Experiment set3IT072 for Pseudomonas sp. RS175

Ferulic Acid carbon source 2.5 mM

Group: carbon source
Media: MME_noCarbon + Ferulic 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-July-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 15 genes in this experiment

For carbon source Ferulic Acid in Pseudomonas sp. RS175

For carbon source Ferulic Acid across organisms

SEED Subsystems

Subsystem	#Specific
Glutathione-dependent pathway of formaldehyde detoxification	2
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Histidine Degradation	1
Methionine Salvage	1
Threonine and Homoserine Biosynthesis	1
dTDP-rhamnose synthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Tyrosine metabolism
• Phenylalanine metabolism
• Alkaloid biosynthesis I
• Biosynthesis of phenylpropanoids
• Methionine metabolism
• Histidine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• 1- and 2-Methylnaphthalene degradation
• Methane metabolism
• Alkaloid biosynthesis II
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of plant hormones
• Glycolysis / Gluconeogenesis
• Fatty acid metabolism
• Ubiquinone and menaquinone biosynthesis
• Glutamate metabolism
• Alanine and aspartate metabolism
• Glycine, serine and threonine metabolism
• Cysteine metabolism
• Lysine biosynthesis
• Arginine and proline metabolism
• gamma-Hexachlorocyclohexane degradation
• Bisphenol A degradation
• Tryptophan metabolism
• Cyanoamino acid metabolism
• Starch and sucrose metabolism
• Nucleotide sugars metabolism
• Toluene and xylene degradation
• 2,4-Dichlorobenzoate degradation
• Naphthalene and anthracene degradation
• 1,4-Dichlorobenzene degradation
• Benzoate degradation via CoA ligation
• 3-Chloroacrylic acid degradation
• Styrene degradation
• Carbon fixation in photosynthetic organisms
• Retinol metabolism
• Limonene and pinene degradation
• Brassinosteroid biosynthesis
• Carotenoid biosynthesis - General
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Isoflavonoid biosynthesis
• Metabolism of xenobiotics by cytochrome P450
• Drug metabolism - cytochrome P450
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

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
3-methylthiopropanoate biosynthesis	1	1	1
acetaldehyde biosynthesis I	1	1	1
L-glutamate degradation II	2	2	1
vanillin and vanillate degradation II	2	2	1
L-phenylalanine biosynthesis III (cytosolic, plants)	2	2	1
ethanol degradation I	2	2	1
L-tyrosine degradation III	4	2	2
L-phenylalanine degradation III	4	2	2
atromentin biosynthesis	2	1	1
malate/L-aspartate shuttle pathway	2	1	1
L-tryptophan degradation IV (via indole-3-lactate)	2	1	1
L-tyrosine degradation II	2	1	1
pyruvate fermentation to ethanol II	2	1	1
L-tyrosine biosynthesis I	3	3	1
ethanol degradation II	3	3	1
CDP-4-dehydro-3,6-dideoxy-D-glucose biosynthesis	3	3	1
formaldehyde oxidation II (glutathione-dependent)	3	3	1
L-phenylalanine biosynthesis I	3	3	1
sulfolactate degradation III	3	2	1
L-asparagine degradation III (mammalian)	3	2	1
pyruvate fermentation to ethanol III	3	2	1
pyruvate fermentation to ethanol I	3	2	1
L-valine degradation II	3	2	1
L-leucine degradation III	3	2	1
L-phenylalanine degradation II (anaerobic)	3	2	1
L-isoleucine degradation II	3	2	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
(R)-cysteate degradation	3	1	1
indole-3-acetate biosynthesis VI (bacteria)	3	1	1
L-methionine degradation III	3	1	1
L-histidine degradation I	4	4	1
phytol degradation	4	3	1
superpathway of L-aspartate and L-asparagine biosynthesis	4	3	1
salidroside biosynthesis	4	2	1
L-tryptophan degradation VIII (to tryptophol)	4	1	1
ethanolamine utilization	5	5	1
L-histidine degradation II	5	5	1
L-tyrosine degradation I	5	5	1
acetylene degradation (anaerobic)	5	4	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
protein S-nitrosylation and denitrosylation	5	3	1
trans-4-hydroxy-L-proline degradation I	5	3	1
CDP-6-deoxy-D-gulose biosynthesis	5	3	1
superpathway of plastoquinol biosynthesis	5	2	1
phenylethanol biosynthesis	5	2	1
(S)-propane-1,2-diol degradation	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	4	1
L-histidine degradation III	6	4	1
superpathway of sulfolactate degradation	6	3	1
coenzyme M biosynthesis II	6	1	1
noradrenaline and adrenaline degradation	13	8	2
3-methylbutanol biosynthesis (engineered)	7	6	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	2
serotonin degradation	7	4	1
anaerobic energy metabolism (invertebrates, cytosol)	7	4	1
S-methyl-5-thio-α-D-ribose 1-phosphate degradation I	7	2	1
L-histidine degradation VI	8	7	1
superpathway of CDP-glucose-derived O-antigen building blocks biosynthesis	8	3	1
butanol and isobutanol biosynthesis (engineered)	8	3	1
superpathway of aromatic amino acid biosynthesis	18	18	2
superpathway of L-methionine biosynthesis (transsulfuration)	9	7	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	5	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	2	1
L-methionine salvage cycle III	11	5	1
L-methionine salvage cycle II (plants)	11	3	1
(S)-reticuline biosynthesis I	11	1	1
tropane alkaloids biosynthesis	11	1	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	12	1
superpathway of C1 compounds oxidation to CO2	12	5	1
L-methionine salvage cycle I (bacteria and plants)	12	4	1
indole-3-acetate biosynthesis II	12	4	1
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	5	1
L-tryptophan degradation V (side chain pathway)	13	1	1
superpathway of rosmarinic acid biosynthesis	14	2	1
mixed acid fermentation	16	12	1
superpathway of hyoscyamine (atropine) and scopolamine biosynthesis	16	3	1
superpathway of anaerobic energy metabolism (invertebrates)	17	8	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	7	1
heterolactic fermentation	18	16	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	1
streptomycin biosynthesis	18	3	1
superpathway of anaerobic sucrose degradation	19	15	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	14	1
superpathway of N-acetylneuraminate degradation	22	15	1
aspartate superpathway	25	22	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	4	1
superpathway of chorismate metabolism	59	43	2
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	20	1