Experiment set1H37 for Shewanella loihica PV-4

a-Ketoglutaric acid disodium salt hydrate carbon source

Group: carbon source
Media: ShewMM_noCarbon + a-Ketoglutaric acid disodium salt hydrate (20 mM), pH=7
Culturing: PV4_ML1, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 3.3 generations
By: Adam on 12/11/2013
Media components: 1.5 g/L Ammonium chloride, 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, 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 8 genes in this experiment

For carbon source a-Ketoglutaric acid disodium salt hydrate in Shewanella loihica PV-4

For carbon source a-Ketoglutaric acid disodium salt hydrate across organisms

SEED Subsystems

Subsystem	#Specific
Entner-Doudoroff Pathway	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Isobutyryl-CoA to Propionyl-CoA Module	1
Methylglyoxal Metabolism	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	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
• Glycolysis / Gluconeogenesis
• Ascorbate and aldarate metabolism
• Fatty acid metabolism
• Urea cycle and metabolism of amino groups
• Lysine degradation
• Arginine and proline metabolism
• Histidine metabolism
• Tryptophan metabolism
• beta-Alanine metabolism
• Glycerolipid metabolism
• Inositol phosphate metabolism
• Pyruvate metabolism
• 1,2-Dichloroethane degradation
• 3-Chloroacrylic acid degradation
• Butanoate metabolism
• Limonene and pinene degradation

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
β-alanine degradation II	2	2	1
phenylethanol degradation	2	1	1
phenylethylamine degradation I	2	1	1
phenylethylamine degradation II	2	1	1
putrescine degradation I	2	1	1
putrescine degradation V	2	1	1
β-alanine degradation I	2	1	1
ethylene glycol degradation	2	1	1
ethanol degradation IV	3	3	1
ethanol degradation II	3	3	1
L-phenylalanine degradation II (anaerobic)	3	2	1
hypotaurine degradation	3	2	1
putrescine degradation IV	3	2	1
ethanol degradation III	3	2	1
styrene degradation	3	1	1
histamine degradation	3	1	1
phytol degradation	4	3	1
fatty acid α-oxidation I (plants)	4	2	1
putrescine degradation III	4	1	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	1	1
D-arabinose degradation II	4	1	1
mitochondrial NADPH production (yeast)	5	4	1
propanoyl-CoA degradation II	5	3	1
acrylate degradation I	5	3	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
octane oxidation	5	2	1
dopamine degradation	5	1	1
3-methyl-branched fatty acid α-oxidation	6	3	1
alkane oxidation	6	1	1
noradrenaline and adrenaline degradation	13	4	2
superpathway of glycol metabolism and degradation	7	5	1
serotonin degradation	7	3	1
ceramide degradation by α-oxidation	7	2	1
2,4-dinitrotoluene degradation	7	1	1
limonene degradation IV (anaerobic)	7	1	1
myo-inositol degradation I	7	1	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	7	1
superpathway of ornithine degradation	8	6	1
L-valine degradation I	8	6	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
aromatic biogenic amine degradation (bacteria)	8	1	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	5	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	4	1
myo-, chiro- and scyllo-inositol degradation	10	1	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	7	1
superpathway of phenylethylamine degradation	11	4	1
superpathway of L-arginine and L-ornithine degradation	13	9	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	4	1
superpathway of pentose and pentitol degradation	42	6	1