Experiment set3H8 for Shewanella oneidensis MR-1

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Gelatin carbon source replicate 1

Group: carbon source
Media: ShewMM_noCarbon + Gelatin (1 mg/ml), pH=7
Culturing: MR1_ML3, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 4.3 generations
By: Adam on 8/18/2013
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 27 genes in this experiment

For carbon source Gelatin in Shewanella oneidensis MR-1

For carbon source Gelatin across organisms

SEED Subsystems

Subsystem #Specific
Arginine and Ornithine Degradation 3
Homogentisate pathway of aromatic compound degradation 2
Acid resistance mechanisms 1
Aromatic amino acid degradation 1
Histidine Degradation 1
Mannose-sensitive hemagglutinin type 4 pilus 1
N-linked Glycosylation in Bacteria 1
Plastoquinone Biosynthesis 1
Polyamine Metabolism 1
Proline, 4-hydroxyproline uptake and utilization 1
Queuosine-Archaeosine Biosynthesis 1
Respiratory dehydrogenases 1 1
Tocopherol Biosynthesis 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
arginine dependent acid resistance 1 1 1
L-proline degradation I 3 3 2
L-tyrosine degradation I 5 5 3
proline to cytochrome bo oxidase electron transfer 2 1 1
L-arginine degradation III (arginine decarboxylase/agmatinase pathway) 2 1 1
putrescine biosynthesis I 2 1 1
L-arginine degradation II (AST pathway) 5 5 2
putrescine biosynthesis II 3 3 1
L-arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway) 3 3 1
L-arginine degradation I (arginase pathway) 3 2 1
gentisate degradation I 3 1 1
plastoquinol-9 biosynthesis I 3 1 1
L-histidine degradation I 4 4 1
superpathway of putrescine biosynthesis 4 2 1
spermidine biosynthesis III 4 2 1
ethene biosynthesis II (microbes) 4 1 1
4-hydroxy-2-nonenal detoxification 4 1 1
L-histidine degradation II 5 3 1
superpathway of plastoquinol biosynthesis 5 2 1
pentachlorophenol degradation 10 3 2
L-histidine degradation III 6 4 1
5-nitroanthranilate degradation 6 2 1
(5R)-carbapenem carboxylate biosynthesis 6 1 1
L-Nδ-acetylornithine biosynthesis 7 5 1
vitamin E biosynthesis (tocopherols) 7 1 1
L-histidine degradation VI 8 7 1
L-citrulline biosynthesis 8 7 1
superpathway of polyamine biosynthesis II 8 6 1
superpathway of polyamine biosynthesis I 8 4 1
glutathione-mediated detoxification I 8 3 1
L-phenylalanine degradation IV (mammalian, via side chain) 9 3 1
gliotoxin biosynthesis 9 2 1
glutathione-mediated detoxification II 9 1 1
3-phenylpropanoate degradation 10 4 1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation 11 6 1
superpathway of L-citrulline metabolism 12 9 1
indole glucosinolate activation (intact plant cell) 12 3 1
camalexin biosynthesis 12 2 1
superpathway of L-arginine and L-ornithine degradation 13 8 1
superpathway of arginine and polyamine biosynthesis 17 13 1