Experiment set6IT084 for Rhodospirillum rubrum S1H

Sodium acetate; Light intensity 38 uM

Group: light
Media: MELiSSA_defined_50mMCarbonate_noCarbon + Sodium acetate (62.5 mM) + Light intensity (38 uM)
Culturing: Rubrum_ML4a, flask, Anaerobic, at 28 (C), shaken=215 rpm
Growth: about 4.9 generations
By: Baptiste on 9/3/19
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 16 genes in this experiment

For light Sodium acetate in Rhodospirillum rubrum S1H

For light Sodium acetate across organisms

SEED Subsystems

Subsystem	#Specific
Branched-Chain Amino Acid Biosynthesis	1
CMP-N-acetylneuraminate Biosynthesis	1
Glycine and Serine Utilization	1
Glycine cleavage system	1
Molybdenum cofactor biosynthesis	1
Photorespiration (oxidative C2 cycle)	1
Riboflavin, FMN and FAD metabolism	1
Serine-glyoxylate cycle	1
Sialic Acid Metabolism	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Valine, leucine and isoleucine biosynthesis
• Pyruvate metabolism
• Riboflavin metabolism
• Fatty acid biosynthesis
• Ubiquinone and menaquinone biosynthesis
• Glycine, serine and threonine metabolism
• Geraniol degradation
• Nucleotide sugars metabolism
• Aminosugars metabolism
• alpha-Linolenic acid metabolism
• 1- and 2-Methylnaphthalene degradation
• Benzoate degradation via CoA ligation
• Limonene and pinene degradation
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
acetate formation from acetyl-CoA (succinate)	1	1	1
UDP-N-acetyl-α-D-mannosamine biosynthesis	1	1	1
pyruvate fermentation to acetate VI	3	3	1
glycine biosynthesis II	3	3	1
glycine cleavage	3	3	1
pyruvate fermentation to acetate V	3	3	1
CMP-N-acetylneuraminate biosynthesis II (bacteria)	3	1	1
flavin biosynthesis I (bacteria and plants)	9	8	2
flavin biosynthesis III (fungi)	9	7	2
6-hydroxymethyl-dihydropterin diphosphate biosynthesis III (Chlamydia)	5	3	1
CMP-N-acetylneuraminate biosynthesis I (eukaryotes)	5	1	1
L-leucine biosynthesis	6	6	1
3-methylbutanol biosynthesis (engineered)	7	6	1
toxoflavin biosynthesis	7	3	1
succinate fermentation to butanoate	7	2	1
TCA cycle VII (acetate-producers)	9	8	1
anaerobic energy metabolism (invertebrates, mitochondrial)	10	7	1
flavin biosynthesis II (archaea)	10	5	1
superpathway of CMP-sialic acids biosynthesis	15	2	1
superpathway of branched chain amino acid biosynthesis	17	17	1
superpathway of anaerobic energy metabolism (invertebrates)	17	14	1
superpathway of UDP-N-acetylglucosamine-derived O-antigen building blocks biosynthesis	24	6	1