Experiment set16IT039 for Pseudomonas fluorescens FW300-N2E2

Nitrate reduction, replicate A

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 3.3 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 21 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	5
Denitrification	4
CBSS-214092.1.peg.3450	2
Experimental tye	1
Heme and Siroheme Biosynthesis	1
Nitrosative stress	1
Polyamine Metabolism	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Queuosine-Archaeosine Biosynthesis	1
Ribonucleotide reduction	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
• Lysine degradation
• Peptidoglycan biosynthesis
• Biotin metabolism
• Porphyrin and chlorophyll metabolism

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
nitrate reduction I (denitrification)	5	5	2
heme b biosynthesis II (oxygen-independent)	4	3	1
nitrate reduction VII (denitrification)	5	5	1
superpathway of heme b biosynthesis from uroporphyrinogen-III	6	4	1
nitrifier denitrification	6	3	1
3,8-divinyl-chlorophyllide a biosynthesis II (anaerobic)	9	3	1
superpathway of bacteriochlorophyll a biosynthesis	26	6	1