Experiment set9IT080 for Sinorhizobium meliloti 1021

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Protocatechuic Acid carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + Protocatechuic 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 12 genes in this experiment

For carbon source Protocatechuic Acid in Sinorhizobium meliloti 1021

For carbon source Protocatechuic Acid across organisms

SEED Subsystems

Subsystem #Specific
Protocatechuate branch of beta-ketoadipate pathway 3
Ammonia assimilation 1
Catechol branch of beta-ketoadipate pathway 1
Chloroaromatic degradation pathway 1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis 1
Glutamine synthetases 1
Nudix proteins (nucleoside triphosphate hydrolases) 1
Peptidoglycan Biosynthesis 1
Protein degradation 1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway #Steps #Present #Specific
3-oxoadipate degradation 2 2 2
L-glutamine biosynthesis I 1 1 1
protocatechuate degradation II (ortho-cleavage pathway) 4 4 2
ammonia assimilation cycle I 2 2 1
acetoacetate degradation (to acetyl CoA) 2 2 1
catechol degradation III (ortho-cleavage pathway) 6 4 3
ammonia assimilation cycle II 2 1 1
aromatic compounds degradation via β-ketoadipate 9 7 4
superpathway of salicylate degradation 7 5 3
4-methylcatechol degradation (ortho cleavage) 7 3 3
5,6-dehydrokavain biosynthesis (engineered) 10 6 4
toluene degradation III (aerobic) (via p-cresol) 11 7 4
polyhydroxybutanoate biosynthesis 3 3 1
benzoyl-CoA biosynthesis 3 3 1
ammonia assimilation cycle III 3 3 1
superpathway of ammonia assimilation (plants) 3 2 1
ketolysis 3 2 1
NAD salvage pathway III (to nicotinamide riboside) 3 2 1
L-aspartate degradation III (anaerobic) 3 1 1
L-aspartate degradation II (aerobic) 3 1 1
Arg/N-end rule pathway (eukaryotic) 14 8 4
(2S)-ethylmalonyl-CoA biosynthesis 4 3 1
catechol degradation to β-ketoadipate 4 2 1
4-sulfocatechol degradation 4 1 1
oleate β-oxidation 35 29 8
valproate β-oxidation 9 5 2
2-methyl-branched fatty acid β-oxidation 14 9 3
NAD salvage pathway II (PNC IV cycle) 5 5 1
(R)- and (S)-3-hydroxybutanoate biosynthesis (engineered) 5 5 1
adipate degradation 5 5 1
gallate degradation II 5 4 1
adipate biosynthesis 5 4 1
L-glutamate degradation V (via hydroxyglutarate) 10 6 2
glutaryl-CoA degradation 5 3 1
ketogenesis 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
isopropanol biosynthesis (engineered) 5 1 1
ethylbenzene degradation (anaerobic) 5 1 1
fatty acid β-oxidation VII (yeast peroxisome) 5 1 1
pyruvate fermentation to hexanol (engineered) 11 7 2
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
mandelate degradation to acetyl-CoA 18 5 3
10-trans-heptadecenoyl-CoA degradation (MFE-dependent, yeast) 6 1 1
jasmonic acid biosynthesis 19 4 3
acetyl-CoA fermentation to butanoate 7 6 1
NAD salvage pathway I (PNC VI cycle) 7 6 1
L-glutamate and L-glutamine biosynthesis 7 5 1
fatty acid β-oxidation I (generic) 7 5 1
benzoyl-CoA degradation I (aerobic) 7 3 1
pyruvate fermentation to butanoate 7 3 1
L-glutamate degradation XI (reductive Stickland reaction) 7 3 1
fatty acid β-oxidation VI (mammalian peroxisome) 7 3 1
mevalonate pathway II (haloarchaea) 7 1 1
mevalonate pathway I (eukaryotes and bacteria) 7 1 1
superpathway of aerobic toluene degradation 30 9 4
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 aromatic compound degradation via 3-oxoadipate 35 10 4
phenylacetate degradation I (aerobic) 9 5 1
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
L-arginine biosynthesis II (acetyl cycle) 10 10 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
NAD salvage (plants) 11 7 1
superpathway of phenylethylamine degradation 11 6 1
(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
L-glutamate degradation VII (to butanoate) 12 4 1
10-cis-heptadecenoyl-CoA degradation (yeast) 12 2 1
10-trans-heptadecenoyl-CoA degradation (reductase-dependent, 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
superpathway of glyoxylate cycle and fatty acid degradation 14 12 1
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
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