Experiment set3IT017 for Pedobacter sp. GW460-11-11-14-LB5

Gly-DL-Asp nitrogen source

Group: nitrogen source
Media: RCH2_defined_Glucose_noNitrogen + Gly-DL-Asp (20 mM), pH=7
Culturing: Pedo557_ML3, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
Growth: about 5.2 generations
By: Adam on 16-May-17
Media components: 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 20 mM D-Glucose, 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: 1748 D5

Specific Phenotypes

For 5 genes in this experiment

For nitrogen source Gly-DL-Asp in Pedobacter sp. GW460-11-11-14-LB5

For nitrogen source Gly-DL-Asp across organisms

SEED Subsystems

Subsystem	#Specific
Acetyl-CoA fermentation to Butyrate	1
Anaerobic respiratory reductases	1
Butanol Biosynthesis	1
Isoleucine degradation	1
Polyhydroxybutyrate metabolism	1
Propionate-CoA to Succinate Module	1
Serine-glyoxylate cycle	1
TCA Cycle	1
Valine degradation	1
n-Phenylalkanoic acid degradation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Butanoate metabolism
• Biosynthesis of plant hormones
• Citrate cycle (TCA cycle)
• Fatty acid elongation in mitochondria
• Fatty acid metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Lysine degradation
• Tryptophan metabolism
• beta-Alanine metabolism
• alpha-Linolenic acid metabolism
• Glyoxylate and dicarboxylate metabolism
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Limonene and pinene degradation
• Caprolactam degradation
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
benzoyl-CoA biosynthesis	3	3	1
glyoxylate cycle	6	4	2
partial TCA cycle (obligate autotrophs)	8	7	2
nitrogen remobilization from senescing leaves	8	6	2
(2S)-ethylmalonyl-CoA biosynthesis	4	2	1
TCA cycle V (2-oxoglutarate synthase)	9	7	2
TCA cycle VI (Helicobacter)	9	7	2
TCA cycle II (plants and fungi)	9	7	2
TCA cycle VII (acetate-producers)	9	6	2
TCA cycle IV (2-oxoglutarate decarboxylase)	9	6	2
superpathway of glyoxylate cycle and fatty acid degradation	14	10	3
2-methyl-branched fatty acid β-oxidation	14	8	3
TCA cycle I (prokaryotic)	10	9	2
TCA cycle III (animals)	10	8	2
fatty acid β-oxidation II (plant peroxisome)	5	4	1
adipate biosynthesis	5	3	1
glutaryl-CoA degradation	5	3	1
adipate degradation	5	3	1
fatty acid β-oxidation IV (unsaturated, even number)	5	1	1
benzoate biosynthesis III (CoA-dependent, non-β-oxidative)	5	1	1
pyruvate fermentation to hexanol (engineered)	11	8	2
reductive TCA cycle I	11	7	2
(8E,10E)-dodeca-8,10-dienol biosynthesis	11	5	2
oleate β-oxidation	35	23	6
superpathway of glyoxylate bypass and TCA	12	9	2
methyl ketone biosynthesis (engineered)	6	4	1
pyruvate fermentation to butanol II (engineered)	6	4	1
fatty acid salvage	6	4	1
L-isoleucine degradation I	6	4	1
propanoate fermentation to 2-methylbutanoate	6	3	1
reductive TCA cycle II	12	5	2
acetyl-CoA fermentation to butanoate	7	4	1
fatty acid β-oxidation VI (mammalian peroxisome)	7	4	1
pyruvate fermentation to butanoate	7	3	1
fatty acid β-oxidation I (generic)	7	3	1
benzoyl-CoA degradation I (aerobic)	7	2	1
mixed acid fermentation	16	12	2
pyruvate fermentation to butanol I	8	3	1
L-valine degradation I	8	3	1
superpathway of Clostridium acetobutylicum acidogenic fermentation	9	5	1
valproate β-oxidation	9	5	1
benzoate biosynthesis I (CoA-dependent, β-oxidative)	9	3	1
phenylacetate degradation I (aerobic)	9	2	1
methylaspartate cycle	19	11	2
L-glutamate degradation V (via hydroxyglutarate)	10	4	1
3-phenylpropanoate degradation	10	3	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	18	2
ethylmalonyl-CoA pathway	11	4	1
gallate degradation III (anaerobic)	11	3	1
superpathway of phenylethylamine degradation	11	2	1
Spodoptera littoralis pheromone biosynthesis	22	3	2
L-glutamate degradation VII (to butanoate)	12	3	1
ethene biosynthesis V (engineered)	25	16	2
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	21	2
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	4	1
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase)	13	3	1
docosahexaenoate biosynthesis III (6-desaturase, mammals)	14	3	1
L-tryptophan degradation III (eukaryotic)	15	5	1
glycerol degradation to butanol	16	9	1
crotonate fermentation (to acetate and cyclohexane carboxylate)	16	3	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	6	1
benzoate fermentation (to acetate and cyclohexane carboxylate)	17	3	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	10	1
toluene degradation VI (anaerobic)	18	3	1
platensimycin biosynthesis	26	6	1
1-butanol autotrophic biosynthesis (engineered)	27	17	1