Experiment set4IT015 for Rhodanobacter denitrificans FW104-10B01

R2A with bismuth(III) chloride 0.03125 mM

Group: stress
Media: R2A + bismuth(III) chloride (0.03125 mM)
Culturing: rhodanobacter_10B01_ML12, 96 deep-well microplate; 0.8 mL volume, Aerobic, at 28 (C), shaken=700 rpm
By: Hans Carlson and Trenton Owens on 22-Jun-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
Growth plate: 3 A6

Specific Phenotypes

For 65 genes in this experiment

For stress bismuth(III) chloride in Rhodanobacter denitrificans FW104-10B01

For stress bismuth(III) chloride across organisms

SEED Subsystems

Subsystem	#Specific
Isoleucine degradation	2
Ribosomal protein S12p Asp methylthiotransferase	2
Valine degradation	2
Acetyl-CoA fermentation to Butyrate	1
Alanine biosynthesis	1
Anaerobic respiratory reductases	1
Biogenesis of c-type cytochromes	1
Branched-Chain Amino Acid Biosynthesis	1
Butanol Biosynthesis	1
Calvin-Benson cycle	1
Cobalt-zinc-cadmium resistance	1
Glycolysis and Gluconeogenesis	1
Glycolysis and Gluconeogenesis, including Archaeal enzymes	1
Hfl operon	1
High affinity phosphate transporter and control of PHO regulon	1
Isobutyryl-CoA to Propionyl-CoA Module	1
Leucine Biosynthesis	1
Leucine Degradation and HMG-CoA Metabolism	1
Mannose Metabolism	1
Methionine Salvage	1
Na(+)-translocating NADH-quinone oxidoreductase and rnf-like group of electron transport complexes	1
Peptidyl-prolyl cis-trans isomerase	1
Periplasmic disulfide interchange	1
Phosphate metabolism	1
Potassium homeostasis	1
Pyruvate Alanine Serine Interconversions	1
Queuosine-Archaeosine Biosynthesis	1
Universal GTPases	1
tRNA processing	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Fatty acid biosynthesis
• Valine, leucine and isoleucine degradation
• Fatty acid metabolism
• Glycolysis / Gluconeogenesis
• Pentose phosphate pathway
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Ubiquinone and menaquinone biosynthesis
• Urea cycle and metabolism of amino groups
• Purine metabolism
• Puromycin biosynthesis
• Methionine metabolism
• Geraniol degradation
• Valine, leucine and isoleucine biosynthesis
• Arginine and proline metabolism
• Nucleotide sugars metabolism
• Glycosaminoglycan degradation
• Lipopolysaccharide biosynthesis
• 1- and 2-Methylnaphthalene degradation
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• Carbon fixation in photosynthetic organisms
• Pantothenate and CoA biosynthesis
• Brassinosteroid biosynthesis
• Caprolactam degradation
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• 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
gondoate biosynthesis (anaerobic)	4	4	2
L-alanine biosynthesis I	2	2	1
octanoyl-[acyl-carrier protein] biosynthesis (mitochondria, yeast)	12	9	6
palmitate biosynthesis III	29	21	13
palmitoleate biosynthesis I (from (5Z)-dodec-5-enoate)	9	8	4
tetradecanoate biosynthesis (mitochondria)	25	17	11
oleate biosynthesis IV (anaerobic)	14	13	6
palmitate biosynthesis II (type II fatty acid synthase)	31	29	13
fatty acid elongation -- saturated	5	4	2
superpathway of fatty acids biosynthesis (E. coli)	53	49	20
8-amino-7-oxononanoate biosynthesis I	11	10	4
superpathway of unsaturated fatty acids biosynthesis (E. coli)	20	18	7
superpathway of fatty acid biosynthesis II (plant)	43	38	15
(5Z)-dodecenoate biosynthesis I	6	6	2
L-phenylalanine biosynthesis I	3	3	1
stearate biosynthesis II (bacteria and plants)	6	5	2
(5Z)-dodecenoate biosynthesis II	6	5	2
stearate biosynthesis IV	6	4	2
L-leucine degradation III	3	2	1
L-valine degradation II	3	2	1
L-isoleucine biosynthesis V	3	2	1
L-isoleucine degradation II	3	2	1
5'-deoxyadenosine degradation I	3	2	1
L-isoleucine degradation III (oxidative Stickland reaction)	3	1	1
L-phenylalanine degradation II (anaerobic)	3	1	1
L-leucine degradation V (oxidative Stickland reaction)	3	1	1
L-valine degradation III (oxidative Stickland reaction)	3	1	1
superpathway of fatty acid biosynthesis I (E. coli)	16	14	5
biotin biosynthesis I	15	14	4
streptorubin B biosynthesis	34	20	9
L-valine biosynthesis	4	4	1
superpathway of L-alanine biosynthesis	4	4	1
fatty acid biosynthesis initiation (mitochondria)	4	2	1
L-phenylalanine degradation III	4	2	1
5'-deoxyadenosine degradation II	4	1	1
anteiso-branched-chain fatty acid biosynthesis	34	24	7
odd iso-branched-chain fatty acid biosynthesis	34	24	7
even iso-branched-chain fatty acid biosynthesis	34	24	7
8-amino-7-oxononanoate biosynthesis IV	5	4	1
cis-vaccenate biosynthesis	5	4	1
superpathway of fatty acid biosynthesis initiation	5	4	1
S-methyl-5-thio-α-D-ribose 1-phosphate degradation III	5	1	1
S-methyl-5-thio-α-D-ribose 1-phosphate degradation II	5	1	1
L-leucine degradation IV (reductive Stickland reaction)	5	1	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
superpathway of branched chain amino acid biosynthesis	17	17	3
L-leucine biosynthesis	6	6	1
L-leucine degradation I	6	5	1
L-isoleucine degradation I	6	4	1
pyruvate fermentation to butanol II (engineered)	6	4	1
L-isoleucine biosynthesis IV	6	4	1
petroselinate biosynthesis	6	2	1
L-isoleucine biosynthesis I (from threonine)	7	7	1
S-methyl-5-thio-α-D-ribose 1-phosphate degradation I	7	6	1
L-isoleucine biosynthesis III	7	4	1
L-isoleucine biosynthesis II	8	6	1
L-valine degradation I	8	3	1
2-allylmalonyl-CoA biosynthesis	8	2	1
sucrose biosynthesis I (from photosynthesis)	9	7	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	2	1
superpathway of L-phenylalanine biosynthesis	10	10	1
glycolysis II (from fructose 6-phosphate)	11	11	1
L-methionine salvage cycle III	11	10	1
L-methionine salvage cycle II (plants)	11	7	1
pyruvate fermentation to hexanol (engineered)	11	7	1
gluconeogenesis III	12	10	1
formaldehyde assimilation III (dihydroxyacetone cycle)	12	10	1
L-methionine salvage cycle I (bacteria and plants)	12	9	1
androstenedione degradation I (aerobic)	25	8	2
superpathway of L-isoleucine biosynthesis I	13	13	1
glycolysis I (from glucose 6-phosphate)	13	12	1
gluconeogenesis I	13	11	1
Calvin-Benson-Bassham cycle	13	9	1
1-butanol autotrophic biosynthesis (engineered)	27	18	2
androstenedione degradation II (anaerobic)	27	6	2
superpathway of testosterone and androsterone degradation	28	8	2
superpathway of glycolysis and the Entner-Doudoroff pathway	17	16	1
oxygenic photosynthesis	17	10	1
superpathway of aromatic amino acid biosynthesis	18	18	1
superpathway of hexitol degradation (bacteria)	18	14	1
superpathway of L-threonine metabolism	18	13	1
superpathway of anaerobic sucrose degradation	19	16	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	14	1
superpathway of cholesterol degradation I (cholesterol oxidase)	42	10	2
superpathway of N-acetylneuraminate degradation	22	16	1
mycolate biosynthesis	205	20	9
superpathway of cholesterol degradation II (cholesterol dehydrogenase)	47	10	2
superpathway of cholesterol degradation III (oxidase)	49	6	2
ethene biosynthesis V (engineered)	25	17	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	23	1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	17	1
superpathway of mycolate biosynthesis	239	21	9
anaerobic aromatic compound degradation (Thauera aromatica)	27	1	1
oleate β-oxidation	35	32	1
superpathway of chorismate metabolism	59	40	1