Experiment set2S503 for Synechocystis sp000284455 PCC 6803

high light; bubbling

Group: light_bubbling
Media: BG11C
Culturing: Synechocystis_PCC6803_ML3, vertical flask bubling 1 % CO2, at 30 (C), shaken=air bubling
By: Luis on 5/12/25
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 29 genes in this experiment

SEED Subsystems

Subsystem	#Specific
DNA repair, UvrABC system	2
Carotenoids	1
Conserved gene cluster possibly involved in RNA metabolism	1
DNA-replication	1
DNA repair, bacterial	1
Glutathione: Non-redox reactions	1
High affinity phosphate transporter and control of PHO regulon	1
Ketoisovalerate oxidoreductase	1
Macromolecular synthesis operon	1
Methylglyoxal Metabolism	1
Peptidoglycan Biosynthesis	1
Phosphate metabolism	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Serine-glyoxylate cycle	1
Sialic Acid Metabolism	1
TCA Cycle	1
UDP-N-acetylmuramate from Fructose-6-phosphate Biosynthesis	1
Ubiquinone Biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Nucleotide sugars metabolism
• Pyruvate metabolism
• Propanoate metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of plant hormones
• Glycolysis / Gluconeogenesis
• Citrate cycle (TCA cycle)
• Fatty acid metabolism
• Ubiquinone and menaquinone biosynthesis
• Puromycin biosynthesis
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• Aminosugars metabolism
• Lipopolysaccharide biosynthesis
• Peptidoglycan biosynthesis
• alpha-Linolenic acid metabolism
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Benzoate degradation via CoA ligation
• Trinitrotoluene degradation
• C5-Branched dibasic acid metabolism
• Brassinosteroid biosynthesis
• Caprolactam degradation
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Biosynthesis of siderophore group nonribosomal peptides
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
acetate and ATP formation from acetyl-CoA III	1	1	1
acetate conversion to acetyl-CoA	1	1	1
menaquinol-4 biosynthesis I	1	1	1
menaquinol-9 biosynthesis	1	1	1
menaquinol-8 biosynthesis	1	1	1
menaquinol-6 biosynthesis	1	1	1
menaquinol-13 biosynthesis	2	2	1
menaquinol-12 biosynthesis	2	2	1
menaquinol-11 biosynthesis	2	2	1
menaquinol-7 biosynthesis	2	2	1
menaquinol-10 biosynthesis	2	2	1
UDP-α-D-glucose biosynthesis	2	1	1
ethanol degradation II	3	3	1
superpathway of acetate utilization and formation	3	3	1
ethanol degradation IV	3	3	1
ethanol degradation III	3	2	1
pyruvate fermentation to acetate V	3	2	1
GDP-α-D-glucose biosynthesis	3	2	1
pyruvate fermentation to acetate VI	3	2	1
methylglyoxal degradation VIII	3	2	1
methylglyoxal degradation I	3	2	1
L-isoleucine biosynthesis V	3	2	1
trehalose degradation V	3	2	1
glycogen biosynthesis I (from ADP-D-Glucose)	4	4	1
sucrose degradation IV (sucrose phosphorylase)	4	3	1
starch degradation V	4	3	1
chitin deacetylation	4	2	1
starch degradation III	4	2	1
UDP-N-acetyl-D-glucosamine biosynthesis I	5	5	1
glucosylglycerol biosynthesis	5	5	1
dTDP-β-L-rhamnose biosynthesis	5	5	1
CDP-6-deoxy-D-gulose biosynthesis	5	3	1
sucrose degradation II (sucrose synthase)	5	3	1
glucose and glucose-1-phosphate degradation	5	3	1
2-methylcitrate cycle I	5	2	1
D-galactose degradation I (Leloir pathway)	5	2	1
adipate degradation	5	1	1
adipate biosynthesis	5	1	1
O-antigen building blocks biosynthesis (E. coli)	11	10	2
TCA cycle VIII (Chlamydia)	6	6	1
L-isoleucine biosynthesis IV	6	4	1
glycogen degradation II	6	4	1
superpathway of UDP-glucose-derived O-antigen building blocks biosynthesis	6	3	1
peptidoglycan maturation (meso-diaminopimelate containing)	12	4	2
2-methylcitrate cycle II	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
lupulone and humulone biosynthesis	6	1	1
adlupulone and adhumulone biosynthesis	6	1	1
incomplete reductive TCA cycle	7	4	1
glycogen degradation I	8	7	1
sucrose biosynthesis II	8	7	1
ubiquinol-8 biosynthesis (early decarboxylation)	8	4	1
superpathway of methylglyoxal degradation	8	2	1
glycogen biosynthesis III (from α-maltose 1-phosphate)	8	2	1
TCA cycle II (plants and fungi)	9	8	1
TCA cycle V (2-oxoglutarate synthase)	9	8	1
sucrose biosynthesis I (from photosynthesis)	9	8	1
reductive glycine pathway of autotrophic CO2 fixation	9	6	1
chitin biosynthesis	9	5	1
cis-geranyl-CoA degradation	9	1	1
superpathway of menaquinol-8 biosynthesis III	9	1	1
superpathway of menaquinol-11 biosynthesis	10	9	1
TCA cycle I (prokaryotic)	10	9	1
superpathway of menaquinol-6 biosynthesis	10	9	1
superpathway of menaquinol-10 biosynthesis	10	9	1
superpathway of menaquinol-13 biosynthesis	10	9	1
superpathway of menaquinol-9 biosynthesis	10	9	1
superpathway of menaquinol-12 biosynthesis	10	9	1
superpathway of menaquinol-8 biosynthesis I	10	9	1
superpathway of menaquinol-7 biosynthesis	10	9	1
TCA cycle III (animals)	10	8	1
starch biosynthesis	10	6	1
superpathway of coenzyme A biosynthesis II (plants)	10	5	1
anaerobic energy metabolism (invertebrates, mitochondrial)	10	5	1
CMP-legionaminate biosynthesis I	10	2	1
superpathway of menaquinol-8 biosynthesis II	10	1	1
colanic acid building blocks biosynthesis	11	10	1
reductive TCA cycle I	11	7	1
superpathway of glyoxylate bypass and TCA	12	9	1
reductive TCA cycle II	12	6	1
superpathway of ubiquinol-8 biosynthesis (early decarboxylation)	12	6	1
peptidoglycan recycling I	14	9	1
superpathway of mycolyl-arabinogalactan-peptidoglycan complex biosynthesis	33	13	2
peptidoglycan biosynthesis IV (Enterococcus faecium)	17	12	1
peptidoglycan biosynthesis II (staphylococci)	17	12	1
superpathway of anaerobic energy metabolism (invertebrates)	17	9	1
streptomycin biosynthesis	18	2	1
superpathway of anaerobic sucrose degradation	19	14	1
methylaspartate cycle	19	9	1
superpathway of dTDP-glucose-derived O-antigen building blocks biosynthesis	19	6	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	19	1
superpathway of UDP-N-acetylglucosamine-derived O-antigen building blocks biosynthesis	24	6	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	21	1
superpathway of chorismate metabolism	59	43	2
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	20	1