Experiment set3IT061 for Pseudomonas sp. RS175

4-Hydroxyphenylpropionic acid carbon source 2.5 mM

Group: carbon source
Media: MME_noCarbon + 4-Hydroxyphenylpropionic acid (2.5 mM), pH=7
Culturing: Pseudomonas_RS175_ML2, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
By: Joshua Elmore on 1-Jul-22
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 30 genes in this experiment

For carbon source 4-Hydroxyphenylpropionic acid in Pseudomonas sp. RS175

For carbon source 4-Hydroxyphenylpropionic acid across organisms

SEED Subsystems

Subsystem	#Specific
Arginine and Ornithine Degradation	4
ABC transporter dipeptide (TC 3.A.1.5.2)	3
Bacterial Chemotaxis	3
ABC transporter oligopeptide (TC 3.A.1.5.1)	2
Biogenesis of cytochrome c oxidases	1
Biotin biosynthesis	1
DNA-replication	1
DNA Repair Base Excision	1
Histidine Degradation	1
Lysine degradation	1
Polyhydroxybutyrate metabolism	1
Terminal cytochrome C oxidases	1
n-Phenylalkanoic acid degradation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Fatty acid metabolism
• Glycolysis / Gluconeogenesis
• Oxidative phosphorylation
• Purine metabolism
• Pyrimidine metabolism
• Glycine, serine and threonine metabolism
• Histidine metabolism
• Tyrosine metabolism
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• 3-Chloroacrylic acid degradation
• Butanoate metabolism
• Retinol metabolism
• Metabolism of xenobiotics by cytochrome P450
• Drug metabolism - cytochrome P450

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
ethanol degradation I	2	2	2
methanol oxidation to formaldehyde II	1	1	1
acetaldehyde biosynthesis I	1	1	1
long-chain fatty acid activation	1	1	1
pyruvate fermentation to ethanol I	3	2	2
pyruvate fermentation to ethanol III	3	2	2
L-threonine degradation IV	2	2	1
phytol degradation	4	3	2
linoleate biosynthesis II (animals)	2	1	1
arsenite to oxygen electron transfer	2	1	1
γ-linolenate biosynthesis II (animals)	2	1	1
pyruvate fermentation to ethanol II	2	1	1
ethanolamine utilization	5	5	2
acetylene degradation (anaerobic)	5	4	2
ethanol degradation II	3	3	1
L-isoleucine degradation II	3	2	1
2-aminoethylphosphonate degradation I	3	2	1
2-hydroxypenta-2,4-dienoate degradation	3	2	1
L-valine degradation II	3	2	1
2-deoxy-D-ribose degradation I	3	2	1
L-leucine degradation III	3	2	1
3-methyl-branched fatty acid α-oxidation	6	3	2
L-methionine degradation III	3	1	1
arsenite to oxygen electron transfer (via azurin)	3	1	1
oleate biosynthesis I (plants)	3	1	1
2-deoxy-α-D-ribose 1-phosphate degradation	3	1	1
alkane biosynthesis II	3	1	1
sulfoacetaldehyde degradation IV	3	1	1
L-histidine degradation I	4	4	1
aerobic respiration I (cytochrome c)	4	3	1
aerobic respiration II (cytochrome c) (yeast)	4	3	1
L-phenylalanine degradation III	4	2	1
salidroside biosynthesis	4	2	1
L-tyrosine degradation III	4	2	1
long chain fatty acid ester synthesis (engineered)	4	1	1
phosphatidylcholine acyl editing	4	1	1
wax esters biosynthesis II	4	1	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	5	2
sporopollenin precursors biosynthesis	18	4	4
L-histidine degradation II	5	5	1
octane oxidation	5	4	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
catechol degradation I (meta-cleavage pathway)	5	2	1
phenylethanol biosynthesis	5	2	1
(S)-propane-1,2-diol degradation	5	2	1
fatty acid salvage	6	6	1
stearate biosynthesis II (bacteria and plants)	6	5	1
L-histidine degradation III	6	4	1
stearate biosynthesis IV	6	4	1
methanol oxidation to carbon dioxide	6	3	1
Fe(II) oxidation	6	3	1
6-gingerol analog biosynthesis (engineered)	6	3	1
superpathway of pyrimidine deoxyribonucleosides degradation	6	3	1
triethylamine degradation	6	1	1
stearate biosynthesis I (animals)	6	1	1
noradrenaline and adrenaline degradation	13	8	2
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	5	2
3-methylbutanol biosynthesis (engineered)	7	6	1
superpathway of purine deoxyribonucleosides degradation	7	5	1
serotonin degradation	7	4	1
capsaicin biosynthesis	7	4	1
catechol degradation II (meta-cleavage pathway)	7	3	1
ceramide degradation by α-oxidation	7	2	1
toluene degradation V (aerobic) (via toluene-cis-diol)	7	2	1
toluene degradation I (aerobic) (via o-cresol)	7	2	1
icosapentaenoate biosynthesis II (6-desaturase, mammals)	7	1	1
arachidonate biosynthesis III (6-desaturase, mammals)	7	1	1
icosapentaenoate biosynthesis III (8-desaturase, mammals)	7	1	1
L-histidine degradation VI	8	7	1
mixed acid fermentation	16	12	2
2-deoxy-D-ribose degradation II	8	4	1
3-phenylpropanoate and 3-(3-hydroxyphenyl)propanoate degradation	8	3	1
butanol and isobutanol biosynthesis (engineered)	8	3	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
p-cumate degradation	8	2	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	7	2
heterolactic fermentation	18	16	2
hexitol fermentation to lactate, formate, ethanol and acetate	19	14	2
meta cleavage pathway of aromatic compounds	10	3	1
suberin monomers biosynthesis	20	3	2
superpathway of fatty acid biosynthesis II (plant)	43	38	4
superpathway of N-acetylneuraminate degradation	22	15	2
p-cymene degradation	11	2	1
naphthalene degradation to acetyl-CoA	12	3	1
L-tryptophan degradation IX	12	2	1
L-tryptophan degradation XII (Geobacillus)	12	2	1
toluene degradation IV (aerobic) (via catechol)	13	4	1
L-tryptophan degradation V (side chain pathway)	13	1	1
palmitate biosynthesis II (type II fatty acid synthase)	31	29	2
cutin biosynthesis	16	1	1
superpathway of L-threonine metabolism	18	13	1
mandelate degradation to acetyl-CoA	18	7	1
superpathway of anaerobic sucrose degradation	19	15	1
superpathway of fatty acids biosynthesis (E. coli)	53	49	2
palmitate biosynthesis III	29	28	1
superpathway of aerobic toluene degradation	30	11	1
oleate β-oxidation	35	30	1
superpathway of aromatic compound degradation via 3-oxoadipate	35	13	1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate	42	10	1