Experiment set1S114 for Synechocystis sp000284455 PCC 6803

growth in full media bubbled with ambient air

Group: carbon dioxide
Media: BG11C, pH=8
Culturing: Synechocystis_PCC6803_ML3, vertical flask, air bubling, growth chamber, continous light, at 30 (C), shaken=air bubling
Growth: about 6.0 generations
By: Luis on 1/13/25
Media components: 17.6 mM Sodium nitrate, 0.2 mM Potassium phosphate dibasic, 0.3 mM Magnesium Sulfate Heptahydrate, 0.24 mM Calcium chloride dihydrate, 28.5 uM Citric Acid, 0.006 g/L Ferric ammonium citrate, 2.4 uM EDTA (disodium salt), 0.2 mM Sodium bicarbonate, 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 18 genes in this experiment

SEED Subsystems

Subsystem	#Specific
Ammonia assimilation	2
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	2
Glycolate, glyoxylate interconversions	1
Photorespiration (oxidative C2 cycle)	1
Restriction-Modification System	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glutamate metabolism
• N-Glycan biosynthesis
• Nitrogen metabolism
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Fructose and mannose metabolism
• Cysteine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• O-Glycan biosynthesis
• High-mannose type N-glycan biosynthesis
• O-Mannosyl glycan biosynthesis
• Keratan sulfate biosynthesis
• Lipopolysaccharide biosynthesis
• Peptidoglycan biosynthesis
• Glycerolipid metabolism
• Glycosylphosphatidylinositol(GPI)-anchor biosynthesis
• Sphingolipid metabolism
• Glycosphingolipid biosynthesis - lacto and neolacto series
• Glycosphingolipid biosynthesis - globo series
• Glycosphingolipid biosynthesis - ganglio series
• Glyoxylate and dicarboxylate metabolism
• Carotenoid biosynthesis - General
• Zeatin biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Flavone and flavonol biosynthesis

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-glutamate biosynthesis I	2	2	2
L-glutamate biosynthesis IV	1	1	1
L-glutamine degradation II	1	1	1
L-glutamine degradation I	1	1	1
ammonia assimilation cycle III	3	3	2
ammonia assimilation cycle I	2	2	1
glycolate and glyoxylate degradation II	2	1	1
L-glutamate and L-glutamine biosynthesis	7	6	3
superpathway of ammonia assimilation (plants)	3	3	1
glycolate and glyoxylate degradation III	3	1	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	4	1
L-asparagine biosynthesis III (tRNA-dependent)	4	4	1
glycolate and glyoxylate degradation I	4	3	1
ergothioneine biosynthesis II (fungi)	5	3	1
protein O-mannosylation II (mammals, core M1 and core M2)	5	1	1
protein O-mannosylation III (mammals, core M3)	5	1	1
ergothioneine biosynthesis I (bacteria)	7	4	1
superpathway of glycol metabolism and degradation	7	4	1
L-citrulline biosynthesis	8	5	1
protein O-mannosylation I (yeast)	8	1	1
photorespiration III	9	9	1
photorespiration II	10	10	1
protein N-glycosylation (Haloferax volcanii)	11	1	1
superpathway of L-citrulline metabolism	12	7	1
protein N-glycosylation initial phase (eukaryotic)	19	1	1