Experiment set5H25 for Shewanella oneidensis MR-1

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L-Alanine nitrogen source

Group: nitrogen source
Media: ShewMM_noNitrogen + L-Alanine (10 mM), pH=7
Culturing: MR1_ML3, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 4.6 generations
By: Adam on 8/21/2013
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)

Specific Phenotypes

For 42 genes in this experiment

For nitrogen source L-Alanine in Shewanella oneidensis MR-1

For nitrogen source L-Alanine across organisms

SEED Subsystems

Subsystem #Specific
Cysteine Biosynthesis 3
Ammonia assimilation 1
CBSS-262719.3.peg.410 1
Carboxysome 1
DNA repair, bacterial DinG and relatives 1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis 1
Heat shock dnaK gene cluster extended 1
MukBEF Chromosome Condensation 1
Proteasome bacterial 1
Proteolysis in bacteria, ATP-dependent 1
Purine conversions 1
Queuosine-Archaeosine Biosynthesis 1
Respiratory dehydrogenases 1 1
Ribosomal protein S12p Asp methylthiotransferase 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-glutamate biosynthesis I 2 2 2
L-glutamine degradation I 1 1 1
L-glutamine degradation II 1 1 1
ammonia assimilation cycle III 3 3 2
NADH to cytochrome bd oxidase electron transfer I 2 2 1
NADH to cytochrome bd oxidase electron transfer II 2 2 1
NADH to cytochrome aa3 oxidase electron transfer 2 1 1
NADH to nitrate electron transfer 2 1 1
NADH to cytochrome bo oxidase electron transfer II 2 1 1
NADH to cytochrome bo oxidase electron transfer I 2 1 1
nitrate reduction VIIIb (dissimilatory) 2 1 1
adenosine ribonucleotides de novo biosynthesis 3 3 1
5-(methoxycarbonylmethoxy)uridine biosynthesis 3 3 1
aerobic respiration III (alternative oxidase pathway) 3 2 1
molybdenum cofactor biosynthesis 3 2 1
L-glutamate and L-glutamine biosynthesis 7 6 2
queuosine biosynthesis I (de novo) 4 4 1
aerobic respiration I (cytochrome c) 4 3 1
aerobic respiration II (cytochrome c) (yeast) 4 3 1
L-asparagine biosynthesis III (tRNA-dependent) 4 1 1
glutaminyl-tRNAgln biosynthesis via transamidation 4 1 1
superpathway of adenosine nucleotides de novo biosynthesis I 5 5 1
queuosine biosynthesis III (queuosine salvage) 5 3 1
mitochondrial NADPH production (yeast) 5 3 1
NAD(P)/NADPH interconversion 6 3 1
Fe(II) oxidation 6 3 1
superpathway of adenosine nucleotides de novo biosynthesis II 7 7 1
L-citrulline biosynthesis 8 7 1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast) 8 5 1
superpathway of L-citrulline metabolism 12 9 1
superpathway of purine nucleotide salvage 14 13 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 histidine, purine, and pyrimidine biosynthesis 46 46 1