Experiment set5IT073 for Pseudomonas fluorescens FW300-N2C3

D-Alanine carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + D-Alanine (20 mM), pH=7
Culturing: pseudo5_N2-C3_1_ML2, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
By: Mark on 12/17/2014
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 14 genes in this experiment

For carbon source D-Alanine in Pseudomonas fluorescens FW300-N2C3

For carbon source D-Alanine across organisms

SEED Subsystems

Subsystem	#Specific
Ammonia assimilation	2
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	2
Glycine and Serine Utilization	1
Hfl operon	1
Isoleucine degradation	1
Multidrug Resistance Efflux Pumps	1
Pyruvate Alanine Serine Interconversions	1
Ton and Tol transport systems	1
Universal GTPases	1
Valine degradation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glycolysis / Gluconeogenesis
• Butanoate metabolism
• Fatty acid metabolism
• Glutamate metabolism
• Glycine, serine and threonine metabolism
• Tyrosine metabolism
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• 1,2-Dichloroethane degradation
• Propanoate metabolism
• 3-Chloroacrylic acid degradation
• Methane metabolism
• Retinol metabolism
• Nitrogen metabolism
• Metabolism of xenobiotics by cytochrome P450
• Drug metabolism - cytochrome P450
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-glutamate biosynthesis I	2	2	2
ethanol degradation I	2	2	2
acetaldehyde biosynthesis I	1	1	1
L-glutamine degradation I	1	1	1
L-glutamine degradation II	1	1	1
L-lactaldehyde degradation (anaerobic)	1	1	1
ammonia assimilation cycle III	3	3	2
pyruvate fermentation to ethanol III	3	2	2
pyruvate fermentation to ethanol I	3	2	2
ethylene glycol degradation	2	2	1
L-threonine degradation IV	2	2	1
pyruvate fermentation to ethanol II	2	1	1
ethanolamine utilization	5	5	2
acetylene degradation (anaerobic)	5	4	2
ethanol degradation II	3	3	1
2-deoxy-D-ribose degradation I	3	2	1
L-isoleucine degradation II	3	2	1
L-valine degradation II	3	2	1
L-leucine degradation III	3	2	1
2-hydroxypenta-2,4-dienoate degradation	3	2	1
L-methionine degradation III	3	1	1
2-deoxy-α-D-ribose 1-phosphate degradation	3	1	1
2-aminoethylphosphonate degradation I	3	1	1
sulfoacetaldehyde degradation IV	3	1	1
L-glutamate and L-glutamine biosynthesis	7	6	2
glutaminyl-tRNAgln biosynthesis via transamidation	4	4	1
L-asparagine biosynthesis III (tRNA-dependent)	4	4	1
phytol degradation	4	3	1
L-phenylalanine degradation III	4	2	1
L-tyrosine degradation III	4	2	1
salidroside biosynthesis	4	2	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	5	2
pyruvate fermentation to isobutanol (engineered)	5	4	1
(S)-propane-1,2-diol degradation	5	2	1
catechol degradation I (meta-cleavage pathway)	5	2	1
phenylethanol biosynthesis	5	2	1
superpathway of pyrimidine deoxyribonucleosides degradation	6	3	1
nucleoside and nucleotide degradation (halobacteria)	6	3	1
triethylamine degradation	6	1	1
noradrenaline and adrenaline degradation	13	8	2
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	5	2
superpathway of glycol metabolism and degradation	7	7	1
3-methylbutanol biosynthesis (engineered)	7	6	1
superpathway of purine deoxyribonucleosides degradation	7	5	1
serotonin degradation	7	4	1
catechol degradation II (meta-cleavage pathway)	7	3	1
toluene degradation V (aerobic) (via toluene-cis-diol)	7	2	1
toluene degradation I (aerobic) (via o-cresol)	7	2	1
mixed acid fermentation	16	12	2
L-citrulline biosynthesis	8	6	1
3-phenylpropanoate and 3-(3-hydroxyphenyl)propanoate degradation	8	4	1
butanol and isobutanol biosynthesis (engineered)	8	3	1
p-cumate degradation	8	2	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	7	2
heterolactic fermentation	18	16	2
hexitol fermentation to lactate, formate, ethanol and acetate	19	15	2
meta cleavage pathway of aromatic compounds	10	3	1
superpathway of N-acetylneuraminate degradation	22	15	2
p-cymene degradation	11	3	1
superpathway of L-citrulline metabolism	12	8	1
superpathway of fucose and rhamnose degradation	12	5	1
naphthalene degradation to acetyl-CoA	12	3	1
L-tryptophan degradation IX	12	2	1
L-tryptophan degradation XII (Geobacillus)	12	2	1
toluene degradation IV (aerobic) (via catechol)	13	4	1
L-tryptophan degradation V (side chain pathway)	13	1	1
superpathway of L-threonine metabolism	18	13	1
mandelate degradation to acetyl-CoA	18	7	1
superpathway of anaerobic sucrose degradation	19	15	1
superpathway of aerobic toluene degradation	30	12	1
superpathway of aromatic compound degradation via 3-oxoadipate	35	14	1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate	42	11	1