Experiment set2IT023 for Shewanella loihica PV-4

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Gelatin carbon source

Group: carbon source
Media: ShewMM_noCarbon + Gelatin (1 mg/ml), pH=7
Culturing: PV4_ML1, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 6.0 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 10 genes in this experiment

For carbon source Gelatin in Shewanella loihica PV-4

For carbon source Gelatin across organisms

SEED Subsystems

Subsystem #Specific
Proline, 4-hydroxyproline uptake and utilization 4
D-Galacturonate and D-Glucuronate Utilization 1
Respiratory dehydrogenases 1 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
trans-4-hydroxy-L-proline degradation II 4 3 3
pyruvate fermentation to acetate VIII 2 2 1
L-carnitine degradation II 3 2 1
D-galactarate degradation II 3 1 1
D-glucarate degradation II 3 1 1
L-lyxonate degradation 3 1 1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast) 8 7 2
dipicolinate biosynthesis 4 3 1
1,2-dichloroethane degradation 4 2 1
mitochondrial NADPH production (yeast) 5 4 1
cytosolic NADPH production (yeast) 5 4 1
D-glucuronate degradation II 5 2 1
D-xylose degradation V 5 1 1
D-xylose degradation III 5 1 1
D-galacturonate degradation II 5 1 1
L-arabinose degradation III 6 2 1
D-arabinose degradation III 6 2 1
L-lysine biosynthesis III 7 6 1
L-lysine biosynthesis VI 7 6 1
lipoprotein posttranslational modification (Gram-negative bacteria) 7 3 1
L-lysine biosynthesis I 9 9 1
L-lysine biosynthesis II 9 7 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 pentose and pentitol degradation 42 6 2
aspartate superpathway 25 24 1
superpathway of microbial D-galacturonate and D-glucuronate degradation 31 7 1