Experiment set1H41 for Shewanella loihica PV-4

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Potassium acetate carbon source

Group: carbon source
Media: ShewMM_noCarbon + Potassium acetate (20 mM), pH=7
Culturing: PV4_ML1, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 2.8 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 15 genes in this experiment

For carbon source Potassium acetate in Shewanella loihica PV-4

For carbon source Potassium acetate across organisms

SEED Subsystems

Subsystem #Specific
Type IV pilus 4
HMG CoA Synthesis 1
Leucine Degradation and HMG-CoA Metabolism 1
Multidrug Resistance Efflux Pumps 1
Proteasome bacterial 1
Proteolysis in bacteria, ATP-dependent 1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate 1
Serine-glyoxylate cycle 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:

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway #Steps #Present #Specific
acrylate degradation II 3 3 1
2-methylcitrate cycle I 5 5 1
glyoxylate cycle 6 6 1
2-methylcitrate cycle II 6 5 1
β-alanine biosynthesis II 6 5 1
L-isoleucine biosynthesis IV 6 4 1
stearate biosynthesis I (animals) 6 1 1
2-carboxy-1,4-naphthoquinol biosynthesis 7 7 1
2-deoxy-D-ribose degradation II 8 3 1
superpathway of demethylmenaquinol-8 biosynthesis I 9 9 1
superpathway of demethylmenaquinol-6 biosynthesis I 9 8 1
superpathway of demethylmenaquinol-9 biosynthesis 9 8 1
superpathway of menaquinol-8 biosynthesis I 10 10 1
superpathway of menaquinol-7 biosynthesis 10 9 1
superpathway of menaquinol-10 biosynthesis 10 9 1
superpathway of menaquinol-11 biosynthesis 10 9 1
superpathway of menaquinol-6 biosynthesis 10 9 1
superpathway of menaquinol-9 biosynthesis 10 9 1
superpathway of coenzyme A biosynthesis II (plants) 10 9 1
superpathway of menaquinol-13 biosynthesis 10 9 1
superpathway of menaquinol-12 biosynthesis 10 9 1
sphingosine and sphingosine-1-phosphate metabolism 10 4 1
superpathway of glyoxylate bypass and TCA 12 10 1
superpathway of glyoxylate cycle and fatty acid degradation 14 11 1
superpathway of phylloquinol biosynthesis 15 7 1
ceramide and sphingolipid recycling and degradation (yeast) 16 4 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
superpathway of chorismate metabolism 59 51 1