Experiment set6IT089 for Pseudomonas fluorescens FW300-N2C3

Nitrate reduction with yeast extract

Group: anaerobic
Media: RCH2_defined + Sodium nitrate (30 mM) + Yeast Extract, pH=7
Culturing: pseudo5_N2-C3_1_ML2, hungate, Anaerobic, at 30 (C), shaken=0 rpm
Growth: about 3.8 generations
By: Jayashree on 10/28/2014
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 20 mM Sodium D,L-Lactate, 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 15 genes in this experiment

For anaerobic Sodium nitrate in Pseudomonas fluorescens FW300-N2C3

For anaerobic Sodium nitrate across organisms

SEED Subsystems

Subsystem	#Specific
Nitrate and nitrite ammonification	4
Denitrification	3
CBSS-214092.1.peg.3450	1
Experimental tye	1
Heme and Siroheme Biosynthesis	1
Molybdenum cofactor biosynthesis	1
Ribonucleotide reduction	1
Transport of Molybdenum	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	4	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