Experiment set2IT018 for Synechococcus elongatus PCC 7942

Flask growth in 60 uE Light-Dark 12:12

Group: light-dark
Media: BG11, pH=7.5
Culturing: SynE_ML6, 100ml Flask, Aerobic, at 30 (C), shaken=150 rpm
Growth: about 6.5 generations
By: Ben Rubin on 9/17/2014
Media components: 1.5 g/L Sodium nitrate, 0.04 g/L Potassium phosphate dibasic, 0.075 g/L Magnesium Sulfate Heptahydrate, 0.036 g/L Calcium chloride dihydrate, 0.006 g/L Citric Acid, 0.006 g/L Ferric ammonium citrate, 0.001 g/L EDTA (disodium salt), 0.02 g/L Sodium carbonate, Trace metal mix A5 (0.00286 g/L Boric Acid, 0.00181 g/L Manganese (II) chloride tetrahydrate, 0.000222 g/L Zinc sulfate heptahydrate, 0.00039 g/L Sodium Molybdate Dihydrate, 7.9e-05 g/L Copper (II) sulfate pentahydrate, 0.0494 mg/L Cobalt(II) nitrate hexahydrate)

Specific Phenotypes

For 20 genes in this experiment

SEED Subsystems

Subsystem	#Specific
Succinate dehydrogenase	3
Conserved gene cluster associated with Met-tRNA formyltransferase	2
Serine-glyoxylate cycle	2
TCA Cycle	2
Terminal cytochrome d ubiquinol oxidases	2
Terminal cytochrome oxidases	2
Bacterial RNA-metabolizing Zn-dependent hydrolases	1
Calvin-Benson cycle	1
Chitin and N-acetylglucosamine utilization	1
Cyanobacterial Circadian Clock	1
Entner-Doudoroff Pathway	1
Glycolysis and Gluconeogenesis	1
Glycolysis and Gluconeogenesis, including Archaeal enzymes	1
N-Acetyl-Galactosamine and Galactosamine Utilization	1
Potassium homeostasis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Pentose phosphate pathway
• Lysine biosynthesis
• Nucleotide sugars metabolism
• Lipopolysaccharide biosynthesis
• Nicotinate and nicotinamide metabolism
• Phenylpropanoid biosynthesis
• Biosynthesis of phenylpropanoids
• Glycolysis / Gluconeogenesis
• Citrate cycle (TCA cycle)
• Fructose and mannose metabolism
• Ubiquinone and menaquinone biosynthesis
• Oxidative phosphorylation
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• Cyanoamino acid metabolism
• Glutathione metabolism
• Starch and sucrose metabolism
• Other glycan degradation
• Aminosugars metabolism
• Glycosaminoglycan degradation
• Sphingolipid metabolism
• Glycosphingolipid biosynthesis - globo series
• Glycosphingolipid biosynthesis - ganglio series
• Naphthalene and anthracene degradation
• 1,4-Dichlorobenzene degradation
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• Carbon fixation in photosynthetic organisms
• Reductive carboxylate cycle (CO2 fixation)
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Caprolactam degradation
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Drug metabolism - other enzymes
• Biosynthesis of alkaloids derived from shikimate pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
aerobic respiration III (alternative oxidase pathway)	3	3	2
neolinustatin bioactivation	3	2	2
linustatin bioactivation	4	2	2
succinate to cytochrome bo oxidase electron transfer	2	1	1
linamarin degradation	2	1	1
succinate to cytochrome bd oxidase electron transfer	2	1	1
lotaustralin degradation	2	1	1
succinate to cytochrome bo quinol oxidase (cyanobacteria, cytoplamic membrane)	2	1	1
succinate to cytochrome c oxidase via plastocyanin (thylakoid membrane)	3	3	1
succinate to chytochrome c oxidase via cytochrome c6 (thylakoid membrane)	3	2	1
chitin degradation II (Vibrio)	6	2	2
cellulose degradation II (fungi)	3	1	1
aerobic respiration I (cytochrome c)	4	3	1
aerobic respiration II (cytochrome c) (yeast)	4	2	1
coumarin biosynthesis (via 2-coumarate)	5	2	1
α-tomatine degradation	6	1	1
chitin degradation III (Serratia)	7	2	1
L-lysine biosynthesis I	9	7	1
sucrose biosynthesis I (from photosynthesis)	9	7	1
TCA cycle III (animals)	10	7	1
peptidoglycan recycling II	10	3	1
glycolysis II (from fructose 6-phosphate)	11	10	1
formaldehyde assimilation III (dihydroxyacetone cycle)	12	10	1
gluconeogenesis III	12	8	1
Calvin-Benson-Bassham cycle	13	13	1
gluconeogenesis I	13	12	1
glycolysis I (from glucose 6-phosphate)	13	11	1
peptidoglycan recycling I	14	10	1
firefly bioluminescence	14	2	1
oxygenic photosynthesis	17	17	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	14	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	14	1
superpathway of hexitol degradation (bacteria)	18	12	1
superpathway of anaerobic sucrose degradation	19	14	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	12	1
superpathway of N-acetylneuraminate degradation	22	15	1
ethene biosynthesis V (engineered)	25	24	1
aspartate superpathway	25	21	1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	21	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	19	1
1-butanol autotrophic biosynthesis (engineered)	27	21	1