Experiment set2IT082 for Pseudomonas fluorescens FW300-N2C3

Ethanol carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + Ethanol (20 mM), pH=7.2
Culturing: pseudo5_N2-C3_1_ML2, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 4.3 generations
By: Jayashree on 6/12/2014
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 19 genes in this experiment

For carbon source Ethanol in Pseudomonas fluorescens FW300-N2C3

For carbon source Ethanol across organisms

SEED Subsystems

Subsystem	#Specific
Ammonia assimilation	1
Cobalt-zinc-cadmium resistance	1
Coenzyme PQQ synthesis	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Ketoisovalerate oxidoreductase	1
Murein hydrolase regulation and cell death	1
Pyrroloquinoline Quinone biosynthesis	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Ribosome biogenesis bacterial	1
TCA Cycle	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glycolysis / Gluconeogenesis
• Pyruvate metabolism
• Propanoate metabolism
• Butanoate metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Citrate cycle (TCA cycle)
• Fatty acid metabolism
• Glutamate metabolism
• Glycine, serine and threonine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Glutathione metabolism
• 1- and 2-Methylnaphthalene degradation
• 1,2-Dichloroethane degradation
• 3-Chloroacrylic acid degradation
• Methane metabolism
• Retinol metabolism
• Nitrogen metabolism
• Metabolism of xenobiotics by cytochrome P450
• Drug metabolism - cytochrome P450
• Biosynthesis of siderophore group nonribosomal peptides
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
ethanol degradation I	2	2	2
L-glutamate biosynthesis I	2	2	2
L-lactaldehyde degradation (anaerobic)	1	1	1
acetate and ATP formation from acetyl-CoA III	1	1	1
L-glutamine degradation II	1	1	1
acetate conversion to acetyl-CoA	1	1	1
acetaldehyde biosynthesis I	1	1	1
L-glutamine degradation I	1	1	1
ammonia assimilation cycle III	3	3	2
ethanol degradation II	3	3	2
pyruvate fermentation to ethanol I	3	2	2
pyruvate fermentation to ethanol III	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 IV	3	3	1
superpathway of acetate utilization and formation	3	3	1
L-isoleucine degradation II	3	2	1
ethanol degradation III	3	2	1
L-leucine degradation III	3	2	1
L-isoleucine biosynthesis V	3	2	1
L-valine degradation II	3	2	1
2-deoxy-D-ribose degradation I	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
L-asparagine biosynthesis III (tRNA-dependent)	4	4	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	4	1
phytol degradation	4	3	1
L-tyrosine degradation III	4	2	1
salidroside biosynthesis	4	2	1
chitin deacetylation	4	2	1
L-phenylalanine degradation III	4	2	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	5	2
2-methylcitrate cycle I	5	5	1
cytosolic NADPH production (yeast)	5	4	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
catechol degradation I (meta-cleavage pathway)	5	2	1
(S)-propane-1,2-diol degradation	5	2	1
phenylethanol biosynthesis	5	2	1
mixed acid fermentation	16	12	3
2-methylcitrate cycle II	6	5	1
β-alanine biosynthesis II	6	5	1
L-isoleucine biosynthesis IV	6	4	1
nucleoside and nucleotide degradation (halobacteria)	6	3	1
superpathway of pyrimidine deoxyribonucleosides degradation	6	3	1
superpathway of bitter acids biosynthesis	18	3	3
lupulone and humulone biosynthesis	6	1	1
colupulone and cohumulone biosynthesis	6	1	1
adlupulone and adhumulone biosynthesis	6	1	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
pyrroloquinoline quinone biosynthesis	7	4	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
partial TCA cycle (obligate autotrophs)	8	8	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	7	1
L-citrulline biosynthesis	8	6	1
nitrogen remobilization from senescing leaves	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
TCA cycle IV (2-oxoglutarate decarboxylase)	9	7	1
TCA cycle VI (Helicobacter)	9	7	1
TCA cycle V (2-oxoglutarate synthase)	9	7	1
TCA cycle VII (acetate-producers)	9	7	1
reductive glycine pathway of autotrophic CO2 fixation	9	5	1
cis-geranyl-CoA degradation	9	3	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	15	2
superpathway of coenzyme A biosynthesis II (plants)	10	9	1
TCA cycle I (prokaryotic)	10	8	1
meta cleavage pathway of aromatic compounds	10	3	1
superpathway of N-acetylneuraminate degradation	22	15	2
reductive TCA cycle I	11	6	1
p-cymene degradation	11	3	1
superpathway of glyoxylate bypass and TCA	12	10	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
methylaspartate cycle	19	10	1
ethene biosynthesis V (engineered)	25	19	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	21	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