Experiment set9IT071 for Ralstonia sp. UNC404CL21Col

Octanoic acid carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + Octanoic acid (10 mM)
Culturing: CL21_ML4_JBEI, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 3.0 generations
By: Allie Pearson on 8/26/19
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 55 genes in this experiment

For carbon source Octanoic acid in Ralstonia sp. UNC404CL21Col

For carbon source Octanoic acid across organisms

SEED Subsystems

Subsystem	#Specific
Trehalose Biosynthesis	3
Cobalt-zinc-cadmium resistance	2
Terminal cytochrome d ubiquinol oxidases	2
Terminal cytochrome oxidases	2
ZZ gjo need homes	2
Bacterial RNA-metabolizing Zn-dependent hydrolases	1
Biotin biosynthesis	1
Branched-Chain Amino Acid Biosynthesis	1
Chorismate: Intermediate for synthesis of PAPA antibiotics, PABA, anthranilate, 3-hydroxyanthranilate and more.	1
Conserved gene cluster associated with Met-tRNA formyltransferase	1
Flagellar motility	1
Flagellum	1
Folate Biosynthesis	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glycogen metabolism	1
Glycolate, glyoxylate interconversions	1
Homogentisate pathway of aromatic compound degradation	1
Hydantoin metabolism	1
Iron acquisition in Vibrio	1
Lipid A modifications	1
Multidrug Resistance Efflux Pumps	1
Peptidyl-prolyl cis-trans isomerase	1
Periplasmic disulfide interchange	1
Photorespiration (oxidative C2 cycle)	1
Potassium homeostasis	1
Purine conversions	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Redox-dependent regulation of nucleus processes	1
Restriction-Modification System	1
Serine-glyoxylate cycle	1
Sulfur oxidation	1
Thioredoxin-disulfide reductase	1
Ton and Tol transport systems	1
Transcription initiation, bacterial sigma factors	1
Transport of Iron	1
cAMP signaling in bacteria	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glutathione metabolism
• Glyoxylate and dicarboxylate metabolism
• Purine metabolism
• Starch and sucrose metabolism
• Nucleotide sugars metabolism
• Folate biosynthesis
• Biosynthesis of phenylpropanoids
• Ascorbate and aldarate metabolism
• Ubiquinone and menaquinone biosynthesis
• Glycine, serine and threonine metabolism
• Lysine biosynthesis
• Benzoxazinone biosynthesis
• Glycosaminoglycan degradation
• Lipopolysaccharide biosynthesis
• Sphingolipid metabolism
• 1,4-Dichlorobenzene degradation
• Nicotinate and nicotinamide metabolism
• Biotin metabolism
• Diterpenoid biosynthesis
• Caprolactam degradation

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
4-aminobenzoate biosynthesis I	2	2	2
cis-cyclopropane fatty acid (CFA) biosynthesis	1	1	1
L-glutamine degradation I	1	1	1
trehalose biosynthesis IV	1	1	1
glycolate and glyoxylate degradation II	2	2	1
L-glutamate biosynthesis I	2	2	1
trehalose biosynthesis I	2	2	1
8-amino-7-oxononanoate biosynthesis II	2	1	1
sterculate biosynthesis	2	1	1
8-amino-7-oxononanoate biosynthesis III	2	1	1
4-aminobenzoate biosynthesis II	2	1	1
purine deoxyribonucleosides degradation II	3	3	1
ammonia assimilation cycle III	3	3	1
adenine and adenosine salvage V	3	2	1
glycolate and glyoxylate degradation III	3	1	1
purine deoxyribonucleosides degradation I	4	4	1
L-asparagine biosynthesis III (tRNA-dependent)	4	4	1
adenine and adenosine salvage III	4	4	1
glycolate and glyoxylate degradation I	4	3	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	3	1
adenosine nucleotides degradation II	5	5	1
8-amino-7-oxononanoate biosynthesis IV	5	5	1
superpathway of tetrahydrofolate biosynthesis	10	9	2
superpathway of candicidin biosynthesis	11	3	2
glyoxylate cycle	6	6	1
superpathway of tetrahydrofolate biosynthesis and salvage	12	11	2
purine ribonucleosides degradation	6	5	1
biotin biosynthesis II	6	5	1
L-glutamate and L-glutamine biosynthesis	7	7	1
superpathway of glycol metabolism and degradation	7	5	1
superpathway of purine deoxyribonucleosides degradation	7	4	1
L-citrulline biosynthesis	8	7	1
glycogen biosynthesis III (from α-maltose 1-phosphate)	8	4	1
photorespiration III	9	5	1
photorespiration I	9	5	1
chloramphenicol biosynthesis	9	1	1
photorespiration II	10	5	1
purine nucleotides degradation II (aerobic)	11	11	1
8-amino-7-oxononanoate biosynthesis I	11	9	1
superpathway of glyoxylate bypass and TCA	12	10	1
superpathway of L-citrulline metabolism	12	9	1
superpathway of glyoxylate cycle and fatty acid degradation	14	11	1
biotin biosynthesis I	15	13	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	22	1
superpathway of chorismate metabolism	59	44	2
mycolate biosynthesis	205	25	3
superpathway of mycolate biosynthesis	239	26	3