Experiment set6IT079 for Rhodospirillum rubrum S1H

Sodium acetate; Light intensity 18 uM

Group: light
Media: MELiSSA_defined_50mMCarbonate_noCarbon + Sodium acetate (62.5 mM) + Light intensity (18 uM)
Culturing: Rubrum_ML4a, flask, Anaerobic, at 28 (C), shaken=215 rpm
Growth: about 5.3 generations
By: Baptiste on 9/2/19
Media components: 0.051 mM Manganese (II) chloride tetrahydrate, 0.0811 mM Magnesium Sulfate Heptahydrate, 3.801 mM Sodium sulfate, 35.33 mM Ammonium chloride, 0.34 mM Calcium chloride dihydrate, 0.068 mM EDTA, 3.601 mM Potassium phosphate monobasic, 0.072 mM Iron (II) sulfate heptahydrate, 50 mM Sodium bicarbonate, 100.4 mM 3-(N-morpholino)propanesulfonic acid, 2.985 mM Potassium phosphate dibasic, 1.902 uM Nickel (II) sulfate hexahydrate, 0.348 uM Zinc sulfate heptahydrate, 0.02 uM Copper (II) sulfate pentahydrate, 1.623 uM Boric Acid, 0.207 uM Sodium Molybdate Dihydrate, 0.06 uM biotin

Specific Phenotypes

For 9 genes in this experiment

For light Sodium acetate in Rhodospirillum rubrum S1H

For light Sodium acetate across organisms

SEED Subsystems

Subsystem	#Specific
Alkylphosphonate utilization	1
Biogenesis of cytochrome c oxidases	1
Conserved gene cluster associated with Met-tRNA formyltransferase	1
Oxidative stress	1
Peptidoglycan Biosynthesis	1
Phosphate metabolism	1
Type IV pilus	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Peptidoglycan biosynthesis
• Carotenoid biosynthesis - General
• Fructose and mannose metabolism
• Puromycin biosynthesis
• Geraniol degradation
• Lysine degradation
• Aminophosphonate metabolism
• N-Glycan biosynthesis
• O-Glycan biosynthesis
• High-mannose type N-glycan biosynthesis
• O-Mannosyl glycan biosynthesis
• Nucleotide sugars metabolism
• Keratan sulfate biosynthesis
• Lipopolysaccharide biosynthesis
• Glycerolipid metabolism
• Glycosylphosphatidylinositol(GPI)-anchor biosynthesis
• alpha-Linolenic acid metabolism
• Sphingolipid metabolism
• Glycosphingolipid biosynthesis - lacto and neolacto series
• Glycosphingolipid biosynthesis - globo series
• Glycosphingolipid biosynthesis - ganglio series
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• Trinitrotoluene degradation
• Biotin metabolism
• Porphyrin and chlorophyll metabolism
• Zeatin biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Flavone and flavonol biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
acetate formation from acetyl-CoA (succinate)	1	1	1
phosphonoacetate degradation	1	1	1
pyruvate fermentation to acetate VI	3	3	1
pyruvate fermentation to acetate V	3	3	1
succinate fermentation to butanoate	7	2	1
peptidoglycan biosynthesis IV (Enterococcus faecium)	17	11	2
peptidoglycan biosynthesis II (staphylococci)	17	11	2
peptidoglycan biosynthesis V (β-lactam resistance)	17	10	2
TCA cycle VII (acetate-producers)	9	8	1
anaerobic energy metabolism (invertebrates, mitochondrial)	10	7	1
peptidoglycan biosynthesis I (meso-diaminopimelate containing)	12	10	1
peptidoglycan maturation (meso-diaminopimelate containing)	12	3	1
peptidoglycan biosynthesis III (mycobacteria)	15	10	1
superpathway of anaerobic energy metabolism (invertebrates)	17	14	1