Experiment set10IT036 for Agrobacterium fabrum C58

4-Aminobutyric acid carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + 4-Aminobutyric acid (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 9 genes in this experiment

For carbon source 4-Aminobutyric acid in Agrobacterium fabrum C58

For carbon source 4-Aminobutyric acid across organisms

SEED Subsystems

Subsystem	#Specific
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	2
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	2
Pyruvate Alanine Serine Interconversions	2
Alanine biosynthesis	1
Entner-Doudoroff Pathway	1
Fermentations: Mixed acid	1
Glycolate, glyoxylate interconversions	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
• Arginine and proline metabolism
• Tryptophan metabolism
• 1- and 2-Methylnaphthalene degradation
• 3-Chloroacrylic acid degradation
• Limonene and pinene degradation
• Ascorbate and aldarate metabolism
• Puromycin biosynthesis
• Alanine and aspartate metabolism
• Glycine, serine and threonine metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Lysine biosynthesis
• Lysine degradation
• Histidine metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• beta-Alanine 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
• Propanoate metabolism
• 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
alanine racemization	1	1	1
acetaldehyde biosynthesis I	1	1	1
ethanol degradation II	3	3	2
putrescine degradation V	2	2	1
phytol degradation	4	3	2
putrescine degradation I	2	1	1
pyruvate fermentation to ethanol II	2	1	1
ethanol degradation I	2	1	1
ethylene glycol degradation	2	1	1
ethanol degradation IV	3	3	1
L-isoleucine degradation II	3	2	1
putrescine degradation IV	3	2	1
ethanol degradation III	3	2	1
L-valine degradation II	3	2	1
L-leucine degradation III	3	2	1
hypotaurine degradation	3	2	1
L-methionine degradation III	3	1	1
pyruvate fermentation to ethanol III	3	1	1
pyruvate fermentation to ethanol I	3	1	1
histamine degradation	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
L-phenylalanine degradation III	4	2	1
fatty acid α-oxidation I (plants)	4	2	1
salidroside biosynthesis	4	1	1
putrescine degradation III	4	1	1
cytidine-5'-diphosphate-glycerol 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
dopamine degradation	5	1	1
(S)-propane-1,2-diol degradation	5	1	1
ethanolamine utilization	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
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 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