Experiment set1S309 for Rhodopseudomonas palustris CGA009

4-Aminobutyric acid carbon source; anaerobic

Group: carbon source
Media: PM + 4-Aminobutyric acid (10 mM) + Sodium bicarbonate (10 mM) + Light intensity (30 µmol photons/m2/s from a 60-W incandescent light bulb)
Culturing: RPal_CGA009_ML8, tube, Anaerobic, at 30 (C)
By: Rpal_Yasu on 9/1/24
Media components: 12.5 mM Disodium phosphate, 12.5 mM Potassium phosphate monobasic, 1 g/L Ammonium Sulfate, 0.1 mM Sodium thiosulfate pentahydrate, 0.002 g/L 4-Aminobenzoic acid, UW concentrated base (0.02 g/L Nitrilotriacetic acid, 0.0289 g/L Magnesium sulfate, 0.00667 g/L Calcium chloride dihydrate, 1.85e-05 g/L ammonium molybdate tetrahydrate, 0.000698 g/L Iron (II) sulfate heptahydrate, 0.00025 g/L EDTA, 0.001095 g/L Zinc sulfate heptahydrate, 0.000154 g/L Manganese (II) sulfate monohydrate, 3.92e-05 g/L Copper (II) sulfate pentahydrate, 2.5e-05 g/L Cobalt(II) nitrate hexahydrate, 1.77e-05 g/L sodium tetraborate decahydrate)

Specific Phenotypes

For 11 genes in this experiment

For carbon source 4-Aminobutyric acid in Rhodopseudomonas palustris CGA009

For carbon source 4-Aminobutyric acid across organisms

SEED Subsystems

Subsystem	#Specific
Utilization of glutathione as a sulphur source	3
Arginine Biosynthesis extended	1
Biotin biosynthesis	1
Glycogen metabolism	1
Sulfur oxidation	1
Trehalose Biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Propanoate metabolism
• Urea cycle and metabolism of amino groups
• Glutamate metabolism
• Alanine and aspartate metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Arginine and proline metabolism
• Tyrosine metabolism
• beta-Alanine metabolism
• Butanoate metabolism
• Biotin metabolism
• Limonene and pinene degradation
• Ascorbate and aldarate metabolism
• Ubiquinone and menaquinone biosynthesis
• Lysine biosynthesis
• Lysine degradation
• Tryptophan metabolism
• Nucleotide sugars metabolism
• Glycosaminoglycan degradation
• Peptidoglycan biosynthesis
• alpha-Linolenic acid metabolism
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Benzoate degradation via CoA ligation
• Ethylbenzene degradation
• Caprolactam degradation
• Alkaloid biosynthesis II
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
4-aminobutanoate degradation III	2	2	2
sulfide oxidation II (flavocytochrome c)	1	1	1
β-alanine degradation II	2	2	1
4-aminobutanoate degradation II	2	1	1
4-aminobutanoate degradation I	2	1	1
L-lysine degradation IV	5	2	2
L-lysine degradation X	6	4	2
L-lysine degradation III	6	2	2
superpathway of 4-aminobutanoate degradation	3	1	1
L-lysine degradation I	7	4	2
biotin biosynthesis from 8-amino-7-oxononanoate I	4	4	1
GABA shunt II	4	2	1
GABA shunt I	4	1	1
L-ornithine biosynthesis I	5	5	1
β-alanine biosynthesis II	6	4	1
4-aminobutanoate degradation V	7	1	1
L-valine degradation I	8	6	1
L-arginine biosynthesis I (via L-ornithine)	9	9	1
L-arginine biosynthesis III (via N-acetyl-L-citrulline)	9	8	1
superpathway of coenzyme A biosynthesis II (plants)	10	8	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	3	1
superpathway of L-arginine and L-ornithine degradation	13	5	1
biotin biosynthesis I	15	13	1
superpathway of arginine and polyamine biosynthesis	17	13	1
nicotine degradation I (pyridine pathway)	17	4	1
superpathway of L-lysine degradation	43	13	2