Experiment set7IT057 for Pseudomonas fluorescens FW300-N2E3

N1B4wt with N2E3m denitrifying replicate C

Group: anaerobic
Media: UGA + Sodium pyruvate (15 mM) + Sodium nitrate (30 mM), pH=6.88
Culturing: pseudo3_N2E3_ML2, 100mL Serum Bottle, Anaerobic, at 30 (C), shaken=175 rpm
Growth: about 3.2 generations
By: Alex Aaring on 6/26/2015

Specific Phenotypes

For 41 genes in this experiment

For anaerobic Sodium pyruvate in Pseudomonas fluorescens FW300-N2E3

For anaerobic Sodium pyruvate across organisms

SEED Subsystems

Subsystem	#Specific
Nitrate and nitrite ammonification	7
Molybdenum cofactor biosynthesis	6
Denitrification	3
Transport of Molybdenum	3
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	2
Cysteine Biosynthesis	1
DNA-replication	1
Formate hydrogenase	1
Maltose and Maltodextrin Utilization	1
Nitrosative stress	1
Oxidative stress	1
Potassium homeostasis	1
Ribosome activity modulation	1
Ribosome biogenesis bacterial	1
TCA Cycle	1
Trehalose Biosynthesis	1
Universal stress protein family	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Citrate cycle (TCA cycle)
• Purine metabolism
• Pyrimidine metabolism
• Benzoate degradation via hydroxylation
• Glutathione metabolism
• Starch and sucrose metabolism
• Glyoxylate and dicarboxylate metabolism
• Methane metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Nitrogen metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
formate oxidation to CO2	1	1	1
NADH to nitrate electron transfer	2	2	1
nitrate reduction IX (dissimilatory)	2	2	1
nitrate reduction III (dissimilatory)	2	2	1
nitrate reduction VIII (dissimilatory)	2	1	1
microcin B17 biosynthesis	3	1	1
protocatechuate degradation II (ortho-cleavage pathway)	4	4	1
oxalate degradation VI	4	1	1
nitrate reduction I (denitrification)	5	4	1
nitrate reduction VII (denitrification)	5	3	1
cytosolic NADPH production (yeast)	5	3	1
oxalate degradation III	5	1	1
molybdopterin biosynthesis	6	4	1
partial TCA cycle (obligate autotrophs)	8	8	1
nitrogen remobilization from senescing leaves	8	6	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	6	1
aromatic compounds degradation via β-ketoadipate	9	9	1
TCA cycle IV (2-oxoglutarate decarboxylase)	9	7	1
TCA cycle VI (Helicobacter)	9	7	1
TCA cycle V (2-oxoglutarate synthase)	9	7	1
TCA cycle VII (acetate-producers)	9	7	1
TCA cycle I (prokaryotic)	10	9	1
toluene degradation III (aerobic) (via p-cresol)	11	7	1
reductive TCA cycle I	11	6	1
superpathway of glyoxylate bypass and TCA	12	11	1
superpathway of C1 compounds oxidation to CO2	12	5	1
purine nucleobases degradation I (anaerobic)	15	6	1
mixed acid fermentation	16	12	1
methylaspartate cycle	19	9	1
purine nucleobases degradation II (anaerobic)	24	16	1
ethene biosynthesis V (engineered)	25	19	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	22	1
superpathway of aerobic toluene degradation	30	11	1
superpathway of aromatic compound degradation via 3-oxoadipate	35	18	1