Experiment set9IT074 for Sinorhizobium meliloti 1021

5-Aminovaleric acid carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + 5-Aminovaleric acid (10 mM)
Culturing: Smeli_ML6_JBEI, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=200 rpm
By: Catharine Adams on 11/8/20
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)

Specific Phenotypes

For 5 genes in this experiment

For carbon source 5-Aminovaleric acid in Sinorhizobium meliloti 1021

For carbon source 5-Aminovaleric acid across organisms

SEED Subsystems

Subsystem	#Specific
Serine-glyoxylate cycle	2
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	1
Acetyl-CoA fermentation to Butyrate	1
Archaeal lipids	1
Butanol Biosynthesis	1
Isobutyryl-CoA to Propionyl-CoA Module	1
Isoprenoid Biosynthesis	1
MLST	1
Polyhydroxybutyrate metabolism	1
Valine degradation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Valine, leucine and isoleucine degradation
• Propanoate metabolism
• Fatty acid metabolism
• Inositol phosphate metabolism
• Fatty acid elongation in mitochondria
• Synthesis and degradation of ketone bodies
• Alanine and aspartate metabolism
• Geraniol degradation
• Lysine degradation
• Benzoate degradation via hydroxylation
• Tryptophan metabolism
• beta-Alanine metabolism
• alpha-Linolenic acid metabolism
• Pyruvate metabolism
• Glyoxylate and dicarboxylate metabolism
• Benzoate degradation via CoA ligation
• Ethylbenzene degradation
• Butanoate metabolism
• Terpenoid biosynthesis
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
acetoacetate degradation (to acetyl CoA)	2	2	1
β-alanine degradation II	2	2	1
β-alanine degradation I	2	1	1
5,6-dehydrokavain biosynthesis (engineered)	10	6	4
polyhydroxybutanoate biosynthesis	3	3	1
benzoyl-CoA biosynthesis	3	3	1
ketolysis	3	2	1
(2S)-ethylmalonyl-CoA biosynthesis	4	3	1
oleate β-oxidation	35	29	8
valproate β-oxidation	9	5	2
2-methyl-branched fatty acid β-oxidation	14	9	3
(R)- and (S)-3-hydroxybutanoate biosynthesis (engineered)	5	5	1
acrylate degradation I	5	4	1
propanoyl-CoA degradation II	5	4	1
ketogenesis	5	3	1
glutaryl-CoA degradation	5	3	1
fatty acid β-oxidation II (plant peroxisome)	5	3	1
9-cis, 11-trans-octadecadienoyl-CoA degradation (isomerase-dependent, yeast)	10	4	2
pyruvate fermentation to acetone	5	2	1
4-hydroxybenzoate biosynthesis III (plants)	5	2	1
ethylbenzene degradation (anaerobic)	5	1	1
fatty acid β-oxidation VII (yeast peroxisome)	5	1	1
isopropanol biosynthesis (engineered)	5	1	1
pyruvate fermentation to hexanol (engineered)	11	7	2
glyoxylate cycle	6	6	1
fatty acid salvage	6	5	1
pyruvate fermentation to butanol II (engineered)	6	4	1
L-isoleucine degradation I	6	4	1
propanoate fermentation to 2-methylbutanoate	6	3	1
4-ethylphenol degradation (anaerobic)	6	2	1
10-trans-heptadecenoyl-CoA degradation (MFE-dependent, yeast)	6	1	1
jasmonic acid biosynthesis	19	4	3
myo-inositol degradation I	7	7	1
superpathway of glyoxylate cycle and fatty acid degradation	14	12	2
acetyl-CoA fermentation to butanoate	7	6	1
fatty acid β-oxidation I (generic)	7	5	1
pyruvate fermentation to butanoate	7	3	1
fatty acid β-oxidation VI (mammalian peroxisome)	7	3	1
2,4-dinitrotoluene degradation	7	1	1
mevalonate pathway II (haloarchaea)	7	1	1
mevalonate pathway I (eukaryotes and bacteria)	7	1	1
L-valine degradation I	8	5	1
pyruvate fermentation to butanol I	8	4	1
2-deoxy-D-ribose degradation II	8	3	1
2-methylpropene degradation	8	2	1
mevalonate pathway IV (archaea)	8	1	1
mevalonate pathway III (Thermoplasma)	8	1	1
isoprene biosynthesis II (engineered)	8	1	1
androstenedione degradation I (aerobic)	25	6	3
superpathway of Clostridium acetobutylicum acidogenic fermentation	9	5	1
benzoate biosynthesis I (CoA-dependent, β-oxidative)	9	3	1
4-oxopentanoate degradation	9	2	1
superpathway of testosterone and androsterone degradation	28	6	3
myo-, chiro- and scyllo-inositol degradation	10	7	1
L-glutamate degradation V (via hydroxyglutarate)	10	6	1
superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate)	10	4	1
3-phenylpropanoate degradation	10	4	1
L-lysine fermentation to acetate and butanoate	10	3	1
methyl tert-butyl ether degradation	10	2	1
superpathway of cholesterol degradation I (cholesterol oxidase)	42	8	4
(8E,10E)-dodeca-8,10-dienol biosynthesis	11	6	1
ethylmalonyl-CoA pathway	11	4	1
superpathway of cholesterol degradation II (cholesterol dehydrogenase)	47	8	4
superpathway of glyoxylate bypass and TCA	12	11	1
L-glutamate degradation VII (to butanoate)	12	4	1
10-trans-heptadecenoyl-CoA degradation (reductase-dependent, yeast)	12	2	1
10-cis-heptadecenoyl-CoA degradation (yeast)	12	2	1
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	6	1
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase)	13	2	1
androstenedione degradation II (anaerobic)	27	4	2
docosahexaenoate biosynthesis III (6-desaturase, mammals)	14	2	1
L-tryptophan degradation III (eukaryotic)	15	3	1
glycerol degradation to butanol	16	12	1
crotonate fermentation (to acetate and cyclohexane carboxylate)	16	3	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	8	1
benzoate fermentation (to acetate and cyclohexane carboxylate)	17	3	1
cholesterol degradation to androstenedione I (cholesterol oxidase)	17	2	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	10	1
toluene degradation VI (anaerobic)	18	3	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	22	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	22	1
platensimycin biosynthesis	26	6	1
superpathway of ergosterol biosynthesis I	26	3	1
1-butanol autotrophic biosynthesis (engineered)	27	21	1
superpathway of cholesterol biosynthesis	38	3	1
superpathway of L-lysine degradation	43	15	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	20	1