Experiment set2IT021 for Shewanella loihica PV-4

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L-Glutamine carbon source

Group: carbon source
Media: ShewMM_noCarbon + L-Glutamine (10 mM), pH=7
Culturing: PV4_ML1, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 4.9 generations
By: Adam on 12/11/2013
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)

Specific Phenotypes

For 20 genes in this experiment

For carbon source L-Glutamine in Shewanella loihica PV-4

For carbon source L-Glutamine across organisms

SEED Subsystems

Subsystem #Specific
Multidrug Resistance Efflux Pumps 2
n-Phenylalkanoic acid degradation 2
Acetyl-CoA fermentation to Butyrate 1
Biogenesis of c-type cytochromes 1
Biotin biosynthesis 1
Butanol Biosynthesis 1
Chorismate Synthesis 1
Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate) 1
Copper homeostasis 1
Isoleucine degradation 1
Mannose-sensitive hemagglutinin type 4 pilus 1
Methicillin resistance in Staphylococci 1
Polyhydroxybutyrate metabolism 1
Teichoic and lipoteichoic acids biosynthesis 1
Terminal cytochrome C oxidases 1
Valine degradation 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
fatty acid β-oxidation III (unsaturated, odd number) 1 1 1
long-chain fatty acid activation 1 1 1
benzoyl-CoA biosynthesis 3 3 2
fatty acid β-oxidation IV (unsaturated, even number) 5 3 3
fatty acid β-oxidation I (generic) 7 6 4
oleate β-oxidation (thioesterase-dependent, yeast) 2 2 1
3-dehydroquinate biosynthesis I 2 2 1
fatty acid salvage 6 5 3
γ-linolenate biosynthesis II (animals) 2 1 1
indole-3-acetate biosynthesis IV (bacteria) 2 1 1
indole-3-acetate biosynthesis III (bacteria) 2 1 1
acrylonitrile degradation I 2 1 1
linoleate biosynthesis II (animals) 2 1 1
arsenite to oxygen electron transfer 2 1 1
oleate β-oxidation 35 33 17
adipate degradation 5 4 2
glutaryl-CoA degradation 5 3 2
fatty acid β-oxidation II (plant peroxisome) 5 3 2
adipate biosynthesis 5 3 2
fatty acid β-oxidation V (unsaturated, odd number, di-isomerase-dependent) 5 2 2
pyruvate fermentation to hexanol (engineered) 11 7 4
(8E,10E)-dodeca-8,10-dienol biosynthesis 11 6 4
2-methyl-branched fatty acid β-oxidation 14 9 5
pyruvate fermentation to butanol II (engineered) 6 5 2
valproate β-oxidation 9 6 3
L-isoleucine degradation I 6 4 2
3-methyl-branched fatty acid α-oxidation 6 3 2
methyl ketone biosynthesis (engineered) 6 3 2
propanoate fermentation to 2-methylbutanoate 6 3 2
6-gingerol analog biosynthesis (engineered) 6 2 2
alkane biosynthesis II 3 1 1
oleate biosynthesis I (plants) 3 1 1
arsenite to oxygen electron transfer (via azurin) 3 1 1
superpathway of acrylonitrile degradation 3 1 1
L-arginine degradation X (arginine monooxygenase pathway) 3 1 1
oleate β-oxidation (reductase-dependent, yeast) 3 1 1
fatty acid β-oxidation VI (mammalian peroxisome) 7 3 2
pyruvate fermentation to butanoate 7 3 2
benzoyl-CoA degradation I (aerobic) 7 2 2
L-valine degradation I 8 6 2
phosphatidylcholine acyl editing 4 3 1
aerobic respiration II (cytochrome c) (yeast) 4 3 1
phytol degradation 4 3 1
aerobic respiration I (cytochrome c) 4 3 1
pyruvate fermentation to butanol I 8 4 2
long chain fatty acid ester synthesis (engineered) 4 2 1
wax esters biosynthesis II 4 1 1
oleate β-oxidation (isomerase-dependent, yeast) 4 1 1
superpathway of Clostridium acetobutylicum acidogenic fermentation 9 5 2
phenylacetate degradation I (aerobic) 9 3 2
benzoate biosynthesis I (CoA-dependent, β-oxidative) 9 3 2
sporopollenin precursors biosynthesis 18 5 4
(R)- and (S)-3-hydroxybutanoate biosynthesis (engineered) 5 4 1
L-glutamate degradation V (via hydroxyglutarate) 10 5 2
9-cis, 11-trans-octadecadienoyl-CoA degradation (isomerase-dependent, yeast) 10 4 2
3-phenylpropanoate degradation 10 4 2
sphingosine and sphingosine-1-phosphate metabolism 10 4 2
4-hydroxybenzoate biosynthesis III (plants) 5 2 1
octane oxidation 5 2 1
Escherichia coli serotype O:15 O antigen biosynthesis 5 1 1
benzoate biosynthesis III (CoA-dependent, non-β-oxidative) 5 1 1
enterobacterial common antigen biosynthesis 5 1 1
Salmonella enterica serotype O:54 O antigen biosynthesis 5 1 1
superpathway of phenylethylamine degradation 11 4 2
stearate biosynthesis II (bacteria and plants) 6 5 1
stearate biosynthesis IV 6 4 1
Fe(II) oxidation 6 3 1
Escherichia coli serotype O:50 O antigen biosynthesis 6 2 1
Escherichia coli serotype O:149/Shigella boydii serotype O1 O antigen biosynthesis 6 2 1
L-glutamate degradation VII (to butanoate) 12 3 2
Escherichia coli serotype O:177 O antigen biosynthesis 6 1 1
Escherichia coli serotype O:56 O antigen biosynthesis 6 1 1
Salmonella enterica serotype O:13 O antigen biosynthesis 6 1 1
stearate biosynthesis I (animals) 6 1 1
Escherichia coli serotype O:77/Salmonella enterica serotype O:6,14 O antigen biosynthesis 6 1 1
superpathway of Clostridium acetobutylicum solventogenic fermentation 13 6 2
chorismate biosynthesis I 7 7 1
superpathway of glyoxylate cycle and fatty acid degradation 14 11 2
Escherichia coli serotype O:2 O antigen biosynthesis 7 2 1
ceramide degradation by α-oxidation 7 2 1
arachidonate biosynthesis III (6-desaturase, mammals) 7 1 1
Salmonella enterica serotype O:39 O antigen biosynthesis 7 1 1
icosapentaenoate biosynthesis II (6-desaturase, mammals) 7 1 1
Escherichia coli serotype O:111/Salmonella enterica serotype O:35 O antigen biosynthesis 7 1 1
Escherichia coli serotype O:85/Salmonella enterica serotype O:17 O antigen biosynthesis 7 1 1
Escherichia coli serotype O:71/Salmonella enterica serotype O:28ac O antigen biosynthesis 7 1 1
Salmonella enterica serotype O:6,7 O antigen biosynthesis 7 1 1
Salmonella enterica serotype O:18 O antigen biosynthesis 7 1 1
Escherichia coli serotype O:152 O antigen biosynthesis 7 1 1
capsaicin biosynthesis 7 1 1
Escherichia coli serotype O:157/Salmonella enterica serotype O:30 O antigen biosynthesis 7 1 1
Escherichia coli serotype O:7 O antigen biosynthesis 7 1 1
Escherichia coli serotype O:1B/Salmonella enterica serotype O:42 O antigen biosynthesis 7 1 1
icosapentaenoate biosynthesis III (8-desaturase, mammals) 7 1 1
Spodoptera littoralis pheromone biosynthesis 22 4 3
L-tryptophan degradation III (eukaryotic) 15 4 2
glycerol degradation to butanol 16 10 2
2-deoxy-D-ribose degradation II 8 3 1
ceramide and sphingolipid recycling and degradation (yeast) 16 4 2
crotonate fermentation (to acetate and cyclohexane carboxylate) 16 4 2
2-methylpropene degradation 8 2 1
Escherichia coli serotype O:107 O antigen biosynthesis 8 1 1
Escherichia coli serotype O:55/Salmonella enterica serotype O:50 O antigen biosynthesis 8 1 1
Escherichia coli serotype O:127 O antigen biosynthesis 8 1 1
Escherichia coli serotype O:51/Salmonella enterica serotype O:57 O antigen biosynthesis 8 1 1
Escherichia coli serotype O:117 O antigen biosynthesis 8 1 1
Escherichia coli serotype O:49 O antigen biosynthesis 8 1 1
Shigella boydii serotype 6 O antigen biosynthesis 8 1 1
Escherichia coli serotype O:52 O antigen biosynthesis 8 1 1
Escherichia coli serotype O:128 O antigen biosynthesis 8 1 1
Escherichia coli serotype O:21/Salmonella enterica serotype O:38 O antigen biosynthesis 8 1 1
Escherichia coli serotype O:86 O antigen biosynthesis 8 1 1
Escherichia coli serotype O:104 O antigen biosynthesis 8 1 1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation 17 8 2
benzoate fermentation (to acetate and cyclohexane carboxylate) 17 4 2
3-hydroxypropanoate/4-hydroxybutanate cycle 18 8 2
toluene degradation VI (anaerobic) 18 4 2
Escherichia coli serotype O:169 O antigen biosynthesis 9 1 1
Escherichia coli serotype O:8 O antigen biosynthesis 9 1 1
Escherichia coli serotype O:183/Shigella boydii serotype O:10 O antigen biosynthesis 9 1 1
superpathway of L-phenylalanine biosynthesis 10 10 1
superpathway of L-tyrosine biosynthesis 10 10 1
superpathway of enterobacterial common antigen biosynthesis 10 3 1
poly(3-O-β-D-glucopyranosyl-N-acetylgalactosamine 1-phosphate) wall teichoic acid biosynthesis 10 2 1
methyl tert-butyl ether degradation 10 2 1
suberin monomers biosynthesis 20 3 2
Escherichia coli serotype O:9a O antigen biosynthesis 10 1 1
Escherichia coli serotype O:9 O antigen biosynthesis 10 1 1
superpathway of fatty acid biosynthesis II (plant) 43 37 4
gallate degradation III (anaerobic) 11 3 1
poly(glycerol phosphate) wall teichoic acid biosynthesis 11 2 1
indole-3-acetate biosynthesis II 12 3 1
10-trans-heptadecenoyl-CoA degradation (reductase-dependent, yeast) 12 2 1
poly(ribitol phosphate) wall teichoic acid biosynthesis I (B. subtilis) 12 2 1
10-cis-heptadecenoyl-CoA degradation (yeast) 12 2 1
androstenedione degradation I (aerobic) 25 6 2
superpathway of L-tryptophan biosynthesis 13 13 1
platensimycin biosynthesis 26 6 2
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase) 13 2 1
1-butanol autotrophic biosynthesis (engineered) 27 21 2
androstenedione degradation II (anaerobic) 27 4 2
superpathway of testosterone and androsterone degradation 28 6 2
superpathway of cholesterol degradation I (cholesterol oxidase) 42 8 3
poly(ribitol phosphate) wall teichoic acid biosynthesis II (S. aureus) 14 2 1
docosahexaenoate biosynthesis III (6-desaturase, mammals) 14 2 1
palmitate biosynthesis II (type II fatty acid synthase) 31 29 2
superpathway of cholesterol degradation II (cholesterol dehydrogenase) 47 8 3
cutin biosynthesis 16 2 1
cholesterol degradation to androstenedione I (cholesterol oxidase) 17 2 1
superpathway of aromatic amino acid biosynthesis 18 18 1
H. pylori 26695 O-antigen biosynthesis 21 1 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 20 1
superpathway of fatty acids biosynthesis (E. coli) 53 50 2
palmitate biosynthesis III 29 21 1
superpathway of chorismate metabolism 59 51 1