Experiment set6IT087 for Herbaspirillum seropedicae SmR1

Carbon source Phenylacetic acid 5 mM

Group: carbon source
Media: RCH2_defined_noCarbon + Phenylacetic acid (5 mM), pH=7
Culturing: HerbieS_ML4a, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
By: Adam on 5/2/18
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 30 mM PIPES sesquisodium salt, Wolfe's mineral mix (0.03 g/L Magnesium Sulfate Heptahydrate, 0.015 g/L Nitrilotriacetic acid, 0.01 g/L Sodium Chloride, 0.005 g/L Manganese (II) sulfate monohydrate, 0.001 g/L Cobalt chloride hexahydrate, 0.001 g/L Zinc sulfate heptahydrate, 0.001 g/L Calcium chloride dihydrate, 0.001 g/L Iron (II) sulfate heptahydrate, 0.00025 g/L Nickel (II) chloride hexahydrate, 0.0002 g/L Aluminum potassium sulfate dodecahydrate, 0.0001 g/L Copper (II) sulfate pentahydrate, 0.0001 g/L Boric Acid, 0.0001 g/L Sodium Molybdate Dihydrate, 0.003 mg/L Sodium selenite pentahydrate), Wolfe's vitamin mix (0.1 mg/L Pyridoxine HCl, 0.05 mg/L 4-Aminobenzoic acid, 0.05 mg/L Lipoic acid, 0.05 mg/L Nicotinic Acid, 0.05 mg/L Riboflavin, 0.05 mg/L Thiamine HCl, 0.05 mg/L calcium pantothenate, 0.02 mg/L biotin, 0.02 mg/L Folic Acid, 0.001 mg/L Cyanocobalamin)
Growth plate: HerbieS_plate B2

Specific Phenotypes

For 17 genes in this experiment

For carbon source Phenylacetic acid in Herbaspirillum seropedicae SmR1

For carbon source Phenylacetic acid across organisms

SEED Subsystems

Subsystem	#Specific
Acetyl-CoA fermentation to Butyrate	2
Aromatic Amin Catabolism	2
Butanol Biosynthesis	2
Isoleucine degradation	2
Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria	2
Polyhydroxybutyrate metabolism	2
Valine degradation	2
n-Phenylalkanoic acid degradation	2
Aromatic amino acid interconversions with aryl acids	1
Multidrug Resistance Efflux Pumps	1
NAD and NADP cofactor biosynthesis global	1
NAD regulation	1
Redox-dependent regulation of nucleus processes	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Butanoate metabolism
• Benzoate degradation via CoA ligation
• Fatty acid metabolism
• Valine, leucine and isoleucine degradation
• Lysine degradation
• Biosynthesis of unsaturated fatty acids
• Tryptophan metabolism
• Propanoate metabolism
• Limonene and pinene degradation
• Ascorbate and aldarate metabolism
• Fatty acid elongation in mitochondria
• Geraniol degradation
• Histidine metabolism
• Phenylalanine metabolism
• Benzoate degradation via hydroxylation
• beta-Alanine metabolism
• alpha-Linolenic acid metabolism
• Pyruvate metabolism
• Ethylbenzene degradation
• Alkaloid biosynthesis I
• Biosynthesis of plant hormones
• Glycolysis / Gluconeogenesis
• Fructose and mannose metabolism
• Fatty acid biosynthesis
• Synthesis and degradation of ketone bodies
• C21-Steroid hormone metabolism
• Urea cycle and metabolism of amino groups
• Glycine, serine and threonine metabolism
• Arginine and proline metabolism
• Tyrosine metabolism
• Bisphenol A degradation
• Nucleotide sugars metabolism
• Polyketide sugar unit biosynthesis
• Aminosugars metabolism
• Lipopolysaccharide biosynthesis
• Glycerolipid metabolism
• Glycerophospholipid metabolism
• Ether lipid metabolism
• Linoleic acid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• 1- and 2-Methylnaphthalene degradation
• Tetrachloroethene degradation
• 1,2-Dichloroethane degradation
• 3-Chloroacrylic acid degradation
• Nicotinate and nicotinamide metabolism
• Retinol metabolism
• Terpenoid biosynthesis
• Diterpenoid biosynthesis
• Carotenoid biosynthesis - General
• Caprolactam degradation
• Anthocyanin biosynthesis
• Alkaloid biosynthesis II
• Insect hormone biosynthesis
• Biosynthesis of type II polyketide backbone
• Biosynthesis of type II polyketide products
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
phenylacetate degradation I (aerobic)	9	9	7
benzoyl-CoA biosynthesis	3	3	2
superpathway of phenylethylamine degradation	11	11	7
3-oxoadipate degradation	2	2	1
acetoacetate degradation (to acetyl CoA)	2	1	1
2-methyl-branched fatty acid β-oxidation	14	9	6
adipate degradation	5	5	2
oleate β-oxidation	35	31	14
adipate biosynthesis	5	4	2
5,6-dehydrokavain biosynthesis (engineered)	10	6	4
fatty acid β-oxidation II (plant peroxisome)	5	3	2
glutaryl-CoA degradation	5	3	2
pyruvate fermentation to hexanol (engineered)	11	7	4
ethanol degradation IV	3	3	1
ketolysis	3	3	1
polyhydroxybutanoate biosynthesis	3	3	1
ethanol degradation II	3	3	1
fatty acid salvage	6	5	2
pyruvate fermentation to butanol II (engineered)	6	4	2
L-isoleucine degradation I	6	4	2
ethanol degradation III	3	2	1
hypotaurine degradation	3	2	1
valproate β-oxidation	9	5	3
propanoate fermentation to 2-methylbutanoate	6	3	2
histamine degradation	3	1	1
fatty acid β-oxidation I (generic)	7	5	2
pyruvate fermentation to butanoate	7	4	2
benzoyl-CoA degradation I (aerobic)	7	3	2
fatty acid β-oxidation VI (mammalian peroxisome)	7	3	2
(8E,10E)-dodeca-8,10-dienol biosynthesis	11	6	3
phytol degradation	4	3	1
pyruvate fermentation to butanol I	8	4	2
(2S)-ethylmalonyl-CoA biosynthesis	4	2	1
fatty acid α-oxidation I (plants)	4	2	1
penicillin G and penicillin V biosynthesis	4	1	1
phenylacetate degradation II (anaerobic)	4	1	1
putrescine degradation III	4	1	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	1	1
superpathway of Clostridium acetobutylicum acidogenic fermentation	9	6	2
benzoate biosynthesis I (CoA-dependent, β-oxidative)	9	3	2
4-hydroxybenzoate biosynthesis III (plants)	5	5	1
NAD salvage pathway V (PNC V cycle)	5	4	1
ketogenesis	5	3	1
mitochondrial NADPH production (yeast)	5	3	1
(R)- and (S)-3-hydroxybutanoate biosynthesis (engineered)	5	3	1
octane oxidation	5	3	1
3-phenylpropanoate degradation	10	5	2
9-cis, 11-trans-octadecadienoyl-CoA degradation (isomerase-dependent, yeast)	10	4	2
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
L-glutamate degradation V (via hydroxyglutarate)	10	4	2
benzoate biosynthesis III (CoA-dependent, non-β-oxidative)	5	2	1
fatty acid β-oxidation IV (unsaturated, even number)	5	2	1
dopamine degradation	5	1	1
pyruvate fermentation to acetone	5	1	1
fatty acid β-oxidation VII (yeast peroxisome)	5	1	1
ethylbenzene degradation (anaerobic)	5	1	1
isopropanol biosynthesis (engineered)	5	1	1
catechol degradation III (ortho-cleavage pathway)	6	6	1
methyl ketone biosynthesis (engineered)	6	3	1
3-methyl-branched fatty acid α-oxidation	6	3	1
L-glutamate degradation VII (to butanoate)	12	4	2
4-ethylphenol degradation (anaerobic)	6	2	1
alkane oxidation	6	1	1
10-trans-heptadecenoyl-CoA degradation (MFE-dependent, yeast)	6	1	1
jasmonic acid biosynthesis	19	5	3
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	5	2
noradrenaline and adrenaline degradation	13	4	2
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase)	13	2	2
superpathway of salicylate degradation	7	7	1
NAD salvage pathway I (PNC VI cycle)	7	6	1
superpathway of glyoxylate cycle and fatty acid degradation	14	10	2
acetyl-CoA fermentation to butanoate	7	4	1
4-methylcatechol degradation (ortho cleavage)	7	4	1
serotonin degradation	7	3	1
mevalonate pathway II (haloarchaea)	7	2	1
mevalonate pathway I (eukaryotes and bacteria)	7	2	1
ceramide degradation by α-oxidation	7	2	1
docosahexaenoate biosynthesis III (6-desaturase, mammals)	14	2	2
limonene degradation IV (anaerobic)	7	1	1
L-tryptophan degradation III (eukaryotic)	15	3	2
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	6	1
glycerol degradation to butanol	16	10	2
L-valine degradation I	8	5	1
2-deoxy-D-ribose degradation II	8	4	1
aromatic biogenic amine degradation (bacteria)	8	3	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
isoprene biosynthesis II (engineered)	8	2	1
2-methylpropene degradation	8	2	1
mevalonate pathway III (Thermoplasma)	8	2	1
mevalonate pathway IV (archaea)	8	2	1
crotonate fermentation (to acetate and cyclohexane carboxylate)	16	3	2
androstenedione degradation I (aerobic)	25	6	3
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	8	2
benzoate fermentation (to acetate and cyclohexane carboxylate)	17	3	2
aromatic compounds degradation via β-ketoadipate	9	9	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	5	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	8	2
4-oxopentanoate degradation	9	2	1
toluene degradation VI (anaerobic)	18	3	2
superpathway of testosterone and androsterone degradation	28	7	3
superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate)	10	5	1
methyl tert-butyl ether degradation	10	3	1
L-lysine fermentation to acetate and butanoate	10	3	1
superpathway of cholesterol degradation I (cholesterol oxidase)	42	8	4
toluene degradation III (aerobic) (via p-cresol)	11	7	1
NAD salvage (plants)	11	6	1
gallate degradation III (anaerobic)	11	3	1
Spodoptera littoralis pheromone biosynthesis	22	4	2
ethylmalonyl-CoA pathway	11	2	1
superpathway of cholesterol degradation II (cholesterol dehydrogenase)	47	8	4
10-cis-heptadecenoyl-CoA degradation (yeast)	12	2	1
10-trans-heptadecenoyl-CoA degradation (reductase-dependent, yeast)	12	2	1
platensimycin biosynthesis	26	6	2
1-butanol autotrophic biosynthesis (engineered)	27	18	2
androstenedione degradation II (anaerobic)	27	4	2
superpathway of NAD biosynthesis in eukaryotes	14	7	1
cholesterol degradation to androstenedione I (cholesterol oxidase)	17	2	1
mandelate degradation to acetyl-CoA	18	13	1
sitosterol degradation to androstenedione	18	1	1
cholesterol degradation to androstenedione II (cholesterol dehydrogenase)	22	2	1
superpathway of cholesterol degradation III (oxidase)	49	4	2
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	17	1
superpathway of ergosterol biosynthesis I	26	6	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	3	1
superpathway of aerobic toluene degradation	30	12	1
superpathway of aromatic compound degradation via 3-oxoadipate	35	21	1
superpathway of cholesterol biosynthesis	38	6	1
superpathway of L-lysine degradation	43	8	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	21	1