Experiment set16IT010 for Pseudomonas putida KT2440

3-methyl-1-butanol carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + 3-methyl-1-butanol (10 mM)
Culturing: Putida_ML5_JBEI, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 5.2 generations
By: Mitchell Thompson on 9/5/19
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 19 genes in this experiment

For carbon source 3-methyl-1-butanol in Pseudomonas putida KT2440

For carbon source 3-methyl-1-butanol across organisms

SEED Subsystems

Subsystem	#Specific
Leucine Degradation and HMG-CoA Metabolism	3
Serine-glyoxylate cycle	3
Catechol branch of beta-ketoadipate pathway	2
Protocatechuate branch of beta-ketoadipate pathway	2
Aromatic amino acid degradation	1
Biotin biosynthesis	1
Calvin-Benson cycle	1
Cobalamin synthesis	1
Coenzyme B12 biosynthesis	1
DNA-binding regulatory proteins, strays	1
DNA repair, bacterial RecFOR pathway	1
Entner-Doudoroff Pathway	1
Flavodoxin	1
Fructose utilization	1
Glycolysis and Gluconeogenesis	1
HMG CoA Synthesis	1
Purine conversions	1
Pyridoxin (Vitamin B6) Biosynthesis	1
Redox-dependent regulation of nucleus processes	1
Rubrerythrin	1
Thioredoxin-disulfide reductase	1
Triacylglycerol metabolism	1
n-Phenylalkanoic acid degradation	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
• Geraniol degradation
• Glycolysis / Gluconeogenesis
• Fatty acid metabolism
• 1- and 2-Methylnaphthalene degradation
• Limonene and pinene degradation
• Biosynthesis of plant hormones
• Fructose and mannose metabolism
• Galactose metabolism
• Ascorbate and aldarate metabolism
• Synthesis and degradation of ketone bodies
• Urea cycle and metabolism of amino groups
• Purine metabolism
• Lysine biosynthesis
• Arginine and proline metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Glutathione metabolism
• Starch and sucrose metabolism
• Nucleotide sugars metabolism
• Aminosugars metabolism
• Glycerophospholipid metabolism
• alpha-Linolenic acid metabolism
• Naphthalene and anthracene degradation
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• Ethylbenzene degradation
• Butanoate metabolism
• Caprolactam degradation
• Alkaloid biosynthesis II
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
long-chain fatty acid activation	1	1	1
adenosine nucleotides degradation III	1	1	1
γ-linolenate biosynthesis II (animals)	2	1	1
linoleate biosynthesis II (animals)	2	1	1
octane oxidation	5	4	2
ketolysis	3	3	1
L-leucine degradation I	6	5	2
3-methyl-branched fatty acid α-oxidation	6	3	2
alkane biosynthesis II	3	1	1
oleate biosynthesis I (plants)	3	1	1
phytol degradation	4	3	1
phospholipid remodeling (phosphatidylethanolamine, yeast)	4	2	1
long chain fatty acid ester synthesis (engineered)	4	1	1
phosphatidylcholine acyl editing	4	1	1
wax esters biosynthesis II	4	1	1
sporopollenin precursors biosynthesis	18	4	4
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
fatty acid salvage	6	6	1
stearate biosynthesis II (bacteria and plants)	6	5	1
stearate biosynthesis IV	6	4	1
6-gingerol analog biosynthesis (engineered)	6	3	1
stearate biosynthesis I (animals)	6	1	1
pyridoxal 5'-phosphate biosynthesis I	7	7	1
capsaicin biosynthesis	7	3	1
ceramide degradation by α-oxidation	7	2	1
icosapentaenoate biosynthesis II (6-desaturase, mammals)	7	1	1
arachidonate biosynthesis III (6-desaturase, mammals)	7	1	1
icosapentaenoate biosynthesis III (8-desaturase, mammals)	7	1	1
2-deoxy-D-ribose degradation II	8	4	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
Entner-Doudoroff pathway I	9	8	1
sucrose biosynthesis I (from photosynthesis)	9	7	1
TCA cycle VI (Helicobacter)	9	7	1
glycolysis IV	10	8	1
suberin monomers biosynthesis	20	4	2
superpathway of fatty acid biosynthesis II (plant)	43	38	4
glycolysis II (from fructose 6-phosphate)	11	9	1
glycolysis III (from glucose)	11	9	1
glycolysis VI (from fructose)	11	7	1
superpathway of pyridoxal 5'-phosphate biosynthesis and salvage	12	11	1
formaldehyde assimilation III (dihydroxyacetone cycle)	12	10	1
homolactic fermentation	12	9	1
gluconeogenesis III	12	9	1
gluconeogenesis I	13	11	1
glycolysis I (from glucose 6-phosphate)	13	10	1
cob(II)yrinate a,c-diamide biosynthesis I (early cobalt insertion)	15	13	1
Bifidobacterium shunt	15	12	1
palmitate biosynthesis II (type II fatty acid synthase)	31	29	2
glycerol degradation to butanol	16	9	1
cutin biosynthesis	16	1	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	14	1
superpathway of glucose and xylose degradation	17	14	1
superpathway of hexitol degradation (bacteria)	18	13	1
heterolactic fermentation	18	12	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	14	1
superpathway of anaerobic sucrose degradation	19	13	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	18	1
superpathway of N-acetylneuraminate degradation	22	12	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	22	1
superpathway of fatty acids biosynthesis (E. coli)	53	51	2
palmitate biosynthesis III	29	28	1
oleate β-oxidation	35	30	1
adenosylcobalamin biosynthesis I (anaerobic)	36	29	1