Experiment set5IT074 for Shewanella loihica PV-4

Compare to:

MinMedia 30C

Group: temperature
Media: ShewMM
Culturing: PV4_ML1, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 5.3 generations
By: Adam on 8/28/2013
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, 20 mM Sodium D,L-Lactate, 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 14 genes in this experiment

SEED Subsystems

Subsystem #Specific
Lactate utilization 6
Methionine Biosynthesis 2
Phosphate metabolism 2
Chorismate Synthesis 1
Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate) 1
L-rhamnose utilization 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
3-dehydroquinate biosynthesis I 2 2 1
S-adenosyl-L-methionine salvage II 3 2 1
methylglyoxal degradation V 3 2 1
S-adenosyl-L-methionine salvage I 4 4 1
L-methionine biosynthesis III 4 3 1
lactate fermentation to acetate, CO2 and hydrogen (Desulfovibrionales) 8 4 2
L-methionine biosynthesis I 5 5 1
seleno-amino acid biosynthesis (plants) 5 3 1
L-methionine biosynthesis II 6 5 1
NAD(P)/NADPH interconversion 6 3 1
chorismate biosynthesis I 7 7 1
superpathway of L-homoserine and L-methionine biosynthesis 8 8 1
superpathway of S-adenosyl-L-methionine biosynthesis 9 9 1
superpathway of L-methionine biosynthesis (transsulfuration) 9 9 1
superpathway of L-tyrosine biosynthesis 10 10 1
superpathway of L-phenylalanine biosynthesis 10 10 1
superpathway of L-methionine biosynthesis (by sulfhydrylation) 12 11 1
superpathway of L-tryptophan biosynthesis 13 13 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II 15 13 1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I 18 18 1
superpathway of aromatic amino acid biosynthesis 18 18 1
superpathway of seleno-compound metabolism 19 8 1
aspartate superpathway 25 24 1
superpathway of chorismate metabolism 59 51 1