Experiment set2H23 for Pseudomonas stutzeri RCH2

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L-Alanine nitrogen source

Group: nitrogen source
Media: RCH2_defined_noNitrogen + L-Alanine (5 mM), pH=7.2
Culturing: psRCH2_ML7, 48 well microplate; Tecan Infinite F200, Aerobic, at 30 (C), shaken=orbital
By: Kelly on 6/20/2013
Media components: 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: 552 B5,B6

Specific Phenotypes

For 13 genes in this experiment

For nitrogen source L-Alanine in Pseudomonas stutzeri RCH2

For nitrogen source L-Alanine across organisms

SEED Subsystems

Subsystem #Specific
Polyamine Metabolism 4
Arginine and Ornithine Degradation 2
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis 2
Acid resistance mechanisms 1
Alanine biosynthesis 1
Branched-Chain Amino Acid Biosynthesis 1
Fructose utilization 1
Glutamate dehydrogenases 1
Proline Synthesis 1
Pyruvate Alanine Serine Interconversions 1
Respiratory dehydrogenases 1 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
arginine dependent acid resistance 1 1 1
L-glutamate biosynthesis III 1 1 1
L-cysteine degradation IV 1 1 1
fructose degradation 1 1 1
L-alanine biosynthesis III 1 1 1
L-alanine degradation I 2 2 1
L-arginine degradation III (arginine decarboxylase/agmatinase pathway) 2 1 1
cytidylyl molybdenum cofactor sulfurylation 2 1 1
putrescine biosynthesis I 2 1 1
putrescine biosynthesis II 3 3 1
L-arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway) 3 3 1
bis(guanylyl molybdopterin) cofactor sulfurylation 3 1 1
thiazole component of thiamine diphosphate biosynthesis II 7 5 2
superpathway of L-alanine biosynthesis 4 4 1
superpathway of putrescine biosynthesis 4 2 1
D-galactosamine and N-acetyl-D-galactosamine degradation 4 1 1
tRNA-uridine 2-thiolation (mammalian mitochondria) 4 1 1
tRNA-uridine 2-thiolation (yeast mitochondria) 4 1 1
spermidine biosynthesis III 4 1 1
[2Fe-2S] iron-sulfur cluster biosynthesis 10 4 2
galactitol degradation 5 2 1
lactose degradation I 5 1 1
tRNA-uridine 2-thiolation (thermophilic bacteria) 5 1 1
N-acetyl-D-galactosamine degradation 5 1 1
superpathway of thiamine diphosphate biosynthesis II 11 9 2
molybdopterin biosynthesis 6 4 1
thiazole component of thiamine diphosphate biosynthesis I 6 4 1
L-glutamate and L-glutamine biosynthesis 7 5 1
superpathway of polyamine biosynthesis I 8 5 1
superpathway of polyamine biosynthesis II 8 5 1
tRNA-uridine 2-thiolation (cytoplasmic) 8 1 1
superpathway of thiamine diphosphate biosynthesis I 10 8 1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation 11 6 1
tRNA-uridine 2-thiolation and selenation (bacteria) 11 5 1
superpathway of L-arginine and L-ornithine degradation 13 8 1
superpathway of arginine and polyamine biosynthesis 17 14 1
superpathway of hexitol degradation (bacteria) 18 13 1