Experiment set2H33 for Shewanella amazonensis SB2B

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Minimal media with Putrescine Dihydrochloride as carbon source

Group: carbon source
Media: ShewMM_noCarbon + Putrescine Dihydrochloride (20 mM), pH=7
Culturing: SB2B_ML5, 48 well microplate; Tecan Infinite F200, Aerobic, at 37 (C), shaken=orbital
By: Jake on 4/15/2013
Media components: 1.5 g/L Ammonium chloride, 1.75 g/L Sodium Chloride, 0.61 g/L Magnesium chloride hexahydrate, 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: 508 A3,A4

Specific Phenotypes

For 19 genes in this experiment

For carbon source Putrescine Dihydrochloride in Shewanella amazonensis SB2B

For carbon source Putrescine Dihydrochloride across organisms

SEED Subsystems

Subsystem #Specific
Bacterial Chemotaxis 2
Autoinducer 2 (AI-2) transport and processing (lsrACDBFGE operon) 1
Bacterial hemoglobins 1
Biogenesis of c-type cytochromes 1
Chorismate: Intermediate for synthesis of PAPA antibiotics, PABA, anthranilate, 3-hydroxyanthranilate and more. 1
Flagellar motility 1
Folate Biosynthesis 1
Isobutyryl-CoA to Propionyl-CoA Module 1
Isoleucine degradation 1
Methionine Biosynthesis 1
Methionine Degradation 1
Methylcitrate cycle 1
Nudix proteins (nucleoside triphosphate hydrolases) 1
Periplasmic disulfide interchange 1
Polyamine Metabolism 1
Propionate-CoA to Succinate Module 1
Tryptophan synthesis 1
Two-component regulatory systems in Campylobacter 1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway #Steps #Present #Specific
L-glutamine degradation I 1 1 1
4-aminobenzoate biosynthesis I 2 2 1
L-glutamate biosynthesis I 2 2 1
putrescine degradation V 2 2 1
4-aminobutanoate degradation III 2 2 1
putrescine degradation II 4 3 2
4-aminobutanoate degradation I 2 1 1
4-aminobutanoate degradation II 2 1 1
acetoacetate degradation (to acetyl CoA) 2 1 1
5,6-dehydrokavain biosynthesis (engineered) 10 6 4
ammonia assimilation cycle III 3 3 1
ketolysis 3 3 1
benzoyl-CoA biosynthesis 3 3 1
polyhydroxybutanoate biosynthesis 3 2 1
chitin degradation II (Vibrio) 6 2 2
superpathway of 4-aminobutanoate degradation 3 1 1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation 11 6 3
S-adenosyl-L-methionine salvage I 4 4 1
superpathway of ornithine degradation 8 6 2
GABA shunt II 4 3 1
(2S)-ethylmalonyl-CoA biosynthesis 4 2 1
GABA shunt I 4 2 1
L-arginine degradation VIII (arginine oxidase pathway) 4 1 1
L-asparagine biosynthesis III (tRNA-dependent) 4 1 1
glutaminyl-tRNAgln biosynthesis via transamidation 4 1 1
L-arginine degradation IX (arginine:pyruvate transaminase pathway) 4 1 1
superpathway of L-arginine and L-ornithine degradation 13 8 3
oleate β-oxidation 35 33 8
valproate β-oxidation 9 6 2
2-methyl-branched fatty acid β-oxidation 14 9 3
2-methylcitrate cycle I 5 5 1
(R)- and (S)-3-hydroxybutanoate biosynthesis (engineered) 5 5 1
autoinducer AI-2 biosynthesis I 5 4 1
ketogenesis 5 3 1
glutaryl-CoA degradation 5 3 1
fatty acid β-oxidation II (plant peroxisome) 5 3 1
9-cis, 11-trans-octadecadienoyl-CoA degradation (isomerase-dependent, yeast) 10 4 2
4-hydroxybenzoate biosynthesis III (plants) 5 2 1
L-lysine degradation IV 5 2 1
isopropanol biosynthesis (engineered) 5 1 1
ethylbenzene degradation (anaerobic) 5 1 1
fatty acid β-oxidation VII (yeast peroxisome) 5 1 1
pyruvate fermentation to acetone 5 1 1
pyruvate fermentation to hexanol (engineered) 11 7 2
(8E,10E)-dodeca-8,10-dienol biosynthesis 11 6 2
2-methylcitrate cycle II 6 5 1
autoinducer AI-2 biosynthesis II (Vibrio) 6 5 1
fatty acid salvage 6 5 1
pyruvate fermentation to butanol II (engineered) 6 4 1
L-isoleucine degradation I 6 4 1
propanoate fermentation to 2-methylbutanoate 6 3 1
L-lysine degradation X 6 2 1
L-lysine degradation III 6 1 1
10-trans-heptadecenoyl-CoA degradation (MFE-dependent, yeast) 6 1 1
4-ethylphenol degradation (anaerobic) 6 1 1
jasmonic acid biosynthesis 19 4 3
L-glutamate and L-glutamine biosynthesis 7 6 1
fatty acid β-oxidation I (generic) 7 6 1
L-cysteine biosynthesis VI (reverse transsulfuration) 7 4 1
acetyl-CoA fermentation to butanoate 7 4 1
4-aminobutanoate degradation V 7 3 1
pyruvate fermentation to butanoate 7 3 1
fatty acid β-oxidation VI (mammalian peroxisome) 7 3 1
chitin degradation III (Serratia) 7 2 1
L-lysine degradation I 7 1 1
mevalonate pathway I (eukaryotes and bacteria) 7 1 1
mevalonate pathway II (haloarchaea) 7 1 1
L-citrulline biosynthesis 8 7 1
L-valine degradation I 8 6 1
pyruvate fermentation to butanol I 8 3 1
2-deoxy-D-ribose degradation II 8 3 1
2-methylpropene degradation 8 2 1
isoprene biosynthesis II (engineered) 8 1 1
mevalonate pathway IV (archaea) 8 1 1
mevalonate pathway III (Thermoplasma) 8 1 1
androstenedione degradation I (aerobic) 25 6 3
superpathway of Clostridium acetobutylicum acidogenic fermentation 9 5 1
benzoate biosynthesis I (CoA-dependent, β-oxidative) 9 3 1
4-oxopentanoate degradation 9 2 1
chloramphenicol biosynthesis 9 1 1
superpathway of testosterone and androsterone degradation 28 6 3
superpathway of tetrahydrofolate biosynthesis 10 8 1
peptidoglycan recycling II 10 5 1
L-glutamate degradation V (via hydroxyglutarate) 10 5 1
3-phenylpropanoate degradation 10 4 1
superpathway of geranylgeranyldiphosphate biosynthesis I (via mevalonate) 10 4 1
L-lysine fermentation to acetate and butanoate 10 3 1
methyl tert-butyl ether degradation 10 2 1
superpathway of cholesterol degradation I (cholesterol oxidase) 42 8 4
ethylmalonyl-CoA pathway 11 2 1
superpathway of candicidin biosynthesis 11 2 1
superpathway of cholesterol degradation II (cholesterol dehydrogenase) 47 8 4
superpathway of tetrahydrofolate biosynthesis and salvage 12 10 1
superpathway of L-citrulline metabolism 12 9 1
L-glutamate degradation VII (to butanoate) 12 3 1
10-cis-heptadecenoyl-CoA degradation (yeast) 12 2 1
10-trans-heptadecenoyl-CoA degradation (reductase-dependent, yeast) 12 2 1
superpathway of Clostridium acetobutylicum solventogenic fermentation 13 5 1
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase) 13 2 1
androstenedione degradation II (anaerobic) 27 4 2
peptidoglycan recycling I 14 11 1
superpathway of glyoxylate cycle and fatty acid degradation 14 11 1
docosahexaenoate biosynthesis III (6-desaturase, mammals) 14 2 1
L-tryptophan degradation III (eukaryotic) 15 4 1
glycerol degradation to butanol 16 9 1
crotonate fermentation (to acetate and cyclohexane carboxylate) 16 3 1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation 17 7 1
nicotine degradation I (pyridine pathway) 17 4 1
benzoate fermentation (to acetate and cyclohexane carboxylate) 17 3 1
cholesterol degradation to androstenedione I (cholesterol oxidase) 17 2 1
3-hydroxypropanoate/4-hydroxybutanate cycle 18 6 1
toluene degradation VI (anaerobic) 18 3 1
sitosterol degradation to androstenedione 18 1 1
superpathway of L-lysine degradation 43 8 2
Spodoptera littoralis pheromone biosynthesis 22 4 1
cholesterol degradation to androstenedione II (cholesterol dehydrogenase) 22 2 1
superpathway of cholesterol degradation III (oxidase) 49 4 2
photosynthetic 3-hydroxybutanoate biosynthesis (engineered) 26 21 1
platensimycin biosynthesis 26 6 1
superpathway of ergosterol biosynthesis I 26 3 1
1-butanol autotrophic biosynthesis (engineered) 27 20 1
superpathway of cholesterol biosynthesis 38 3 1
Methanobacterium thermoautotrophicum biosynthetic metabolism 56 22 1
superpathway of chorismate metabolism 59 50 1