Experiment set2IT031 for Synechococcus elongatus PCC 7942

Flask grown to static phase (untill yellowing)

Group: stationary phase
Media: BG11, pH=7.5
Culturing: SynE_ML6, 100ml Flask, Aerobic, at 30 (C), shaken=150 rpm
Growth: about 4.5 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 56 genes in this experiment

SEED Subsystems

Subsystem	#Specific
CO2 uptake, carboxysome	2
Coenzyme F420 synthesis	2
Glycolate, glyoxylate interconversions	2
Photorespiration (oxidative C2 cycle)	2
Glutathione: Biosynthesis and gamma-glutamyl cycle	1
Glutathione: Non-redox reactions	1
Ketoisovalerate oxidoreductase	1
Methylglyoxal Metabolism	1
Peptidoglycan Biosynthesis	1
Pyruvate Alanine Serine Interconversions	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Rhamnose containing glycans	1
Streptococcus pyogenes recombinatorial zone	1
Utilization of glutathione as a sulphur source	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:

• Taurine and hypotaurine metabolism
• Pyruvate metabolism
• Glyoxylate and dicarboxylate metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Glycolysis / Gluconeogenesis
• Oxidative phosphorylation
• Puromycin biosynthesis
• Arginine and proline metabolism
• Selenoamino acid metabolism
• Cyanoamino acid metabolism
• Glutathione metabolism
• Nucleotide sugars metabolism
• Streptomycin biosynthesis
• Polyketide sugar unit biosynthesis
• Peptidoglycan biosynthesis
• Arachidonic acid metabolism
• alpha-Linolenic acid metabolism
• Trinitrotoluene degradation
• Propanoate metabolism
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• mTOR signaling pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-alanine degradation IV	1	1	1
acetate conversion to acetyl-CoA	1	1	1
acetate and ATP formation from acetyl-CoA III	1	1	1
CO2 fixation into oxaloacetate (anaplerotic)	2	2	1
glycolate and glyoxylate degradation II	2	1	1
glutathione degradation (DUG pathway)	2	1	1
ethanol degradation IV	3	3	1
cyanate degradation	3	3	1
ethanol degradation II	3	3	1
L-isoleucine biosynthesis V	3	2	1
methylglyoxal degradation VIII	3	2	1
superpathway of acetate utilization and formation	3	2	1
methylglyoxal degradation I	3	2	1
ethanol degradation III	3	2	1
glycolate and glyoxylate degradation III	3	1	1
glycolate and glyoxylate degradation I	4	2	1
dTDP-N-acetylthomosamine biosynthesis	4	2	1
chitin deacetylation	4	2	1
dTDP-N-acetylviosamine biosynthesis	4	2	1
dTDP-β-D-fucofuranose biosynthesis	4	2	1
dTDP-6-deoxy-α-D-allose biosynthesis	4	2	1
creatinine degradation I	4	1	1
dTDP-β-L-rhamnose biosynthesis	5	5	1
dTDP-4-O-demethyl-β-L-noviose biosynthesis	5	3	1
dTDP-3-acetamido-α-D-fucose biosynthesis	5	2	1
dTDP-α-D-mycaminose biosynthesis	5	2	1
2-methylcitrate cycle I	5	2	1
dTDP-3-acetamido-3,6-dideoxy-α-D-glucose biosynthesis	5	2	1
peptido-conjugates in tissue regeneration biosynthesis	17	3	3
L-isoleucine biosynthesis IV	6	4	1
γ-glutamyl cycle	6	4	1
dTDP-L-daunosamine biosynthesis	6	3	1
dTDP-sibirosamine biosynthesis	6	3	1
peptidoglycan maturation (meso-diaminopimelate containing)	12	4	2
2-methylcitrate cycle II	6	2	1
dTDP-α-D-ravidosamine and dTDP-4-acetyl-α-D-ravidosamine biosynthesis	6	2	1
dTDP-D-desosamine biosynthesis	6	2	1
superpathway of bitter acids biosynthesis	18	3	3
β-alanine biosynthesis II	6	1	1
colupulone and cohumulone biosynthesis	6	1	1
leukotriene biosynthesis	6	1	1
adlupulone and adhumulone biosynthesis	6	1	1
lupulone and humulone biosynthesis	6	1	1
C4 photosynthetic carbon assimilation cycle, NADP-ME type	7	4	1
superpathway of glycol metabolism and degradation	7	3	1
dTDP-β-L-digitoxose biosynthesis	7	3	1
dTDP-β-L-olivose biosynthesis	7	3	1
dTDP-β-L-mycarose biosynthesis	7	2	1
dTDP-β-L-megosamine biosynthesis	8	3	1
dTDP-β-L-4-epi-vancosamine biosynthesis	8	3	1
superpathway of methylglyoxal degradation	8	2	1
photorespiration III	9	8	1
photorespiration I	9	8	1
reductive glycine pathway of autotrophic CO2 fixation	9	6	1
dTDP-α-D-forosamine biosynthesis	9	3	1
dTDP-α-D-olivose, dTDP-α-D-oliose and dTDP-α-D-mycarose biosynthesis	9	3	1
cis-geranyl-CoA degradation	9	1	1
photorespiration II	10	8	1
superpathway of coenzyme A biosynthesis II (plants)	10	5	1
peptidoglycan recycling II	10	3	1
superpathway of enterobacterial common antigen biosynthesis	10	3	1
O-antigen building blocks biosynthesis (E. coli)	11	10	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	7	1
3-hydroxypropanoate cycle	13	4	1
glyoxylate assimilation	13	3	1
peptidoglycan recycling I	14	10	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	7	1
hypoglycin biosynthesis	14	3	1
peptidoglycan biosynthesis IV (Enterococcus faecium)	17	12	1
peptidoglycan biosynthesis II (staphylococci)	17	12	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	4	1
superpathway of the 3-hydroxypropanoate cycle	18	4	1
superpathway of dTDP-glucose-derived O-antigen building blocks biosynthesis	19	6	1
superpathway of novobiocin biosynthesis	19	3	1
superpathway of erythromycin biosynthesis	19	2	1
superpathway of megalomicin A biosynthesis	22	3	1
superpathway of dTDP-glucose-derived antibiotic building blocks biosynthesis	23	3	1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	33	13	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	19	1