Experiment set2IT004 for Rhodanobacter denitrificans FW104-10B01

R2A with Manganese (II) chloride tetrahydrate 6.25 mM

Group: stress
Media: R2A + Manganese (II) chloride tetrahydrate (6.25 mM)
Culturing: rhodanobacter_10B01_ML12, 96 deep-well microplate; 0.8 mL volume, Aerobic, at 30 (C), shaken=700 rpm
By: Hans on 2/27/21
Media components: 0.5 g/L Bacto Peptone, 0.5 g/L casamino acids, 0.5 g/L Yeast Extract, 0.5 g/L D-Glucose, 0.5 g/L Starch, 0.3 g/L Potassium phosphate dibasic, 0.05 g/L Magnesium Sulfate Heptahydrate, 0.3 g/L Sodium pyruvate

Specific Phenotypes

For 15 genes in this experiment

For stress Manganese (II) chloride tetrahydrate in Rhodanobacter denitrificans FW104-10B01

For stress Manganese (II) chloride tetrahydrate across organisms

SEED Subsystems

Subsystem	#Specific
Peptidoglycan Biosynthesis	2
Acetyl-CoA fermentation to Butyrate	1
Anaerobic respiratory reductases	1
Bacterial Cytoskeleton	1
Butanol Biosynthesis	1
Conserved gene cluster associated with Met-tRNA formyltransferase	1
Isobutyryl-CoA to Propionyl-CoA Module	1
Isoleucine degradation	1
Phosphate metabolism	1
Proteolysis in bacteria, ATP-dependent	1
Type IV pilus	1
Valine degradation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Peptidoglycan biosynthesis
• Fatty acid metabolism
• Valine, leucine and isoleucine degradation
• Carotenoid biosynthesis - General
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Biosynthesis of plant hormones
• Fructose and mannose metabolism
• Ubiquinone and menaquinone biosynthesis
• Purine metabolism
• Geraniol degradation
• Lysine degradation
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• N-Glycan biosynthesis
• O-Glycan biosynthesis
• High-mannose type N-glycan biosynthesis
• O-Mannosyl glycan biosynthesis
• Keratan sulfate biosynthesis
• Lipopolysaccharide biosynthesis
• Glycerolipid metabolism
• Glycosylphosphatidylinositol(GPI)-anchor biosynthesis
• Sphingolipid metabolism
• Glycosphingolipid biosynthesis - lacto and neolacto series
• Glycosphingolipid biosynthesis - globo series
• Glycosphingolipid biosynthesis - ganglio series
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• Biotin metabolism
• Porphyrin and chlorophyll metabolism
• Brassinosteroid biosynthesis
• Zeatin biosynthesis
• Caprolactam degradation
• Phenylpropanoid biosynthesis
• Flavone and flavonol biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
pyruvate fermentation to butanol II (engineered)	6	4	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
pyruvate fermentation to hexanol (engineered)	11	7	1
peptidoglycan biosynthesis I (meso-diaminopimelate containing)	12	10	1
peptidoglycan maturation (meso-diaminopimelate containing)	12	4	1
peptidoglycan biosynthesis III (mycobacteria)	15	10	1
1-butanol autotrophic biosynthesis (engineered)	27	18	1
oleate β-oxidation	35	32	1