Experiment set3H15 for Shewanella amazonensis SB2B

L-Lysine nitrogen source

Group: nitrogen source
Media: ShewMM_noNitrogen + L-Lysine (20 mM), pH=7
Culturing: SB2B_ML5, 48 well microplate; Tecan Infinite F200, Aerobic, at 37 (C), shaken=orbital
By: Jake on 4/24/2013
Media components: 1.75 g/L Sodium Chloride, 0.61 g/L Magnesium chloride hexahydrate, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 20 mM Sodium D,L-Lactate, 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: 510 D1, D2

Specific Phenotypes

For 13 genes in this experiment

For nitrogen source L-Lysine in Shewanella amazonensis SB2B

For nitrogen source L-Lysine across organisms

SEED Subsystems

Subsystem	#Specific
Arginine and Ornithine Degradation	4
Isoleucine degradation	2
Polyamine Metabolism	2
Valine degradation	2
Acetyl-CoA fermentation to Butyrate	1
Arginine Biosynthesis extended	1
Butanol Biosynthesis	1
Leucine Degradation and HMG-CoA Metabolism	1
Lysine Biosynthesis DAP Pathway	1
Polyhydroxybutyrate metabolism	1
Ribosome biogenesis bacterial	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:

• Fatty acid metabolism
• Arginine and proline metabolism
• Lysine degradation
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• Valine, leucine and isoleucine degradation
• Tryptophan metabolism
• Fatty acid elongation in mitochondria
• Urea cycle and metabolism of amino groups
• Geraniol degradation
• Lysine biosynthesis
• Limonene and pinene degradation
• Caprolactam degradation
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of plant hormones
• Fatty acid biosynthesis
• Bile acid biosynthesis
• Pyrimidine metabolism
• Histidine metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• beta-Alanine metabolism
• Glutathione metabolism
• Lipopolysaccharide biosynthesis
• Glycerophospholipid metabolism
• Ether lipid metabolism
• alpha-Linolenic acid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• 1- and 2-Methylnaphthalene degradation
• Propanoate metabolism
• Ethylbenzene degradation
• Diterpenoid biosynthesis
• Carotenoid biosynthesis - General
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of type II polyketide backbone
• Biosynthesis of terpenoids and steroids

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
fatty acid β-oxidation III (unsaturated, odd number)	1	1	1
benzoyl-CoA biosynthesis	3	3	2
L-arginine degradation II (AST pathway)	5	5	3
fatty acid β-oxidation IV (unsaturated, even number)	5	3	3
fatty acid β-oxidation I (generic)	7	6	4
oleate β-oxidation (thioesterase-dependent, yeast)	2	2	1
pseudouridine degradation	2	1	1
putrescine biosynthesis III	2	1	1
oleate β-oxidation	35	33	16
adipate degradation	5	4	2
adipate biosynthesis	5	3	2
fatty acid β-oxidation II (plant peroxisome)	5	3	2
glutaryl-CoA degradation	5	3	2
fatty acid β-oxidation V (unsaturated, odd number, di-isomerase-dependent)	5	2	2
pyruvate fermentation to hexanol (engineered)	11	7	4
(8E,10E)-dodeca-8,10-dienol biosynthesis	11	6	4
2-methyl-branched fatty acid β-oxidation	14	9	5
2-oxoisovalerate decarboxylation to isobutanoyl-CoA	3	3	1
L-proline biosynthesis III (from L-ornithine)	3	3	1
L-ornithine biosynthesis II	3	3	1
fatty acid salvage	6	5	2
valproate β-oxidation	9	6	3
pyruvate fermentation to butanol II (engineered)	6	4	2
L-isoleucine degradation I	6	4	2
L-arginine degradation I (arginase pathway)	3	2	1
methyl ketone biosynthesis (engineered)	6	3	2
propanoate fermentation to 2-methylbutanoate	6	3	2
oleate β-oxidation (reductase-dependent, yeast)	3	1	1
fatty acid β-oxidation VI (mammalian peroxisome)	7	3	2
pyruvate fermentation to butanoate	7	3	2
benzoyl-CoA degradation I (aerobic)	7	2	2
L-valine degradation I	8	6	2
L-arginine degradation VI (arginase 2 pathway)	4	3	1
superpathway of putrescine biosynthesis	4	2	1
pyruvate fermentation to butanol I	8	3	2
oleate β-oxidation (isomerase-dependent, yeast)	4	1	1
superpathway of Clostridium acetobutylicum acidogenic fermentation	9	5	2
benzoate biosynthesis I (CoA-dependent, β-oxidative)	9	3	2
phenylacetate degradation I (aerobic)	9	2	2
L-ornithine biosynthesis I	5	5	1
(R)- and (S)-3-hydroxybutanoate biosynthesis (engineered)	5	5	1
L-arginine degradation XIII (reductive Stickland reaction)	5	4	1
L-glutamate degradation V (via hydroxyglutarate)	10	5	2
9-cis, 11-trans-octadecadienoyl-CoA degradation (isomerase-dependent, yeast)	10	4	2
3-phenylpropanoate degradation	10	4	2
4-hydroxybenzoate biosynthesis III (plants)	5	2	1
benzoate biosynthesis III (CoA-dependent, non-β-oxidative)	5	1	1
superpathway of phenylethylamine degradation	11	3	2
6-gingerol analog biosynthesis (engineered)	6	2	1
L-glutamate degradation VII (to butanoate)	12	3	2
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	5	2
superpathway of glyoxylate cycle and fatty acid degradation	14	11	2
L-Nδ-acetylornithine biosynthesis	7	5	1
Spodoptera littoralis pheromone biosynthesis	22	4	3
L-tryptophan degradation III (eukaryotic)	15	4	2
L-citrulline biosynthesis	8	7	1
superpathway of ornithine degradation	8	6	1
superpathway of polyamine biosynthesis II	8	6	1
superpathway of polyamine biosynthesis I	8	5	1
glycerol degradation to butanol	16	9	2
2-methylpropene degradation	8	2	1
crotonate fermentation (to acetate and cyclohexane carboxylate)	16	3	2
superpathway of arginine and polyamine biosynthesis	17	14	2
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	7	2
benzoate fermentation (to acetate and cyclohexane carboxylate)	17	3	2
L-arginine biosynthesis I (via L-ornithine)	9	9	1
L-lysine biosynthesis I	9	9	1
L-arginine biosynthesis III (via N-acetyl-L-citrulline)	9	8	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	6	2
toluene degradation VI (anaerobic)	18	3	2
L-arginine biosynthesis II (acetyl cycle)	10	9	1
methyl tert-butyl ether degradation	10	2	1
gallate degradation III (anaerobic)	11	3	1
superpathway of L-citrulline metabolism	12	9	1
10-cis-heptadecenoyl-CoA degradation (yeast)	12	2	1
10-trans-heptadecenoyl-CoA degradation (reductase-dependent, yeast)	12	2	1
androstenedione degradation I (aerobic)	25	6	2
superpathway of L-arginine and L-ornithine degradation	13	8	1
platensimycin biosynthesis	26	6	2
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase)	13	2	1
1-butanol autotrophic biosynthesis (engineered)	27	20	2
androstenedione degradation II (anaerobic)	27	4	2
superpathway of testosterone and androsterone degradation	28	6	2
superpathway of cholesterol degradation I (cholesterol oxidase)	42	8	3
docosahexaenoate biosynthesis III (6-desaturase, mammals)	14	2	1
superpathway of cholesterol degradation II (cholesterol dehydrogenase)	47	8	3
superpathway of hyoscyamine (atropine) and scopolamine biosynthesis	16	3	1
cholesterol degradation to androstenedione I (cholesterol oxidase)	17	2	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	17	1
cholesterol degradation to androstenedione II (cholesterol dehydrogenase)	22	2	1
superpathway of cholesterol degradation III (oxidase)	49	4	2
aspartate superpathway	25	23	1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	21	1