Experiment set1H6 for Shewanella amazonensis SB2B

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Minimal media with Potassium acetate as carbon source

Group: carbon source
Media: ShewMM_noCarbon + Potassium acetate (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: 509 A7,A8

Specific Phenotypes

For 6 genes in this experiment

For carbon source Potassium acetate in Shewanella amazonensis SB2B

For carbon source Potassium acetate across organisms

SEED Subsystems

Subsystem #Specific
Photorespiration (oxidative C2 cycle) 2
Serine-glyoxylate cycle 2
2-phosphoglycolate salvage 1
Glycolate, glyoxylate interconversions 1
HMG CoA Synthesis 1
Leucine Degradation and HMG-CoA Metabolism 1
Pyruvate Alanine Serine Interconversions 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:

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway #Steps #Present #Specific
L-aspartate degradation I 1 1 1
glycine biosynthesis III 1 1 1
L-aspartate biosynthesis 1 1 1
L-glutamate degradation II 2 2 1
malate/L-aspartate shuttle pathway 2 2 1
L-serine biosynthesis II 4 2 2
L-serine biosynthesis I 3 3 1
L-cysteine biosynthesis IX (Trichomonas vaginalis) 3 2 1
L-asparagine degradation III (mammalian) 3 2 1
acrylate degradation II 3 1 1
sulfolactate degradation III 3 1 1
(R)-cysteate degradation 3 1 1
superpathway of L-serine and glycine biosynthesis I 4 4 1
superpathway of L-aspartate and L-asparagine biosynthesis 4 4 1
photorespiration III 9 7 2
photorespiration I 9 7 2
2-methylcitrate cycle I 5 5 1
photorespiration II 10 8 2
superpathway of L-threonine biosynthesis 6 6 1
glyoxylate cycle 6 6 1
2-methylcitrate cycle II 6 5 1
TCA cycle VIII (Chlamydia) 6 5 1
β-alanine biosynthesis II 6 4 1
L-isoleucine biosynthesis IV 6 4 1
superpathway of sulfolactate degradation 6 2 1
stearate biosynthesis I (animals) 6 1 1
coenzyme M biosynthesis II 6 1 1
formaldehyde assimilation I (serine pathway) 13 8 2
anaerobic energy metabolism (invertebrates, cytosol) 7 5 1
2-deoxy-D-ribose degradation II 8 3 1
superpathway of sulfate assimilation and cysteine biosynthesis 9 9 1
superpathway of L-methionine biosynthesis (transsulfuration) 9 8 1
superpathway of coenzyme A biosynthesis II (plants) 10 8 1
sphingosine and sphingosine-1-phosphate metabolism 10 4 1
C4 photosynthetic carbon assimilation cycle, NAD-ME type 11 8 1
superpathway of L-methionine biosynthesis (by sulfhydrylation) 12 11 1
superpathway of glyoxylate bypass and TCA 12 10 1
superpathway of L-isoleucine biosynthesis I 13 13 1
superpathway of glyoxylate cycle and fatty acid degradation 14 11 1
C4 photosynthetic carbon assimilation cycle, PEPCK type 14 9 1
ceramide and sphingolipid recycling and degradation (yeast) 16 4 1
superpathway of anaerobic energy metabolism (invertebrates) 17 10 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I 18 17 1
aspartate superpathway 25 23 1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass 26 22 1
palmitate biosynthesis III 29 21 1
palmitate biosynthesis II (type II fatty acid synthase) 31 29 1
superpathway of fatty acid biosynthesis II (plant) 43 37 1
superpathway of fatty acids biosynthesis (E. coli) 53 50 1
Methanobacterium thermoautotrophicum biosynthetic metabolism 56 22 1