Experiment set1S142 for Synechocystis sp000284455 PCC 6803

growth in full media and 10 mM glucose= photomixotrophic growth

Group: nitrogen source
Media: BG11C + D-Glucose (10 mM)
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

Specific Phenotypes

For 46 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
CO2 uptake, carboxysome	3
Alanine biosynthesis	2
DNA-replication	2
Bacterial hemoglobins	1
Campylobacter Iron Metabolism	1
Conserved gene cluster associated with Met-tRNA formyltransferase	1
Cyanobacterial Circadian Clock	1
DNA repair, bacterial UvrD and related helicases	1
Folate Biosynthesis	1
Fructose utilization	1
Glutathione: Non-redox reactions	1
Methylglyoxal Metabolism	1
NAD and NADP cofactor biosynthesis global	1
Pentose phosphate pathway	1
Peptidoglycan Biosynthesis	1
Purine conversions	1
RNA processing and degradation, bacterial	1
Ribosomal protein S12p Asp methylthiotransferase	1
Transcription factors bacterial	1
Two cell division clusters relating to chromosome partitioning	1
cAMP signaling in bacteria	1
tRNA processing	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Purine metabolism
• Puromycin biosynthesis
• Lipopolysaccharide biosynthesis
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of alkaloids derived from shikimate pathway
• Pentose phosphate pathway
• Ubiquinone and menaquinone biosynthesis
• Oxidative phosphorylation
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• Nucleotide sugars metabolism
• alpha-Linolenic acid metabolism
• Pyruvate metabolism
• Naphthalene and anthracene degradation
• Trinitrotoluene degradation
• Thiamine metabolism
• Nicotinate and nicotinamide metabolism
• Folate biosynthesis
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Biosynthesis of phenylpropanoids
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
menaquinol-4 biosynthesis I	1	1	1
NADP biosynthesis	1	1	1
L-cysteine degradation IV	1	1	1
menaquinol-8 biosynthesis	1	1	1
L-alanine biosynthesis III	1	1	1
menaquinol-9 biosynthesis	1	1	1
menaquinol-6 biosynthesis	1	1	1
menaquinol-10 biosynthesis	2	2	1
menaquinol-11 biosynthesis	2	2	1
NAD phosphorylation and transhydrogenation	2	2	1
menaquinol-13 biosynthesis	2	2	1
menaquinol-12 biosynthesis	2	2	1
menaquinol-7 biosynthesis	2	2	1
adenine and adenosine salvage I	2	1	1
guanine and guanosine salvage II	2	1	1
cytidylyl molybdenum cofactor sulfurylation	2	1	1
guanine and guanosine salvage I	2	1	1
adenine and adenosine salvage II	2	1	1
methylglyoxal degradation VIII	3	2	1
methylglyoxal degradation I	3	2	1
NAD phosphorylation and dephosphorylation	3	2	1
L-serine degradation	3	2	1
L-cysteine degradation II	3	2	1
L-methionine degradation II	3	2	1
L-tryptophan degradation II (via pyruvate)	3	2	1
D-serine degradation	3	2	1
bis(guanylyl molybdopterin) cofactor sulfurylation	3	1	1
superpathway of guanine and guanosine salvage	3	1	1
adenine salvage	3	1	1
thiazole component of thiamine diphosphate biosynthesis II	7	5	2
superpathway of L-alanine biosynthesis	4	2	1
tRNA-uridine 2-thiolation (yeast mitochondria)	4	1	1
tRNA-uridine 2-thiolation (mammalian mitochondria)	4	1	1
pentose phosphate pathway (non-oxidative branch) I	5	5	1
cytosolic NADPH production (yeast)	5	3	1
mitochondrial NADPH production (yeast)	5	2	1
felinine and 3-methyl-3-sulfanylbutan-1-ol biosynthesis	5	2	1
[2Fe-2S] iron-sulfur cluster biosynthesis	10	2	2
tRNA-uridine 2-thiolation (thermophilic bacteria)	5	1	1
superpathway of thiamine diphosphate biosynthesis II	11	8	2
L-threonine degradation I	6	5	1
thiazole component of thiamine diphosphate biosynthesis I	6	3	1
NAD(P)/NADPH interconversion	6	3	1
L-methionine biosynthesis II	6	3	1
molybdopterin biosynthesis	6	1	1
L-isoleucine biosynthesis I (from threonine)	7	7	1
superpathway of purine nucleotide salvage	14	11	2
glycine betaine degradation III	7	3	1
glyphosate degradation III	7	2	1
pentose phosphate pathway	8	8	1
L-mimosine degradation	8	4	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	4	1
glutathione-mediated detoxification I	8	3	1
glycine betaine degradation I	8	3	1
superpathway of methylglyoxal degradation	8	2	1
(aminomethyl)phosphonate degradation	8	2	1
tRNA-uridine 2-thiolation (cytoplasmic)	8	1	1
formaldehyde assimilation II (assimilatory RuMP Cycle)	9	7	1
superpathway of menaquinol-8 biosynthesis III	9	1	1
Rubisco shunt	10	10	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-7 biosynthesis	10	9	1
superpathway of menaquinol-8 biosynthesis I	10	9	1
superpathway of menaquinol-12 biosynthesis	10	9	1
superpathway of menaquinol-11 biosynthesis	10	9	1
superpathway of menaquinol-6 biosynthesis	10	9	1
superpathway of thiamine diphosphate biosynthesis I	10	6	1
superpathway of menaquinol-8 biosynthesis II	10	1	1
tRNA-uridine 2-thiolation and selenation (bacteria)	11	2	1
formaldehyde assimilation III (dihydroxyacetone cycle)	12	10	1
superpathway of L-isoleucine biosynthesis I	13	13	1
hypoglycin biosynthesis	14	4	1
Bifidobacterium shunt	15	13	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	12	1
superpathway of branched chain amino acid biosynthesis	17	17	1
superpathway of glucose and xylose degradation	17	14	1
superpathway of L-threonine metabolism	18	11	1
purine nucleobases degradation II (anaerobic)	24	11	1
superpathway of chorismate metabolism	59	43	1