Experiment set8IT056 for Pseudomonas fluorescens FW300-N1B4

Nitrate reduction, replicate A, timepoint 2

Group: denitrifying
Media: Chakraborty_Basal + Sodium pyruvate (15 mM) + Sodium nitrate (30 mM)
Culturing: pseudo1_N1B4_ML1, 150mL Serum Bottle, Anaerobic, at 27 (C), shaken=0 rpm
Growth: about 3.8 generations
By: Alex Aaring on 03/13/16
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 0.3792 g/L Sodium phosphate monobasic, 0.9713 g/L Disodium phosphate, 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 15 genes in this experiment

For denitrifying Sodium pyruvate in Pseudomonas fluorescens FW300-N1B4

For denitrifying Sodium pyruvate across organisms

SEED Subsystems

Subsystem	#Specific
Terminal cytochrome C oxidases	3
Conserved gene cluster possibly involved in RNA metabolism	1
Cysteine Biosynthesis	1
Denitrification	1
Fermentations: Mixed acid	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Isoleucine degradation	1
Methionine Biosynthesis	1
NAD and NADP cofactor biosynthesis global	1
NAD regulation	1
Redox-dependent regulation of nucleus processes	1
Valine degradation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Fatty acid metabolism
• Nicotinate and nicotinamide metabolism
• Glycolysis / Gluconeogenesis
• Oxidative phosphorylation
• Glycine, serine and threonine metabolism
• Cysteine metabolism
• Valine, leucine and isoleucine degradation
• Lysine biosynthesis
• Tyrosine metabolism
• beta-Alanine metabolism
• Glutathione metabolism
• Nucleotide sugars metabolism
• Lipopolysaccharide biosynthesis
• Sphingolipid metabolism
• 1- and 2-Methylnaphthalene degradation
• 1,4-Dichlorobenzene degradation
• Propanoate metabolism
• 3-Chloroacrylic acid degradation
• Retinol metabolism
• Sulfur metabolism
• Caprolactam degradation
• Metabolism of xenobiotics by cytochrome P450
• Drug metabolism - cytochrome P450

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
acetaldehyde biosynthesis I	1	1	1
ethanol degradation I	2	2	1
L-cysteine biosynthesis I	2	2	1
pyruvate fermentation to ethanol II	2	1	1
arsenite to oxygen electron transfer	2	1	1
ethanol degradation II	3	3	1
L-leucine degradation III	3	2	1
pyruvate fermentation to ethanol I	3	2	1
L-isoleucine degradation II	3	2	1
L-valine degradation II	3	2	1
pyruvate fermentation to ethanol III	3	2	1
L-methionine degradation III	3	1	1
arsenite to oxygen electron transfer (via azurin)	3	1	1
aldoxime degradation	3	1	1
L-cysteine biosynthesis VII (from S-sulfo-L-cysteine)	4	3	1
phytol degradation	4	3	1
aerobic respiration II (cytochrome c) (yeast)	4	3	1
aerobic respiration I (cytochrome c)	4	3	1
salidroside biosynthesis	4	2	1
L-phenylalanine degradation III	4	2	1
L-tyrosine degradation III	4	2	1
cytidine-5'-diphosphate-glycerol biosynthesis	4	1	1
N-3-oxalyl-L-2,3-diaminopropanoate biosynthesis	4	1	1
ethanolamine utilization	5	5	1
acetylene degradation (anaerobic)	5	4	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
NAD salvage pathway V (PNC V cycle)	5	3	1
seleno-amino acid biosynthesis (plants)	5	3	1
phenylethanol biosynthesis	5	2	1
(S)-propane-1,2-diol degradation	5	2	1
Fe(II) oxidation	6	3	1
D-cycloserine biosynthesis	6	1	1
noradrenaline and adrenaline degradation	13	8	2
3-methylbutanol biosynthesis (engineered)	7	6	1
NAD salvage pathway I (PNC VI cycle)	7	5	1
serotonin degradation	7	4	1
L-cysteine biosynthesis VI (reverse transsulfuration)	7	3	1
butanol and isobutanol biosynthesis (engineered)	8	3	1
superpathway of sulfate assimilation and cysteine biosynthesis	9	9	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	5	1
NAD salvage (plants)	11	6	1
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	6	1
L-tryptophan degradation V (side chain pathway)	13	1	1
superpathway of NAD biosynthesis in eukaryotes	14	6	1
mixed acid fermentation	16	12	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	8	1
heterolactic fermentation	18	15	1
superpathway of anaerobic sucrose degradation	19	15	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	14	1
superpathway of seleno-compound metabolism	19	6	1
superpathway of N-acetylneuraminate degradation	22	13	1