Experiment set1S311 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	4
Acetoin, butanediol metabolism	1
Biotin biosynthesis	1
Branched-Chain Amino Acid Biosynthesis	1
Glycogen metabolism	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
• Butanoate metabolism
• Glutamate metabolism
• Alanine and aspartate metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Tyrosine metabolism
• beta-Alanine metabolism
• Limonene and pinene degradation
• Ascorbate and aldarate metabolism
• Ubiquinone and menaquinone biosynthesis
• Urea cycle and metabolism of amino groups
• Valine, leucine and isoleucine biosynthesis
• Lysine biosynthesis
• Arginine and proline metabolism
• Tryptophan metabolism
• Nucleotide sugars metabolism
• Glycosaminoglycan degradation
• alpha-Linolenic acid metabolism
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Benzoate degradation via CoA ligation
• Ethylbenzene degradation
• C5-Branched dibasic acid metabolism
• Pantothenate and CoA biosynthesis
• Biotin metabolism
• Caprolactam degradation
• Alkaloid biosynthesis II
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
4-aminobutanoate degradation III	2	2	2
β-alanine degradation II	2	2	1
pyruvate fermentation to (R)-acetoin II	2	1	1
4-aminobutanoate degradation I	2	1	1
4-aminobutanoate degradation II	2	1	1
L-lysine degradation IV	5	2	2
L-lysine degradation X	6	4	2
pyruvate fermentation to (R)-acetoin I	3	2	1
pyruvate fermentation to (S)-acetoin	3	2	1
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
L-valine biosynthesis	4	4	1
GABA shunt II	4	2	1
GABA shunt I	4	1	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
superpathway of (R,R)-butanediol biosynthesis	5	2	1
L-isoleucine biosynthesis IV	6	4	1
β-alanine biosynthesis II	6	4	1
superpathway of 2,3-butanediol biosynthesis	6	2	1
L-isoleucine biosynthesis I (from threonine)	7	7	1
L-isoleucine biosynthesis III	7	4	1
4-aminobutanoate degradation V	7	1	1
L-valine degradation I	8	6	1
L-isoleucine biosynthesis II	8	5	1
superpathway of branched chain amino acid biosynthesis	17	17	2
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-isoleucine biosynthesis I	13	13	1
superpathway of L-arginine and L-ornithine degradation	13	5	1
biotin biosynthesis I	15	13	1
nicotine degradation I (pyridine pathway)	17	4	1
superpathway of L-threonine metabolism	18	12	1
superpathway of L-lysine degradation	43	13	2