Experiment set3IT010 for Pedobacter sp. GW460-11-11-14-LB5

Glycine nitrogen source

Group: nitrogen source
Media: RCH2_defined_Glucose_noNitrogen + Glycine (20 mM), pH=7
Culturing: Pedo557_ML3, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
Growth: about 4.5 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 B5

Specific Phenotypes

For 8 genes in this experiment

For nitrogen source Glycine in Pedobacter sp. GW460-11-11-14-LB5

For nitrogen source Glycine across organisms

SEED Subsystems

Subsystem	#Specific
Acetyl-CoA fermentation to Butyrate	1
Butanol Biosynthesis	1
DNA-binding regulatory proteins, strays	1
Folate Biosynthesis	1
Isoleucine degradation	1
One-carbon metabolism by tetrahydropterines	1
Oxidative stress	1
Polyhydroxybutyrate metabolism	1
Serine-glyoxylate cycle	1
Thioredoxin-disulfide reductase	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
• 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
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• One carbon pool by folate
• Limonene and pinene degradation
• Caprolactam degradation
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
benzoyl-CoA biosynthesis	3	3	1
(2S)-ethylmalonyl-CoA biosynthesis	4	2	1
2-methyl-branched fatty acid β-oxidation	14	8	3
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
(8E,10E)-dodeca-8,10-dienol biosynthesis	11	5	2
oleate β-oxidation	35	23	6
methyl ketone biosynthesis (engineered)	6	4	1
L-isoleucine degradation I	6	4	1
pyruvate fermentation to butanol II (engineered)	6	4	1
fatty acid salvage	6	4	1
propanoate fermentation to 2-methylbutanoate	6	3	1
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
pyruvate fermentation to butanol I	8	3	1
L-valine degradation I	8	3	1
folate transformations III (E. coli)	9	8	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
L-glutamate degradation V (via hydroxyglutarate)	10	4	1
3-phenylpropanoate degradation	10	3	1
folate transformations II (plants)	11	9	1
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
folate transformations I	13	8	1
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	4	1
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase)	13	3	1
superpathway of glyoxylate cycle and fatty acid degradation	14	10	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