Experiment set2H39 for Pseudomonas stutzeri RCH2

Sodium butyrate carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + Sodium butyrate (10 mM), pH=7.2
Culturing: psRCH2_ML7, 48 well microplate; Tecan Infinite F200, Aerobic, at 30 (C), shaken=orbital
By: Kelly on 6/20/2013
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 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)
Growth plate: 552 F7,F8

Specific Phenotypes

For 44 genes in this experiment

For carbon source Sodium butyrate in Pseudomonas stutzeri RCH2

For carbon source Sodium butyrate across organisms

SEED Subsystems

Subsystem	#Specific
Bacterial hemoglobins	2
DNA repair, bacterial	2
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	2
Alginate metabolism	1
Ethanolamine utilization	1
Fermentations: Lactate	1
Fermentations: Mixed acid	1
Folate Biosynthesis	1
Glutathione: Non-redox reactions	1
Glycine reductase, sarcosine reductase and betaine reductase	1
Mannose Metabolism	1
N-linked Glycosylation in Bacteria	1
Peptidoglycan Biosynthesis	1
Photorespiration (oxidative C2 cycle)	1
Polyamine Metabolism	1
Proteolysis in bacteria, ATP-dependent	1
Selenocysteine metabolism	1
Serine-glyoxylate cycle	1
SigmaB stress responce regulation	1
Thioredoxin-disulfide reductase	1
Threonine anaerobic catabolism gene cluster	1
Transcription initiation, bacterial sigma factors	1
Wyeosine-MimG Biosynthesis	1
cAMP signaling in bacteria	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Fructose and mannose metabolism
• Nucleotide sugars metabolism
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• Glyoxylate and dicarboxylate metabolism
• Fatty acid biosynthesis
• Purine metabolism
• Pyrimidine metabolism
• Glycine, serine and threonine metabolism
• Geraniol degradation
• Tyrosine metabolism
• Benzoate degradation via hydroxylation
• Tryptophan metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Taurine and hypotaurine metabolism
• Glutathione metabolism
• N-Glycan biosynthesis
• O-Glycan biosynthesis
• High-mannose type N-glycan biosynthesis
• O-Mannosyl glycan biosynthesis
• Keratan sulfate biosynthesis
• Lipopolysaccharide biosynthesis
• Peptidoglycan biosynthesis
• Glycerolipid metabolism
• Glycosylphosphatidylinositol(GPI)-anchor biosynthesis
• Sphingolipid metabolism
• Glycosphingolipid biosynthesis - lacto and neolacto series
• Glycosphingolipid biosynthesis - globo series
• Glycosphingolipid biosynthesis - ganglio series
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• Butanoate metabolism
• One carbon pool by folate
• Methane metabolism
• Folate biosynthesis
• Porphyrin and chlorophyll metabolism
• Limonene and pinene degradation
• Carotenoid biosynthesis - General
• Zeatin biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Flavone and flavonol biosynthesis
• Metabolism of xenobiotics by cytochrome P450
• Drug metabolism - cytochrome P450
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide backbone
• Biosynthesis of phenylpropanoids
• 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
acetate formation from acetyl-CoA (succinate)	1	1	1
acetate and ATP formation from acetyl-CoA I	2	2	1
glycolate and glyoxylate degradation II	2	2	1
UDP-2-acetamido-4-amino-2,4,6-trideoxy-α-D-galactose biosynthesis	2	2	1
UDP-N-acetyl-α-D-quinovosamine biosynthesis	2	2	1
glycine degradation (reductive Stickland reaction)	2	1	1
UDP-N-acetyl-α-D-fucosamine biosynthesis	2	1	1
thioredoxin pathway	2	1	1
dTMP de novo biosynthesis (mitochondrial)	3	3	1
L-serine biosynthesis I	3	3	1
pyruvate fermentation to acetate II	3	3	1
pyruvate fermentation to acetate V	3	3	1
superpathway of acetate utilization and formation	3	3	1
tetrahydrofolate biosynthesis I	3	3	1
glyoxylate cycle	6	5	2
pyruvate fermentation to acetate VI	3	2	1
pyruvate fermentation to acetate I	3	2	1
UDP-yelosamine biosynthesis	3	2	1
pyruvate fermentation to acetate IV	3	2	1
pyruvate fermentation to acetate VII	3	2	1
UDP-N,N'-diacetylbacillosamine biosynthesis	3	1	1
Arg/N-end rule pathway (eukaryotic)	14	8	4
GDP-mannose biosynthesis	4	4	1
pyruvate fermentation to acetate and (S)-lactate I	4	4	1
superpathway of L-serine and glycine biosynthesis I	4	4	1
pyruvate fermentation to acetate and lactate II	4	3	1
tetrahydromonapterin biosynthesis	4	3	1
chitin deacetylation	4	2	1
UDP-N-acetyl-β-L-fucosamine biosynthesis	4	1	1
4-hydroxy-2-nonenal detoxification	4	1	1
UDP-N-acetyl-β-L-quinovosamine biosynthesis	4	1	1
adipate degradation	5	5	1
ethanolamine utilization	5	5	1
acetylene degradation (anaerobic)	5	4	1
(S)-propane-1,2-diol degradation	5	3	1
pentachlorophenol degradation	10	3	2
fatty acid salvage	6	6	1
CMP-pseudaminate biosynthesis	6	6	1
superpathway of glyoxylate bypass and TCA	12	11	2
L-threonine degradation I	6	5	1
methanogenesis from acetate	6	2	1
superpathway of glyoxylate cycle and fatty acid degradation	14	11	2
superpathway of glycol metabolism and degradation	7	5	1
acetyl-CoA fermentation to butanoate	7	4	1
D-xylose degradation IV	7	2	1
succinate fermentation to butanoate	7	2	1
CMP-diacetamido-8-epilegionaminic acid biosynthesis	7	1	1
lactate fermentation to acetate, CO2 and hydrogen (Desulfovibrionales)	8	3	1
L-arabinose degradation IV	8	3	1
glutathione-mediated detoxification I	8	3	1
superpathway of sulfate assimilation and cysteine biosynthesis	9	9	1
folate transformations III (E. coli)	9	9	1
TCA cycle VII (acetate-producers)	9	8	1
reductive glycine pathway of autotrophic CO2 fixation	9	5	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	5	1
superpathway of Clostridium acetobutylicum acidogenic fermentation	9	5	1
superpathway of L-alanine fermentation (Stickland reaction)	9	4	1
gliotoxin biosynthesis	9	1	1
glutathione-mediated detoxification II	9	1	1
superpathway of tetrahydrofolate biosynthesis	10	8	1
anaerobic energy metabolism (invertebrates, mitochondrial)	10	5	1
L-lysine fermentation to acetate and butanoate	10	3	1
folate transformations II (plants)	11	10	1
colanic acid building blocks biosynthesis	11	10	1
gallate degradation III (anaerobic)	11	5	1
oleate β-oxidation	35	30	3
superpathway of tetrahydrofolate biosynthesis and salvage	12	10	1
superpathway of UDP-N-acetylglucosamine-derived O-antigen building blocks biosynthesis	24	9	2
indole glucosinolate activation (intact plant cell)	12	3	1
camalexin biosynthesis	12	2	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	23	2
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	5	1
2-methyl-branched fatty acid β-oxidation	14	10	1
superpathway of GDP-mannose-derived O-antigen building blocks biosynthesis	14	9	1
crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA cycle (engineered)	14	1	1
Bifidobacterium shunt	15	15	1
purine nucleobases degradation I (anaerobic)	15	6	1
mixed acid fermentation	16	12	1
superpathway of anaerobic energy metabolism (invertebrates)	17	9	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	8	1
superpathway of L-threonine metabolism	18	13	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	16	1
superpathway of methanogenesis	21	2	1
superpathway of N-acetylneuraminate degradation	22	14	1
purine nucleobases degradation II (anaerobic)	24	16	1
superpathway of pentose and pentitol degradation	42	7	1
superpathway of L-lysine degradation	43	11	1
superpathway of chorismate metabolism	59	44	1