Experiment set2IT006 for Shewanella loihica PV-4

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Sodium succinate dibasic hexahydrate carbon source

Group: carbon source
Media: ShewMM_noCarbon + Sodium succinate dibasic hexahydrate (10 mM), pH=7
Culturing: PV4_ML1, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 4.3 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 3 genes in this experiment

For carbon source Sodium succinate dibasic hexahydrate in Shewanella loihica PV-4

For carbon source Sodium succinate dibasic hexahydrate across organisms

SEED Subsystems

Subsystem #Specific
Calvin-Benson 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
Rubisco shunt 10 9 1
Calvin-Benson-Bassham cycle 13 11 1
oxygenic photosynthesis 17 12 1
ethene biosynthesis V (engineered) 25 19 1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered) 26 20 1
1-butanol autotrophic biosynthesis (engineered) 27 21 1