Experiment set11IT006 for Agrobacterium fabrum C58

Beta-alanine carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + Beta-alanine (10 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 15 genes in this experiment

For carbon source Beta-alanine in Agrobacterium fabrum C58

For carbon source Beta-alanine across organisms

SEED Subsystems

Subsystem	#Specific
Pyruvate Alanine Serine Interconversions	3
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	2
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	1
Alanine biosynthesis	1
Entner-Doudoroff Pathway	1
Fermentations: Mixed acid	1
Homogentisate pathway of aromatic compound degradation	1
Methylglyoxal Metabolism	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Respiratory dehydrogenases 1	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
• Alanine and aspartate metabolism
• Valine, leucine and isoleucine degradation
• Arginine and proline metabolism
• Tryptophan metabolism
• beta-Alanine metabolism
• 1- and 2-Methylnaphthalene degradation
• Propanoate metabolism
• 3-Chloroacrylic acid degradation
• Limonene and pinene degradation
• Ascorbate and aldarate metabolism
• Puromycin biosynthesis
• Glycine, serine and threonine metabolism
• Geraniol degradation
• Lysine biosynthesis
• Lysine degradation
• Histidine metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• D-Alanine metabolism
• Nucleotide sugars metabolism
• Glycerolipid metabolism
• alpha-Linolenic acid metabolism
• Pyruvate metabolism
• Naphthalene and anthracene degradation
• 1,2-Dichloroethane degradation
• Trinitrotoluene degradation
• Butanoate metabolism
• Retinol metabolism
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Nitrogen metabolism
• Alkaloid biosynthesis I
• Metabolism of xenobiotics by cytochrome P450
• Insect hormone biosynthesis
• Drug metabolism - cytochrome P450

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-alanine degradation I	2	2	2
acetaldehyde biosynthesis I	1	1	1
alanine racemization	1	1	1
ethanol degradation II	3	3	2
putrescine degradation V	2	2	1
β-alanine degradation II	2	2	1
phytol degradation	4	3	2
pyruvate fermentation to ethanol II	2	1	1
putrescine degradation I	2	1	1
ethanol degradation I	2	1	1
ethylene glycol degradation	2	1	1
ethanol degradation IV	3	3	1
ethanol degradation III	3	2	1
putrescine degradation IV	3	2	1
hypotaurine degradation	3	2	1
L-isoleucine degradation II	3	2	1
L-valine degradation II	3	2	1
L-leucine degradation III	3	2	1
L-methionine degradation III	3	1	1
histamine degradation	3	1	1
pyruvate fermentation to ethanol III	3	1	1
pyruvate fermentation to ethanol I	3	1	1
noradrenaline and adrenaline degradation	13	4	4
serotonin degradation	7	3	2
L-tyrosine degradation III	4	2	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	2	1
fatty acid α-oxidation I (plants)	4	2	1
L-phenylalanine degradation III	4	2	1
putrescine degradation III	4	1	1
D-arabinose degradation II	4	1	1
salidroside biosynthesis	4	1	1
cytidine-5'-diphosphate-glycerol biosynthesis	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
phenylethanol biosynthesis	5	1	1
ethanolamine utilization	5	1	1
(S)-propane-1,2-diol degradation	5	1	1
dopamine degradation	5	1	1
acetylene degradation (anaerobic)	5	1	1
3-methyl-branched fatty acid α-oxidation	6	3	1
β-alanine biosynthesis II	6	3	1
alkane oxidation	6	1	1
3-methylbutanol biosynthesis (engineered)	7	6	1
anaerobic energy metabolism (invertebrates, cytosol)	7	5	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
ansatrienin biosynthesis	9	1	1
superpathway of coenzyme A biosynthesis II (plants)	10	7	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
cyclosporin A biosynthesis	15	2	1
mixed acid fermentation	16	9	1
superpathway of anaerobic energy metabolism (invertebrates)	17	13	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