Experiment set1S331 for Rhodopseudomonas palustris CGA009

L-Leucine carbon source; anaerobic

Group: carbon source
Media: PM + L-Leucine (4.5 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 22 genes in this experiment

For carbon source L-Leucine in Rhodopseudomonas palustris CGA009

For carbon source L-Leucine across organisms

SEED Subsystems

Subsystem	#Specific
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	5
Leucine Degradation and HMG-CoA Metabolism	3
Serine-glyoxylate cycle	3
HMG CoA Synthesis	2
Aromatic amino acid interconversions with aryl acids	1
Catechol branch of beta-ketoadipate pathway	1
Fatty Acid Biosynthesis FASII	1
Glutaredoxins	1
Glutathione: Redox cycle	1
Homogentisate pathway of aromatic compound degradation	1
Lysine degradation	1
Protocatechuate branch of beta-ketoadipate pathway	1
mycolic acid synthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Valine, leucine and isoleucine degradation
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• Biosynthesis of unsaturated fatty acids
• Fructose and mannose metabolism
• Ascorbate and aldarate metabolism
• Fatty acid biosynthesis
• Synthesis and degradation of ketone bodies
• C21-Steroid hormone metabolism
• Glycine, serine and threonine metabolism
• Geraniol degradation
• Bisphenol A degradation
• Nucleotide sugars metabolism
• Polyketide sugar unit biosynthesis
• Aminosugars metabolism
• Linoleic acid metabolism
• 1- and 2-Methylnaphthalene degradation
• Tetrachloroethene degradation
• Retinol metabolism
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of type II polyketide products
• Biosynthesis of alkaloids derived from shikimate pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
ketolysis	3	3	1
L-leucine degradation I	6	5	2
octanoyl-[acyl-carrier protein] biosynthesis (mitochondria, yeast)	12	12	3
gondoate biosynthesis (anaerobic)	4	4	1
palmitate biosynthesis III	29	28	7
tetradecanoate biosynthesis (mitochondria)	25	23	6
palmitate biosynthesis II (type II fatty acid synthase)	31	29	7
palmitoleate biosynthesis I (from (5Z)-dodec-5-enoate)	9	8	2
benzoyl-CoA degradation III (anaerobic)	9	7	2
oleate biosynthesis IV (anaerobic)	14	13	3
superpathway of fatty acids biosynthesis (E. coli)	53	49	11
fatty acid elongation -- saturated	5	5	1
superpathway of unsaturated fatty acids biosynthesis (E. coli)	20	18	4
cis-vaccenate biosynthesis	5	4	1
8-amino-7-oxononanoate biosynthesis IV	5	4	1
superpathway of fatty acid biosynthesis II (plant)	43	38	8
8-amino-7-oxononanoate biosynthesis I	11	9	2
odd iso-branched-chain fatty acid biosynthesis	34	30	6
even iso-branched-chain fatty acid biosynthesis	34	30	6
anteiso-branched-chain fatty acid biosynthesis	34	30	6
(5Z)-dodecenoate biosynthesis I	6	6	1
stearate biosynthesis II (bacteria and plants)	6	5	1
(5Z)-dodecenoate biosynthesis II	6	5	1
stearate biosynthesis IV	6	4	1
petroselinate biosynthesis	6	2	1
streptorubin B biosynthesis	34	20	5
benzoyl-CoA degradation II (anaerobic)	7	2	1
biotin biosynthesis I	15	13	2
superpathway of fatty acid biosynthesis I (E. coli)	16	16	2
2-allylmalonyl-CoA biosynthesis	8	2	1
TCA cycle VI (Helicobacter)	9	8	1
benzoate fermentation (to acetate and cyclohexane carboxylate)	17	7	1
toluene degradation VI (anaerobic)	18	5	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	8	1
mycolate biosynthesis	205	26	5
superpathway of mycolate biosynthesis	239	27	5