginine and L-ornithine degradation	13	9	1
superpathway of rosmarinic acid biosynthesis	14	1	1
superpathway of anaerobic energy metabolism (invertebrates)	17	8	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	4	1
superpathway of chorismate metabolism	59	42	2
superpathway of L-lysine degradation	43	17	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	20	1