Experiment set3IT070 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 16 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	3
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Histidine Degradation	1
Methionine Salvage	1
Terminal cytochrome C oxidases	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
• Alkaloid biosynthesis I
• Histidine metabolism
• Phenylalanine metabolism
• Methane metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Ubiquinone and menaquinone biosynthesis
• Methionine metabolism
• Tryptophan metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Carotenoid biosynthesis - General
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Alkaloid biosynthesis II
• Biosynthesis of plant hormones
• Glycolysis / Gluconeogenesis
• Fatty acid metabolism
• Oxidative phosphorylation
• 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
• Benzoxazinone biosynthesis
• Cyanoamino acid metabolism
• Toluene and xylene degradation
• 2,4-Dichlorobenzoate degradation
• 1,4-Dichlorobenzene degradation
• Benzoate degradation via CoA ligation
• 3-Chloroacrylic acid degradation
• Styrene degradation
• Carbon fixation in photosynthetic organisms
• Retinol metabolism
• Porphyrin and chlorophyll metabolism
• Limonene and pinene degradation
• Brassinosteroid biosynthesis
• Anthocyanin biosynthesis
• Isoflavonoid biosynthesis
• Metabolism of xenobiotics by cytochrome P450
• Insect hormone biosynthesis
• 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
3-methylthiopropanoate biosynthesis	1	1	1
acetaldehyde biosynthesis I	1	1	1
L-aspartate biosynthesis	1	1	1
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
L-aspartate degradation I	1	1	1
formaldehyde oxidation II (glutathione-dependent)	3	3	2
ethanol degradation I	2	2	1
L-phenylalanine biosynthesis III (cytosolic, plants)	2	2	1
L-glutamate degradation II	2	2	1
vanillin and vanillate degradation II	2	2	1
L-phenylalanine degradation III	4	2	2
L-tyrosine degradation III	4	2	2
arsenite to oxygen electron transfer	2	1	1
L-tryptophan degradation IV (via indole-3-lactate)	2	1	1
pyruvate fermentation to ethanol II	2	1	1
malate/L-aspartate shuttle pathway	2	1	1
atromentin biosynthesis	2	1	1
L-tyrosine degradation II	2	1	1
ethanol degradation II	3	3	1
L-tyrosine biosynthesis I	3	3	1
L-phenylalanine biosynthesis I	3	3	1
methylglyoxal degradation I	3	2	1
sulfolactate degradation III	3	2	1
pyruvate fermentation to ethanol I	3	2	1
methylglyoxal degradation VIII	3	2	1
pyruvate fermentation to ethanol III	3	2	1
L-valine degradation II	3	2	1
L-phenylalanine degradation II (anaerobic)	3	2	1
L-isoleucine degradation II	3	2	1
L-leucine degradation III	3	2	1
L-asparagine degradation III (mammalian)	3	2	1
L-methionine degradation III	3	1	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
arsenite to oxygen electron transfer (via azurin)	3	1	1
indole-3-acetate biosynthesis VI (bacteria)	3	1	1
(R)-cysteate degradation	3	1	1
L-histidine degradation I	4	4	1
superpathway of L-aspartate and L-asparagine biosynthesis	4	3	1
aerobic respiration II (cytochrome c) (yeast)	4	3	1
aerobic respiration I (cytochrome c)	4	3	1
phytol degradation	4	3	1
salidroside biosynthesis	4	2	1
L-tryptophan degradation VIII (to tryptophol)	4	1	1
L-tyrosine degradation I	5	5	1
L-histidine degradation II	5	5	1
ethanolamine utilization	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
(S)-propane-1,2-diol degradation	5	2	1
phenylethanol biosynthesis	5	2	1
superpathway of plastoquinol biosynthesis	5	2	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
L-tryptophan degradation XIII (reductive Stickland reaction)	5	1	1
L-phenylalanine degradation VI (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
L-histidine degradation III	6	4	1
TCA cycle VIII (Chlamydia)	6	4	1
Fe(II) oxidation	6	3	1
superpathway of sulfolactate degradation	6	3	1
superpathway of C1 compounds oxidation to CO2	12	5	2
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 methylglyoxal degradation	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
tropane alkaloids biosynthesis	11	1	1
(S)-reticuline biosynthesis I	11	1	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	12	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
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