Experiment set9IT089 for Ralstonia sp. UNC404CL21Col

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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 56 genes in this experiment

For carbon source Octanoic acid in Ralstonia sp. UNC404CL21Col

For carbon source Octanoic acid across organisms

SEED Subsystems

Subsystem #Specific
ZZ gjo need homes 3
Cobalt-zinc-cadmium resistance 2
Trehalose Biosynthesis 2
Alkanesulfonate assimilation 1
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
Heat shock dnaK gene cluster extended 1
Hydantoin metabolism 1
Iron acquisition in Vibrio 1
Lipid A modifications 1
Multidrug Resistance Efflux Pumps 1
Proteolysis in bacteria, ATP-dependent 1
Purine conversions 1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate 1
Redox-dependent regulation of nucleus processes 1
Serine-glyoxylate cycle 1
Soluble cytochromes and functionally related electron carriers 1
Sulfur oxidation 1
Terminal cytochrome d ubiquinol oxidases 1
Terminal cytochrome oxidases 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:

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway #Steps #Present #Specific
4-aminobenzoate biosynthesis I 2 2 2
L-glutamine degradation I 1 1 1
L-glutamate biosynthesis I 2 2 1
trehalose biosynthesis I 2 2 1
4-aminobenzoate biosynthesis II 2 1 1
8-amino-7-oxononanoate biosynthesis II 2 1 1
8-amino-7-oxononanoate biosynthesis III 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
L-asparagine biosynthesis III (tRNA-dependent) 4 4 1
purine deoxyribonucleosides degradation I 4 4 1
adenine and adenosine salvage III 4 4 1
glutaminyl-tRNAgln biosynthesis via transamidation 4 3 1
8-amino-7-oxononanoate biosynthesis IV 5 5 1
adenosine nucleotides degradation II 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
biotin biosynthesis II 6 5 1
purine ribonucleosides degradation 6 5 1
L-glutamate and L-glutamine biosynthesis 7 7 1
superpathway of purine deoxyribonucleosides degradation 7 4 1
L-citrulline biosynthesis 8 7 1
chloramphenicol biosynthesis 9 1 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