Experiment set1S143 for Synechocystis sp000284455 PCC 6803

growth in full media and 10 mM glucose= photoheterotrophic growth

Group: nitrogen source
Media: BG11C + D-Glucose (10 mM) + DCMU (20 uM)
Culturing: Synechocystis_PCC6803_ML3, flask, 100 rpm orbital shaking, growth chamber, continous light, at 30 (C), shaken=100 rpm
Growth: about 4.0 generations
By: Luis on 1/20/25
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 5 genes in this experiment

For nitrogen source D-Glucose in Synechocystis sp000284455 PCC 6803

For nitrogen source D-Glucose across organisms

SEED Subsystems

Subsystem	#Specific
Entner-Doudoroff Pathway	1
Glycogen metabolism	1
NAD and NADP cofactor biosynthesis global	1
Pentose phosphate pathway	1
Serine-glyoxylate cycle	1
TCA Cycle	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glutamate metabolism
• Butanoate metabolism
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of plant hormones
• Citrate cycle (TCA cycle)
• Pentose phosphate pathway
• Tyrosine metabolism
• Glutathione metabolism
• Starch and sucrose metabolism
• Pyruvate metabolism
• Glyoxylate and dicarboxylate metabolism
• Carbon fixation in photosynthetic organisms
• Reductive carboxylate cycle (CO2 fixation)
• Nicotinate and nicotinamide metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from terpenoid and polyketide

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
NADP biosynthesis	1	1	1
4-aminobutanoate degradation III	2	2	1
malate/L-aspartate shuttle pathway	2	2	1
NAD phosphorylation and transhydrogenation	2	2	1
4-aminobutanoate degradation I	2	2	1
cytosolic NADPH production (yeast)	5	3	2
pentose phosphate pathway (oxidative branch) I	3	3	1
NAD phosphorylation and dephosphorylation	3	2	1
superpathway of 4-aminobutanoate degradation	3	2	1
N-methylpyrrolidone degradation	3	1	1
4-aminobutanoate degradation IV	3	1	1
GABA shunt II	4	4	1
glycogen biosynthesis I (from ADP-D-Glucose)	4	4	1
GABA shunt I	4	3	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	4	2
mitochondrial NADPH production (yeast)	5	2	1
TCA cycle VIII (Chlamydia)	6	6	1
glyoxylate cycle	6	4	1
formaldehyde oxidation I	6	3	1
NAD(P)/NADPH interconversion	6	3	1
L-lysine biosynthesis VI	7	7	1
anaerobic energy metabolism (invertebrates, cytosol)	7	4	1
incomplete reductive TCA cycle	7	4	1
pyruvate fermentation to propanoate I	7	2	1
pentose phosphate pathway	8	8	1
TCA cycle V (2-oxoglutarate synthase)	9	8	1
TCA cycle II (plants and fungi)	9	8	1
TCA cycle IV (2-oxoglutarate decarboxylase)	9	8	1
L-lysine biosynthesis I	9	7	1
Entner-Doudoroff pathway I	9	7	1
L-lysine biosynthesis II	9	6	1
TCA cycle I (prokaryotic)	10	9	1
TCA cycle III (animals)	10	8	1
starch biosynthesis	10	6	1
reductive TCA cycle I	11	7	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	6	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	5	1
L-glutamate degradation VIII (to propanoate)	11	2	1
superpathway of glyoxylate bypass and TCA	12	9	1
gluconeogenesis III	12	8	1
reductive TCA cycle II	12	6	1
gluconeogenesis I	13	12	1
formaldehyde assimilation I (serine pathway)	13	8	1
superpathway of L-arginine and L-ornithine degradation	13	6	1
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	4	1
superpathway of glyoxylate cycle and fatty acid degradation	14	7	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	12	1
mixed acid fermentation	16	12	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	14	1
superpathway of glucose and xylose degradation	17	14	1
superpathway of anaerobic energy metabolism (invertebrates)	17	9	1
heterolactic fermentation	18	14	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	12	1
methylaspartate cycle	19	9	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	19	1
aspartate superpathway	25	19	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	21	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	20	1