Experiment set2IT030 for Synechococcus elongatus PCC 7942

Flask grown at 18C

Group: temperature
Media: BG11, pH=7.5
Culturing: SynE_ML6, 100ml Flask, Aerobic, at 18 (C), shaken=150 rpm
Growth: about 6.8 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 68 genes in this experiment

SEED Subsystems

Subsystem	#Specific
High affinity phosphate transporter and control of PHO regulon	3
Phosphate metabolism	3
Synechocystis experimental	3
Coenzyme F420 synthesis	2
Glycolate, glyoxylate interconversions	2
Heat shock dnaK gene cluster extended	2
Methionine Salvage	2
Photorespiration (oxidative C2 cycle)	2
2-phosphoglycolate salvage	1
Bacterial Cell Division	1
CO2 uptake, carboxysome	1
Carboxysome	1
Conserved gene cluster associated with Met-tRNA formyltransferase	1
Cyanate hydrolysis	1
NAD and NADP cofactor biosynthesis global	1
Nudix proteins (nucleoside triphosphate hydrolases)	1
Peptidoglycan Biosynthesis	1
Phycobilisome	1
Protein chaperones	1
RNA processing and degradation, bacterial	1
Respiratory dehydrogenases 1	1
Rhamnose containing glycans	1
Ribosome biogenesis bacterial	1
Two cell division clusters relating to chromosome partitioning	1
Type IV pilus	1
Ubiquinone Biosynthesis	1
cAMP signaling in bacteria	1
dTDP-rhamnose synthesis	1
linker unit-arabinogalactan synthesis	1
tRNA aminoacylation, Asp and Asn	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Porphyrin and chlorophyll metabolism
• Ubiquinone and menaquinone biosynthesis
• Purine metabolism
• Methionine metabolism
• Lipopolysaccharide biosynthesis
• Peptidoglycan biosynthesis
• Glyoxylate and dicarboxylate metabolism
• Carotenoid biosynthesis - General
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Pentose phosphate pathway
• Urea cycle and metabolism of amino groups
• Puromycin biosynthesis
• Pyrimidine metabolism
• Alanine and aspartate metabolism
• Lysine degradation
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• Starch and sucrose metabolism
• Nucleotide sugars metabolism
• Streptomycin biosynthesis
• Polyketide sugar unit biosynthesis
• Glycerolipid metabolism
• alpha-Linolenic acid metabolism
• Naphthalene and anthracene degradation
• Trinitrotoluene degradation
• Nicotinate and nicotinamide metabolism
• Biotin metabolism
• Folate biosynthesis
• Nitrogen metabolism
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Aminoacyl-tRNA biosynthesis
• Biosynthesis of vancomycin group antibiotics
• Biosynthesis of alkaloids derived from shikimate pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
S-methyl-5'-thioadenosine degradation II	1	1	1
3-methylthiopropanoate biosynthesis	1	1	1
cellulose biosynthesis	1	1	1
CO2 fixation into oxaloacetate (anaplerotic)	2	2	1
glycerol degradation V	2	1	1
pseudouridine degradation	2	1	1
glycerol degradation II	2	1	1
glycolate and glyoxylate degradation II	2	1	1
cyanate degradation	3	3	1
5'-deoxyadenosine degradation I	3	2	1
glycolate and glyoxylate degradation III	3	1	1
dTDP-6-deoxy-α-D-allose biosynthesis	4	2	1
glycolate and glyoxylate degradation I	4	2	1
dTDP-N-acetylviosamine biosynthesis	4	2	1
dTDP-N-acetylthomosamine biosynthesis	4	2	1
dTDP-β-D-fucofuranose biosynthesis	4	2	1
superpathway of glycerol degradation to 1,3-propanediol	4	1	1
photorespiration III	9	8	2
dTDP-β-L-rhamnose biosynthesis	5	5	1
photorespiration II	10	8	2
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
dTDP-3-acetamido-3,6-dideoxy-α-D-glucose biosynthesis	5	2	1
L-methionine salvage cycle III	11	9	2
dTDP-sibirosamine biosynthesis	6	3	1
dTDP-L-daunosamine biosynthesis	6	3	1
dTDP-α-D-ravidosamine and dTDP-4-acetyl-α-D-ravidosamine biosynthesis	6	2	1
dTDP-D-desosamine biosynthesis	6	2	1
S-methyl-5-thio-α-D-ribose 1-phosphate degradation I	7	5	1
C4 photosynthetic carbon assimilation cycle, NADP-ME type	7	4	1
dTDP-β-L-digitoxose biosynthesis	7	3	1
dTDP-β-L-olivose biosynthesis	7	3	1
superpathway of glycol metabolism and degradation	7	3	1
dTDP-β-L-mycarose biosynthesis	7	2	1
dTDP-β-L-4-epi-vancosamine biosynthesis	8	3	1
dTDP-β-L-megosamine biosynthesis	8	3	1
ubiquinol-8 biosynthesis (early decarboxylation)	8	3	1
ubiquinol-9 biosynthesis (early decarboxylation)	8	3	1
ubiquinol-9 biosynthesis (late decarboxylation)	8	2	1
ubiquinol-7 biosynthesis (early decarboxylation)	8	1	1
ubiquinol-6 biosynthesis (late decarboxylation)	8	1	1
ubiquinol-7 biosynthesis (late decarboxylation)	8	1	1
ubiquinol-10 biosynthesis (early decarboxylation)	8	1	1
peptidoglycan biosynthesis II (staphylococci)	17	12	2
peptidoglycan biosynthesis IV (Enterococcus faecium)	17	12	2
peptidoglycan biosynthesis V (β-lactam resistance)	17	11	2
photorespiration I	9	8	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
ubiquinol-6 biosynthesis from 4-aminobenzoate (yeast)	9	1	1
ubiquinol-10 biosynthesis (late decarboxylation)	9	1	1
ubiquinol-8 biosynthesis (late decarboxylation)	9	1	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
L-methionine salvage cycle II (plants)	11	6	1
superpathway of ubiquinol-6 biosynthesis (late decarboxylation)	11	1	1
peptidoglycan biosynthesis I (meso-diaminopimelate containing)	12	11	1
L-methionine salvage cycle I (bacteria and plants)	12	8	1
superpathway of ubiquinol-8 biosynthesis (early decarboxylation)	12	5	1
peptidoglycan maturation (meso-diaminopimelate containing)	12	4	1
3-hydroxypropanoate cycle	13	4	1
glyoxylate assimilation	13	3	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	7	1
peptidoglycan biosynthesis III (mycobacteria)	15	11	1
glycerol degradation to butanol	16	8	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	1
superpathway of the 3-hydroxypropanoate cycle	18	4	1
3-hydroxypropanoate/4-hydroxybutanate 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
tRNA charging	21	20	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
colibactin biosynthesis	38	7	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	19	1
superpathway of chorismate metabolism	59	40	1