Experiment set11IT008 for Agrobacterium fabrum C58

1,5-Pentanediol carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + 1,5-Pentanediol (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 5 genes in this experiment

For carbon source 1,5-Pentanediol in Agrobacterium fabrum C58

For carbon source 1,5-Pentanediol across organisms

SEED Subsystems

Subsystem	#Specific
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	2
Entner-Doudoroff Pathway	1
Fermentations: Mixed acid	1
Glycolate, glyoxylate interconversions	1
Homogentisate pathway of aromatic compound degradation	1
Methylglyoxal Metabolism	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glycolysis / Gluconeogenesis
• Fatty acid metabolism
• Urea cycle and metabolism of amino groups
• Arginine and proline metabolism
• Tryptophan metabolism
• 1- and 2-Methylnaphthalene degradation
• 3-Chloroacrylic acid degradation
• Limonene and pinene degradation
• Ascorbate and aldarate metabolism
• Glycine, serine and threonine metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Lysine biosynthesis
• Lysine degradation
• Histidine metabolism
• Tyrosine metabolism
• beta-Alanine metabolism
• Glycerolipid metabolism
• Pyruvate metabolism
• Naphthalene and anthracene degradation
• 1,2-Dichloroethane degradation
• Propanoate metabolism
• Butanoate metabolism
• Retinol metabolism
• Metabolism of xenobiotics by cytochrome P450
• Drug metabolism - cytochrome P450

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
acetaldehyde biosynthesis I	1	1	1
ethanol degradation II	3	3	2
putrescine degradation V	2	2	1
phytol degradation	4	3	2
ethylene glycol degradation	2	1	1
putrescine degradation I	2	1	1
ethanol degradation I	2	1	1
pyruvate fermentation to ethanol II	2	1	1
ethanol degradation IV	3	3	1
putrescine degradation IV	3	2	1
L-valine degradation II	3	2	1
hypotaurine degradation	3	2	1
ethanol degradation III	3	2	1
L-isoleucine degradation II	3	2	1
L-leucine degradation III	3	2	1
pyruvate fermentation to ethanol III	3	1	1
pyruvate fermentation to ethanol I	3	1	1
L-methionine degradation III	3	1	1
histamine degradation	3	1	1
noradrenaline and adrenaline degradation	13	4	4
serotonin degradation	7	3	2
fatty acid α-oxidation I (plants)	4	2	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	2	1
L-tyrosine degradation III	4	2	1
L-phenylalanine degradation III	4	2	1
cytidine-5'-diphosphate-glycerol biosynthesis	4	1	1
putrescine degradation III	4	1	1
salidroside biosynthesis	4	1	1
D-arabinose degradation II	4	1	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
mitochondrial NADPH production (yeast)	5	3	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
octane oxidation	5	2	1
acetylene degradation (anaerobic)	5	1	1
phenylethanol biosynthesis	5	1	1
ethanolamine utilization	5	1	1
dopamine degradation	5	1	1
(S)-propane-1,2-diol degradation	5	1	1
3-methyl-branched fatty acid α-oxidation	6	3	1
alkane oxidation	6	1	1
3-methylbutanol biosynthesis (engineered)	7	6	1
superpathway of glycol metabolism and degradation	7	4	1
ceramide degradation by α-oxidation	7	2	1
limonene degradation IV (anaerobic)	7	1	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	6	1
superpathway of ornithine degradation	8	4	1
butanol and isobutanol biosynthesis (engineered)	8	3	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
aromatic biogenic amine degradation (bacteria)	8	1	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	5	1
superpathway of fermentation (Chlamydomonas reinhardtii)	9	3	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	6	1
superpathway of L-arginine and L-ornithine degradation	13	8	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 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
superpathway of pentose and pentitol degradation	42	16	1