Experiment set1IT041 for Pseudomonas fluorescens FW300-N1B4

LB with Paraquat dichloride 0.016 mg/mL

Group: stress
Media: LB + Paraquat dichloride (0.016 mg/ml), pH=7
Culturing: pseudo1_N1B4_ML1, 48 well microplate; Tecan Infinite F200, Aerobic, at 28 (C), shaken=orbital
By: Jayashree on 4/23/2014
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride
Growth plate: 889 D1,D2

Specific Phenotypes

For 14 genes in this experiment

For stress Paraquat dichloride in Pseudomonas fluorescens FW300-N1B4

For stress Paraquat dichloride across organisms

SEED Subsystems

Subsystem	#Specific
Choline and Betaine Uptake and Betaine Biosynthesis	2
Acid resistance mechanisms	1
Arginine and Ornithine Degradation	1
Central meta-cleavage pathway of aromatic compound degradation	1
Entner-Doudoroff Pathway	1
Glutathione-regulated potassium-efflux system and associated functions	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Lysine degradation	1
Methylglyoxal Metabolism	1
Polyamine Metabolism	1
Potassium homeostasis	1
Proteolysis in bacteria, ATP-dependent	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Arginine and proline metabolism
• Urea cycle and metabolism of amino groups
• Lysine degradation
• Tryptophan metabolism
• beta-Alanine metabolism
• Propanoate metabolism
• Butanoate metabolism
• Limonene and pinene degradation
• Glycolysis / Gluconeogenesis
• Ascorbate and aldarate metabolism
• Fatty acid metabolism
• Glutamate metabolism
• Alanine and aspartate metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Lysine biosynthesis
• Histidine metabolism
• Nucleotide sugars metabolism
• Glycerolipid metabolism
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• 1,2-Dichloroethane degradation
• 3-Chloroacrylic acid degradation

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
4-aminobutanoate degradation III	2	2	2
arginine dependent acid resistance	1	1	1
4-aminobutanoate degradation I	2	2	1
L-arginine degradation III (arginine decarboxylase/agmatinase pathway)	2	2	1
ethylene glycol degradation	2	2	1
putrescine biosynthesis I	2	2	1
putrescine degradation V	2	2	1
4-aminobutanoate degradation II	2	2	1
putrescine degradation I	2	1	1
L-lysine degradation IV	5	5	2
putrescine biosynthesis II	3	3	1
ethanol degradation IV	3	3	1
CDP-4-dehydro-3,6-dideoxy-D-glucose biosynthesis	3	3	1
superpathway of 4-aminobutanoate degradation	3	3	1
L-arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway)	3	3	1
ethanol degradation II	3	3	1
L-lysine degradation X	6	5	2
ethanol degradation III	3	2	1
hypotaurine degradation	3	2	1
putrescine degradation IV	3	2	1
L-lysine degradation III	6	2	2
histamine degradation	3	1	1
L-lysine degradation I	7	4	2
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	9	3
superpathway of putrescine biosynthesis	4	3	1
L-arginine degradation IX (arginine:pyruvate transaminase pathway)	4	3	1
putrescine degradation III	4	3	1
phytol degradation	4	3	1
GABA shunt I	4	2	1
fatty acid α-oxidation I (plants)	4	2	1
L-arginine degradation VIII (arginine oxidase pathway)	4	2	1
GABA shunt II	4	2	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	2	1
D-arabinose degradation II	4	1	1
spermidine biosynthesis III	4	1	1
superpathway of L-arginine and L-ornithine degradation	13	11	3
octane oxidation	5	4	1
mitochondrial NADPH production (yeast)	5	4	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
dopamine degradation	5	2	1
3-methyl-branched fatty acid α-oxidation	6	3	1
alkane oxidation	6	1	1
noradrenaline and adrenaline degradation	13	8	2
superpathway of glycol metabolism and degradation	7	7	1
serotonin degradation	7	4	1
4-aminobutanoate degradation V	7	2	1
ceramide degradation by α-oxidation	7	2	1
limonene degradation IV (anaerobic)	7	1	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	7	1
superpathway of ornithine degradation	8	6	1
superpathway of polyamine biosynthesis II	8	5	1
superpathway of polyamine biosynthesis I	8	5	1
aromatic biogenic amine degradation (bacteria)	8	3	1
superpathway of CDP-glucose-derived O-antigen building blocks biosynthesis	8	3	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
Entner-Doudoroff pathway II (non-phosphorylative)	9	7	1
superpathway of arginine and polyamine biosynthesis	17	14	1
nicotine degradation I (pyridine pathway)	17	5	1
superpathway of L-lysine degradation	43	19	2
superpathway of pentose and pentitol degradation	42	11	1