Experiment set16IT036 for Pseudomonas fluorescens FW300-N2E2

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

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 28 genes in this experiment

For denitrifying Sodium pyruvate in Pseudomonas fluorescens FW300-N2E2

For denitrifying Sodium pyruvate across organisms

SEED Subsystems

Subsystem	#Specific
Nitrate and nitrite ammonification	6
Denitrification	4
CBSS-214092.1.peg.3450	3
Experimental tye	1
Folate Biosynthesis	1
Glycine Biosynthesis	1
Glycine and Serine Utilization	1
Glycolysis and Gluconeogenesis	1
Glycolysis and Gluconeogenesis, including Archaeal enzymes	1
Heme and Siroheme Biosynthesis	1
LMPTP YwlE cluster	1
Methionine Biosynthesis	1
Nitrosative stress	1
Photorespiration (oxidative C2 cycle)	1
Polyamine Metabolism	1
Pyridoxin (Vitamin B6) Biosynthesis	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
Queuosine-Archaeosine Biosynthesis	1
Ribonucleotide reduction	1
Serine-glyoxylate cycle	1
Serine Biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Nitrogen metabolism
• Purine metabolism
• Pyrimidine metabolism
• Glycine, serine and threonine metabolism
• Lysine degradation
• Cyanoamino acid metabolism
• Peptidoglycan biosynthesis
• Pyruvate metabolism
• One carbon pool by folate
• Methane metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Vitamin B6 metabolism
• Biotin metabolism
• Porphyrin and chlorophyll metabolism

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
glycine biosynthesis I	1	1	1
nitrate reduction I (denitrification)	5	5	2
pyridoxal 5'-phosphate salvage I	6	6	2
dTMP de novo biosynthesis (mitochondrial)	3	3	1
glycine degradation	3	3	1
superpathway of L-serine and glycine biosynthesis I	4	4	1
heme b biosynthesis II (oxygen-independent)	4	3	1
glycine betaine degradation II (mammalian)	4	1	1
pyridoxal 5'-phosphate salvage II (plants)	9	6	2
nitrate reduction VII (denitrification)	5	5	1
folate polyglutamylation	5	4	1
folate transformations II (plants)	11	10	2
superpathway of pyridoxal 5'-phosphate biosynthesis and salvage	12	12	2
superpathway of heme b biosynthesis from uroporphyrinogen-III	6	4	1
nitrifier denitrification	6	3	1
glycine betaine degradation III	7	7	1
pyridoxal 5'-phosphate biosynthesis I	7	7	1
glycine betaine degradation I	8	6	1
4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis II	8	5	1
folate transformations III (E. coli)	9	9	1
photorespiration III	9	5	1
photorespiration I	9	5	1
3,8-divinyl-chlorophyllide a biosynthesis II (anaerobic)	9	3	1
glycolysis V (Pyrococcus)	10	7	1
photorespiration II	10	6	1
glycolysis II (from fructose 6-phosphate)	11	9	1
gluconeogenesis I	13	11	1
glycolysis I (from glucose 6-phosphate)	13	10	1
folate transformations I	13	9	1
formaldehyde assimilation I (serine pathway)	13	6	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
purine nucleobases degradation II (anaerobic)	24	16	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