Experiment set2H37 for Shewanella amazonensis SB2B

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Minimal media with Thymidine as carbon source

Group: carbon source
Media: ShewMM_noCarbon + Thymidine (10 mM), pH=7
Culturing: SB2B_ML5, 48 well microplate; Tecan Infinite F200, Aerobic, at 37 (C), shaken=orbital
By: Jake on 4/15/2013
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)
Growth plate: 508 B3,B4

Specific Phenotypes

For 5 genes in this experiment

For carbon source Thymidine in Shewanella amazonensis SB2B

For carbon source Thymidine across organisms

SEED Subsystems

Subsystem #Specific
Chitin and N-acetylglucosamine utilization 1
Entner-Doudoroff Pathway 1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria 1
Methylglyoxal Metabolism 1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate 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
putrescine degradation V 2 2 1
phenylethylamine degradation II 2 1 1
ethylene glycol degradation 2 1 1
phenylethylamine degradation I 2 1 1
putrescine degradation I 2 1 1
phenylethanol degradation 2 1 1
ethanol degradation IV 3 3 1
ethanol degradation II 3 3 1
hypotaurine degradation 3 2 1
NAD salvage pathway III (to nicotinamide riboside) 3 2 1
ethanol degradation III 3 2 1
L-phenylalanine degradation II (anaerobic) 3 2 1
putrescine degradation IV 3 2 1
histamine degradation 3 1 1
styrene degradation 3 1 1
UTP and CTP dephosphorylation I 7 5 2
purine nucleotides degradation II (aerobic) 11 8 3
phytol degradation 4 3 1
inosine 5'-phosphate degradation 4 3 1
fatty acid α-oxidation I (plants) 4 2 1
guanosine nucleotides degradation III 4 2 1
adenosine nucleotides degradation I 8 3 2
purine nucleotides degradation I (plants) 12 4 3
L-tryptophan degradation X (mammalian, via tryptamine) 4 1 1
putrescine degradation III 4 1 1
D-arabinose degradation II 4 1 1
guanosine nucleotides degradation II 4 1 1
guanosine nucleotides degradation I 4 1 1
mitochondrial NADPH production (yeast) 5 3 1
adenosine nucleotides degradation II 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
superpathway of purines degradation in plants 18 4 3
superpathway of guanosine nucleotides degradation (plants) 6 1 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
ureide biosynthesis 7 3 1
ceramide degradation by α-oxidation 7 2 1
limonene degradation IV (anaerobic) 7 1 1
superpathway of ornithine degradation 8 6 1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast) 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 3 1
tunicamycin biosynthesis 9 1 1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation 11 6 1
superpathway of phenylethylamine degradation 11 3 1
NAD salvage (plants) 11 3 1
superpathway of L-arginine and L-ornithine degradation 13 8 1
anaerobic aromatic compound degradation (Thauera aromatica) 27 2 1
superpathway of pentose and pentitol degradation 42 6 1