Experiment set16IT038 for Pseudomonas fluorescens FW300-N2E2

Nitrate reduction in presence of wild-type Pseudomonas N2-E3; replicate C

Group: denitrifying
Media: Chakraborty_Basal + Sodium pyruvate (15 mM) + Sodium nitrate (30 mM)
Culturing: pseudo6_N2E2_ML5b, 150mL Serum Bottle, Anaerobic, at 27 (C), shaken=0 rpm
Growth: about 3.7 generations
By: Alex Aaring on 27-Jan-17
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 24 genes in this experiment

For denitrifying Sodium pyruvate in Pseudomonas fluorescens FW300-N2E2

For denitrifying Sodium pyruvate across organisms

SEED Subsystems

Subsystem	#Specific
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	5
Nitrate and nitrite ammonification	5
CBSS-214092.1.peg.3450	2
Experimental tye	1
Fermentations: Mixed acid	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Glycolysis and Gluconeogenesis	1
Glycolysis and Gluconeogenesis, including Archaeal enzymes	1
Heme and Siroheme Biosynthesis	1
Polyamine Metabolism	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
Ribonucleotide reduction	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glycolysis / Gluconeogenesis
• Fatty acid metabolism
• Purine metabolism
• Pyrimidine metabolism
• Glycine, serine and threonine metabolism
• Lysine degradation
• Tyrosine metabolism
• Peptidoglycan biosynthesis
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• 3-Chloroacrylic acid degradation
• Reductive carboxylate cycle (CO2 fixation)
• Biotin metabolism
• Retinol metabolism
• Porphyrin and chlorophyll metabolism
• Nitrogen metabolism
• 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
pyruvate fermentation to ethanol II	2	1	1
ethanol degradation II	3	3	1
pyruvate fermentation to ethanol I	3	2	1
pyruvate fermentation to ethanol III	3	2	1
L-isoleucine degradation II	3	2	1
L-leucine degradation III	3	2	1
L-valine degradation II	3	2	1
L-methionine degradation III	3	1	1
heme b biosynthesis II (oxygen-independent)	4	3	1
phytol degradation	4	3	1
L-phenylalanine degradation III	4	2	1
salidroside biosynthesis	4	2	1
L-tyrosine degradation III	4	2	1
cytidine-5'-diphosphate-glycerol biosynthesis	4	1	1
nitrate reduction I (denitrification)	5	5	1
nitrate reduction VII (denitrification)	5	5	1
ethanolamine utilization	5	5	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
acetylene degradation (anaerobic)	5	4	1
(S)-propane-1,2-diol degradation	5	2	1
phenylethanol biosynthesis	5	2	1
superpathway of heme b biosynthesis from uroporphyrinogen-III	6	4	1
noradrenaline and adrenaline degradation	13	8	2
3-methylbutanol biosynthesis (engineered)	7	6	1
serotonin degradation	7	4	1
butanol and isobutanol biosynthesis (engineered)	8	3	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	5	1
3,8-divinyl-chlorophyllide a biosynthesis II (anaerobic)	9	3	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	14	2
superpathway of anaerobic sucrose degradation	19	14	2
glycolysis V (Pyrococcus)	10	7	1
glycolysis II (from fructose 6-phosphate)	11	9	1
superpathway of N-acetylneuraminate degradation	22	13	2
gluconeogenesis I	13	11	1
glycolysis I (from glucose 6-phosphate)	13	10	1
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	5	1
L-tryptophan degradation V (side chain pathway)	13	1	1
mixed acid fermentation	16	12	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	14	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	7	1
heterolactic fermentation	18	15	1
superpathway of hexitol degradation (bacteria)	18	12	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	21	1
superpathway of bacteriochlorophyll a biosynthesis	26	6	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	21	1