Experiment set7H33 for Pseudomonas stutzeri RCH2

RCH2 defined media with Nalidixic acid sodium salt 0.001 mg/ml

Group: stress
Media: RCH2_defined_no_vitamin + Nalidixic acid sodium salt (0.001 mg/ml), pH=7.2
Culturing: psRCH2_ML7, 48 well microplate; Tecan Infinite F200, Aerobic, at 30 (C), shaken=orbital
By: Adam on 8/13/2013
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)
Growth plate: 644 E3,E4

Specific Phenotypes

For 16 genes in this experiment

For stress Nalidixic acid sodium salt in Pseudomonas stutzeri RCH2

For stress Nalidixic acid sodium salt across organisms

SEED Subsystems

Subsystem	#Specific
DNA repair, bacterial	2
DNA-replication	1
DNA repair, bacterial DinG and relatives	1
Entner-Doudoroff Pathway	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Lysine Biosynthesis DAP Pathway	1
Methylglyoxal Metabolism	1
Multidrug Resistance Efflux Pumps	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Ton and Tol transport systems	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glycolysis / Gluconeogenesis
• Fatty acid metabolism
• Pyruvate metabolism
• 3-Chloroacrylic acid degradation
• Butanoate metabolism
• Ascorbate and aldarate metabolism
• Urea cycle and metabolism of amino groups
• Glycine, serine and threonine metabolism
• Valine, leucine and isoleucine degradation
• Lysine biosynthesis
• Lysine degradation
• Arginine and proline metabolism
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• beta-Alanine metabolism
• Glycerolipid metabolism
• 1- and 2-Methylnaphthalene degradation
• 1,2-Dichloroethane degradation
• Propanoate metabolism
• Retinol metabolism
• Limonene and pinene degradation
• Metabolism of xenobiotics by cytochrome P450
• Drug metabolism - cytochrome P450

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
ethanol degradation I	2	2	2
acetaldehyde biosynthesis I	1	1	1
ethanol degradation II	3	3	2
pyruvate fermentation to ethanol I	3	2	2
pyruvate fermentation to ethanol III	3	2	2
L-threonine degradation IV	2	2	1
putrescine degradation V	2	2	1
phytol degradation	4	3	2
phenylethylamine degradation I	2	1	1
pyruvate fermentation to ethanol II	2	1	1
ethylene glycol degradation	2	1	1
phenylethanol degradation	2	1	1
putrescine degradation I	2	1	1
phenylethylamine degradation II	2	1	1
ethanolamine utilization	5	5	2
acetylene degradation (anaerobic)	5	4	2
ethanol degradation IV	3	3	1
L-isoleucine degradation II	3	2	1
L-valine degradation II	3	2	1
hypotaurine degradation	3	2	1
putrescine degradation IV	3	2	1
L-phenylalanine degradation II (anaerobic)	3	2	1
ethanol degradation III	3	2	1
L-leucine degradation III	3	2	1
2-hydroxypenta-2,4-dienoate degradation	3	1	1
sulfoacetaldehyde degradation IV	3	1	1
histamine degradation	3	1	1
styrene degradation	3	1	1
2-deoxy-D-ribose degradation I	3	1	1
L-methionine degradation III	3	1	1
2-aminoethylphosphonate degradation I	3	1	1
2-deoxy-α-D-ribose 1-phosphate degradation	3	1	1
noradrenaline and adrenaline degradation	13	4	4
serotonin degradation	7	3	2
fatty acid α-oxidation I (plants)	4	2	1
L-tyrosine degradation III	4	2	1
L-phenylalanine degradation III	4	2	1
salidroside biosynthesis	4	1	1
putrescine degradation III	4	1	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	1	1
D-arabinose degradation II	4	1	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	5	2
pyruvate fermentation to isobutanol (engineered)	5	4	1
mitochondrial NADPH production (yeast)	5	3	1
octane oxidation	5	3	1
(S)-propane-1,2-diol degradation	5	3	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
phenylethanol biosynthesis	5	1	1
catechol degradation I (meta-cleavage pathway)	5	1	1
dopamine degradation	5	1	1
3-methyl-branched fatty acid α-oxidation	6	3	1
superpathway of pyrimidine deoxyribonucleosides degradation	6	2	1
triethylamine degradation	6	1	1
alkane oxidation	6	1	1
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	6	2
3-methylbutanol biosynthesis (engineered)	7	6	1
superpathway of glycol metabolism and degradation	7	5	1
superpathway of purine deoxyribonucleosides degradation	7	2	1
ceramide degradation by α-oxidation	7	2	1
toluene degradation V (aerobic) (via toluene-cis-diol)	7	1	1
limonene degradation IV (anaerobic)	7	1	1
catechol degradation II (meta-cleavage pathway)	7	1	1
toluene degradation I (aerobic) (via o-cresol)	7	1	1
mixed acid fermentation	16	12	2
superpathway of ornithine degradation	8	6	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	5	1
butanol and isobutanol biosynthesis (engineered)	8	3	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
p-cumate degradation	8	1	1
3-phenylpropanoate and 3-(3-hydroxyphenyl)propanoate degradation	8	1	1
aromatic biogenic amine degradation (bacteria)	8	1	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	8	2
L-lysine biosynthesis I	9	9	1
heterolactic fermentation	18	15	2
Entner-Doudoroff pathway II (non-phosphorylative)	9	5	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	3	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	16	2
meta cleavage pathway of aromatic compounds	10	3	1
superpathway of N-acetylneuraminate degradation	22	14	2
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	6	1
superpathway of phenylethylamine degradation	11	4	1
p-cymene degradation	11	1	1
L-tryptophan degradation XII (Geobacillus)	12	1	1
naphthalene degradation to acetyl-CoA	12	1	1
L-tryptophan degradation IX	12	1	1
superpathway of L-arginine and L-ornithine degradation	13	8	1
toluene degradation IV (aerobic) (via catechol)	13	3	1
L-tryptophan degradation V (side chain pathway)	13	1	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	1
superpathway of L-threonine metabolism	18	13	1
mandelate degradation to acetyl-CoA	18	9	1
superpathway of anaerobic sucrose degradation	19	15	1
aspartate superpathway	25	22	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	3	1
superpathway of aerobic toluene degradation	30	7	1
superpathway of aromatic compound degradation via 3-oxoadipate	35	11	1
superpathway of pentose and pentitol degradation	42	7	1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate	42	5	1