Experiment set5H32 for Shewanella amazonensis SB2B

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Minimal media, 20C

Group: temperature
Media: ShewMM
Culturing: SB2B_ML5, tube, Aerobic, at 20 (C), shaken=orbital
Growth: about 3.3 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 6 genes in this experiment

SEED Subsystems

Subsystem #Specific
Mannose-sensitive hemagglutinin type 4 pilus 2
Calvin-Benson cycle 1
Rhamnose containing glycans 1
dTDP-rhamnose synthesis 1
linker unit-arabinogalactan synthesis 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
S-adenosyl-L-methionine biosynthesis 1 1 1
S-adenosyl-L-methionine salvage II 3 2 1
L-methionine degradation I (to L-homocysteine) 3 1 1
ethene biosynthesis I (plants) 3 1 1
S-adenosyl-L-methionine salvage I 4 4 1
2'-deoxymugineic acid phytosiderophore biosynthesis 4 1 1
dTDP-β-L-rhamnose biosynthesis 5 5 1
superpathway of L-cysteine biosynthesis (mammalian) 5 1 1
L-cysteine biosynthesis VI (reverse transsulfuration) 7 4 1
superpathway of S-adenosyl-L-methionine biosynthesis 9 8 1
Rubisco shunt 10 9 1
O-antigen building blocks biosynthesis (E. coli) 11 10 1
L-methionine salvage cycle III 11 6 1
L-methionine salvage cycle II (plants) 11 4 1
L-methionine salvage cycle I (bacteria and plants) 12 6 1
Calvin-Benson-Bassham cycle 13 11 1
superpathway of L-methionine salvage and degradation 16 5 1
oxygenic photosynthesis 17 12 1
superpathway of dTDP-glucose-derived O-antigen building blocks biosynthesis 19 6 1
aspartate superpathway 25 23 1
ethene biosynthesis V (engineered) 25 19 1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered) 26 21 1
1-butanol autotrophic biosynthesis (engineered) 27 20 1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis 33 12 1