Experiment set2H47 for Shewanella oneidensis MR-1

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Sodium propionate carbon source replicate 1

Group: carbon source
Media: ShewMM_noCarbon + Sodium propionate (10 mM), pH=7
Culturing: MR1_ML3, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 3.6 generations
By: Adam on 8/18/2013
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 38 genes in this experiment

For carbon source Sodium propionate in Shewanella oneidensis MR-1

For carbon source Sodium propionate across organisms

SEED Subsystems

Subsystem #Specific
Proteolysis in bacteria, ATP-dependent 2
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate 2
Serine-glyoxylate cycle 2
Alkylphosphonate utilization 1
Allantoin Utilization 1
Biogenesis of c-type cytochromes 1
CBSS-262719.3.peg.410 1
D-galactarate, D-glucarate and D-glycerate catabolism 1
Flagellum 1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria 1
Glycine Biosynthesis 1
Glycine and Serine Utilization 1
Lactate utilization 1
Methylcitrate cycle 1
Periplasmic disulfide interchange 1
Photorespiration (oxidative C2 cycle) 1
Propionate-CoA to Succinate Module 1
Proteasome bacterial 1
Purine conversions 1
Redox-dependent regulation of nucleus processes 1
Synechocystis experimental 1
Threonine 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
L-threonine degradation III (to methylglyoxal) 3 2 2
L-threonine degradation II 2 2 1
aminopropanol phosphate biosynthesis II 4 2 2
indole-3-acetate biosynthesis IV (bacteria) 2 1 1
indole-3-acetate biosynthesis III (bacteria) 2 1 1
acrylonitrile degradation I 2 1 1
2-O-α-mannosyl-D-glycerate degradation 2 1 1
adenosine ribonucleotides de novo biosynthesis 3 3 1
L-arginine degradation X (arginine monooxygenase pathway) 3 1 1
superpathway of acrylonitrile degradation 3 1 1
glycolate and glyoxylate degradation I 4 3 1
D-glucarate degradation I 4 2 1
D-galactarate degradation I 4 2 1
2-methylcitrate cycle I 5 5 1
superpathway of adenosine nucleotides de novo biosynthesis I 5 5 1
superpathway of D-glucarate and D-galactarate degradation 5 2 1
glyoxylate cycle 6 6 1
2-methylcitrate cycle II 6 5 1
superpathway of adenosine nucleotides de novo biosynthesis II 7 7 1
superpathway of glycol metabolism and degradation 7 5 1
2-deoxy-D-ribose degradation II 8 4 1
superpathway of L-threonine metabolism 18 15 2
photorespiration I 9 7 1
photorespiration III 9 7 1
Entner-Doudoroff pathway II (non-phosphorylative) 9 5 1
photorespiration II 10 8 1
peptidoglycan recycling II 10 4 1
superpathway of glyoxylate bypass and TCA 12 10 1
indole-3-acetate biosynthesis II 12 3 1
formaldehyde assimilation I (serine pathway) 13 8 1
superpathway of purine nucleotide salvage 14 13 1
superpathway of glyoxylate cycle and fatty acid degradation 14 11 1
peptidoglycan recycling I 14 9 1
superpathway of purine nucleotides de novo biosynthesis I 21 21 1
superpathway of purine nucleotides de novo biosynthesis II 26 26 1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass 26 22 1
superpathway of microbial D-galacturonate and D-glucuronate degradation 31 6 1
superpathway of histidine, purine, and pyrimidine biosynthesis 46 46 1