Experiment set10IT053 for Agrobacterium fabrum C58

Propan-1-ol carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + Propan-1-ol (5 mM), pH=7
Culturing: Agro_ML11, 24-well plate, Aerobic, at 28 (C), shaken=200 rpm
By: Mitchell Thompson on 1/6/22
Media components: 40 mM 3-(N-morpholino)propanesulfonic acid, 4 mM Tricine, 1.32 mM Potassium phosphate dibasic, 0.01 mM Iron (II) sulfate heptahydrate, 9.5 mM Ammonium chloride, 0.276 mM Aluminum potassium sulfate dodecahydrate, 0.0005 mM Calcium chloride, 0.525 mM Magnesium chloride hexahydrate, 50 mM Sodium Chloride, 3e-09 M Ammonium heptamolybdate tetrahydrate, 4e-07 M Boric Acid, 3e-08 M Cobalt chloride hexahydrate, 1e-08 M Copper (II) sulfate pentahydrate, 8e-08 M Manganese (II) chloride tetrahydrate, 1e-08 M Zinc sulfate heptahydrate

Specific Phenotypes

For 10 genes in this experiment

For carbon source Propan-1-ol in Agrobacterium fabrum C58

For carbon source Propan-1-ol across organisms

SEED Subsystems

Subsystem	#Specific
Propionyl-CoA to Succinyl-CoA Module	3
Serine-glyoxylate cycle	2
Cobalamin synthesis	1
Coenzyme B12 biosynthesis	1
Fermentations: Mixed acid	1
Glutathione: Non-redox reactions	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
tRNA splicing	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 degradation
• Propanoate metabolism
• Metabolism of xenobiotics by cytochrome P450
• Drug metabolism - cytochrome P450
• Glycolysis / Gluconeogenesis
• Pentose phosphate pathway
• Fatty acid metabolism
• Glycine, serine and threonine metabolism
• Tyrosine metabolism
• Glutathione metabolism
• Lipopolysaccharide biosynthesis
• 1- and 2-Methylnaphthalene degradation
• 3-Chloroacrylic acid degradation
• Nicotinate and nicotinamide metabolism
• Retinol metabolism
• Porphyrin and chlorophyll metabolism

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
propanoyl CoA degradation I	3	3	3
acetaldehyde biosynthesis I	1	1	1
2-oxobutanoate degradation I	4	3	3
ethanol degradation I	2	1	1
aminopropanol phosphate biosynthesis I	2	1	1
pyruvate fermentation to ethanol II	2	1	1
ethanol degradation II	3	3	1
L-leucine degradation III	3	2	1
L-isoleucine degradation II	3	2	1
L-valine degradation II	3	2	1
pyruvate fermentation to ethanol III	3	1	1
L-methionine degradation III	3	1	1
pyruvate fermentation to ethanol I	3	1	1
conversion of succinate to propanoate	3	1	1
anaerobic energy metabolism (invertebrates, mitochondrial)	10	8	3
pyruvate fermentation to propanoate I	7	4	2
phytol degradation	4	3	1
L-phenylalanine degradation III	4	2	1
L-tyrosine degradation III	4	2	1
4-hydroxy-2-nonenal detoxification	4	1	1
cytidine-5'-diphosphate-glycerol biosynthesis	4	1	1
salidroside biosynthesis	4	1	1
3-hydroxypropanoate cycle	13	8	3
pyruvate fermentation to isobutanol (engineered)	5	4	1
pentachlorophenol degradation	10	4	2
acetylene degradation (anaerobic)	5	1	1
ethanolamine utilization	5	1	1
phenylethanol biosynthesis	5	1	1
(S)-propane-1,2-diol degradation	5	1	1
superpathway of L-methionine salvage and degradation	16	8	3
L-glutamate degradation VIII (to propanoate)	11	4	2
superpathway of anaerobic energy metabolism (invertebrates)	17	13	3
3-hydroxypropanoate/4-hydroxybutanate cycle	18	11	3
superpathway of the 3-hydroxypropanoate cycle	18	8	3
methylaspartate cycle	19	12	3
(S)-lactate fermentation to propanoate, acetate and hydrogen	13	5	2
noradrenaline and adrenaline degradation	13	4	2
3-methylbutanol biosynthesis (engineered)	7	6	1
serotonin degradation	7	3	1
crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA cycle (engineered)	14	3	2
butanol and isobutanol biosynthesis (engineered)	8	3	1
glutathione-mediated detoxification I	8	3	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	3	1
gliotoxin biosynthesis	9	2	1
glutathione-mediated detoxification II	9	1	1
ethylmalonyl-CoA pathway	11	3	1
indole glucosinolate activation (intact plant cell)	12	3	1
camalexin biosynthesis	12	2	1
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	5	1
L-tryptophan degradation V (side chain pathway)	13	1	1
mixed acid fermentation	16	9	1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	5	1
heterolactic fermentation	18	12	1
superpathway of L-threonine metabolism	18	11	1
superpathway of anaerobic sucrose degradation	19	13	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	10	1
superpathway of N-acetylneuraminate degradation	22	12	1
adenosylcobalamin biosynthesis II (aerobic)	33	29	1
adenosylcobalamin biosynthesis I (anaerobic)	36	26	1
mycolate biosynthesis	205	21	1
superpathway of mycolate biosynthesis	239	22	1