Experiment set4IT077 for Shewanella sp. ANA-3

Anaerobic growth with fumarate as e acceptor

Group: anaerobic
Media: ShewMM + Sodium Fumarate dibasic (30 mM) + Yeast Extract (0.1 g/L), pH=7
Culturing: ANA3_ML1, hungate, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 2.2 generations
By: Mark on 1/14/2015
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 13 genes in this experiment

For anaerobic Sodium Fumarate dibasic in Shewanella sp. ANA-3

For anaerobic Sodium Fumarate dibasic across organisms

SEED Subsystems

Subsystem	#Specific
Menaquinone and Phylloquinone Biosynthesis	3
Butanol Biosynthesis	1
Fermentations: Mixed acid	1

Metabolic Maps

Color code by fitness: see overview map or list of maps.

Maps containing gene(s) with specific phenotypes:

• Ubiquinone and menaquinone biosynthesis
• Butanoate metabolism
• Biosynthesis of phenylpropanoids
• Citrate cycle (TCA cycle)
• Oxidative phosphorylation
• Pyruvate metabolism
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Biosynthesis of siderophore group nonribosomal peptides
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
2-carboxy-1,4-naphthoquinol biosynthesis	7	7	5
superpathway of demethylmenaquinol-8 biosynthesis I	9	9	5
superpathway of demethylmenaquinol-9 biosynthesis	9	8	5
superpathway of demethylmenaquinol-6 biosynthesis I	9	8	5
superpathway of menaquinol-8 biosynthesis I	10	10	5
superpathway of menaquinol-10 biosynthesis	10	9	5
superpathway of menaquinol-12 biosynthesis	10	9	5
superpathway of menaquinol-6 biosynthesis	10	9	5
superpathway of menaquinol-13 biosynthesis	10	9	5
superpathway of menaquinol-11 biosynthesis	10	9	5
superpathway of menaquinol-9 biosynthesis	10	9	5
superpathway of menaquinol-7 biosynthesis	10	9	5
reductive monocarboxylic acid cycle	2	1	1
salicylate biosynthesis I	2	1	1
pyruvate fermentation to ethanol I	3	3	1
pyruvate fermentation to acetate IV	3	3	1
salicylate biosynthesis II	3	2	1
2,3-dihydroxybenzoate biosynthesis	3	2	1
superpathway of phylloquinol biosynthesis	15	8	5
L-threonine degradation I	6	6	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	7	1
vibriobactin biosynthesis	9	2	1
enterobactin biosynthesis	11	5	1
superpathway of chorismate metabolism	59	51	5
bacillibactin biosynthesis	12	4	1
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	7	1
mixed acid fermentation	16	15	1
superpathway of L-threonine metabolism	18	15	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	14	1
superpathway of N-acetylneuraminate degradation	22	16	1