Experiment set2IT028 for Pseudomonas fluorescens FW300-N2E2

D-Alanine carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + D-Alanine (20 mM), pH=7
Culturing: pseudo6_N2E2_ML5, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
By: Mark on 3/9/2015
Media components: 0.25 g/L Ammonium chloride, 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 33 genes in this experiment

For carbon source D-Alanine in Pseudomonas fluorescens FW300-N2E2

For carbon source D-Alanine across organisms

SEED Subsystems

Subsystem	#Specific
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	5
Coenzyme PQQ synthesis	2
Polyamine Metabolism	2
Pyrroloquinoline Quinone biosynthesis	2
Acid resistance mechanisms	1
Arginine and Ornithine Degradation	1
Branched-Chain Amino Acid Biosynthesis	1
Cobalt-zinc-cadmium resistance	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glycine and Serine Utilization	1
Glycolysis and Gluconeogenesis	1
Glycolysis and Gluconeogenesis, including Archaeal enzymes	1
Hfl operon	1
Pyruvate Alanine Serine Interconversions	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
Ribosome biogenesis bacterial	1
Twin-arginine translocation system	1
Universal GTPases	1

Metabolic Maps

Color code by fitness: see overview map or list of maps.

Maps containing gene(s) with specific phenotypes:

• Urea cycle and metabolism of amino groups
• Arginine and proline metabolism
• Tryptophan metabolism
• Glycolysis / Gluconeogenesis
• Glycine, serine and threonine metabolism
• Histidine metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Glutathione metabolism
• Pyruvate metabolism
• 1,2-Dichloroethane degradation
• Propanoate metabolism
• Butanoate metabolism
• Methane metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Alkaloid biosynthesis I
• Drug metabolism - cytochrome P450
• Biosynthesis of siderophore group nonribosomal peptides
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
adenosine nucleotides degradation III	1	1	1
cadaverine biosynthesis	1	1	1
arginine dependent acid resistance	1	1	1
L-arginine degradation III (arginine decarboxylase/agmatinase pathway)	2	2	1
putrescine biosynthesis I	2	2	1
phenylethylamine degradation I	2	2	1
superpathway of putrescine biosynthesis	4	3	2
putrescine biosynthesis III	2	1	1
superpathway of polyamine biosynthesis I	8	5	3
putrescine biosynthesis II	3	3	1
L-arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway)	3	3	1
aminopropylcadaverine biosynthesis	3	1	1
L-tryptophan degradation VI (via tryptamine)	3	1	1
noradrenaline and adrenaline degradation	13	8	4
pyrroloquinoline quinone biosynthesis	7	4	2
putrescine degradation II	4	4	1
superpathway of ornithine degradation	8	7	2
putrescine degradation III	4	3	1
superpathway of polyamine biosynthesis II	8	5	2
aromatic biogenic amine degradation (bacteria)	8	4	2
salidroside biosynthesis	4	2	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	2	1
melatonin degradation II	4	1	1
spermidine biosynthesis III	4	1	1
superpathway of L-arginine and L-ornithine degradation	13	11	3
dopamine degradation	5	2	1
phenylethanol biosynthesis	5	2	1
desferrioxamine E biosynthesis	5	1	1
desferrioxamine B biosynthesis	5	1	1
lupanine biosynthesis	5	1	1
bisucaberin biosynthesis	5	1	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	9	2
superpathway of arginine and polyamine biosynthesis	17	14	3
L-lysine degradation X	6	5	1
serotonin degradation	7	4	1
L-lysine degradation I	7	4	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	5	1
glycolysis V (Pyrococcus)	10	7	1
glycolysis II (from fructose 6-phosphate)	11	9	1
superpathway of phenylethylamine degradation	11	6	1
superpathway of melatonin degradation	11	1	1
gluconeogenesis I	13	11	1
glycolysis I (from glucose 6-phosphate)	13	10	1
superpathway of hyoscyamine (atropine) and scopolamine biosynthesis	16	3	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	14	1
superpathway of hexitol degradation (bacteria)	18	12	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	1
superpathway of anaerobic sucrose degradation	19	14	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	14	1
superpathway of N-acetylneuraminate degradation	22	13	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	21	1
superpathway of L-lysine degradation	43	19	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	21	1