Experiment set16IT011 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 3.2 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 34 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
Iron acquisition in Vibrio	4
Serine-glyoxylate cycle	4
Leucine Degradation and HMG-CoA Metabolism	3
Catechol branch of beta-ketoadipate pathway	2
Glutathione-dependent pathway of formaldehyde detoxification	2
Multidrug Resistance Efflux Pumps	2
Multidrug efflux pump in Campylobacter jejuni (CmeABC operon)	2
Protocatechuate branch of beta-ketoadipate pathway	2
Transport of Iron	2
ABC transporter dipeptide (TC 3.A.1.5.2)	1
Aromatic amino acid degradation	1
Biotin biosynthesis	1
Calvin-Benson cycle	1
Campylobacter Iron Metabolism	1
Cobalamin synthesis	1
Cobalt-zinc-cadmium resistance	1
Coenzyme B12 biosynthesis	1
Control of cell elongation - division cycle in Bacilli	1
Cysteine Biosynthesis	1
DNA-binding regulatory proteins, strays	1
DNA Repair Base Excision	1
DNA repair, bacterial	1
DNA repair, bacterial RecFOR pathway	1
Entner-Doudoroff Pathway	1
Flavodoxin	1
Fructose utilization	1
Glycolysis and Gluconeogenesis	1
HMG CoA Synthesis	1
Proline Synthesis	1
Purine conversions	1
Pyridoxin (Vitamin B6) Biosynthesis	1
Redox-dependent regulation of nucleus processes	1
Rubrerythrin	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:

• Glycolysis / Gluconeogenesis
• Fatty acid metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• 1- and 2-Methylnaphthalene degradation
• Urea cycle and metabolism of amino groups
• Arginine and proline metabolism
• Tyrosine metabolism
• Methane metabolism
• Limonene and pinene degradation
• Biosynthesis of plant hormones
• Fructose and mannose metabolism
• Galactose metabolism
• Ascorbate and aldarate metabolism
• Synthesis and degradation of ketone bodies
• Purine metabolism
• Glycine, serine and threonine metabolism
• Lysine biosynthesis
• Tryptophan 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
• 3-Chloroacrylic acid degradation
• Ethylbenzene degradation
• Butanoate metabolism
• Retinol metabolism
• Caprolactam degradation
• Alkaloid biosynthesis II
• Metabolism of xenobiotics by cytochrome P450
• Drug metabolism - cytochrome P450
• 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
acetaldehyde biosynthesis I	1	1	1
adenosine nucleotides degradation III	1	1	1
long-chain fatty acid activation	1	1	1
formaldehyde oxidation II (glutathione-dependent)	3	3	2
phytol degradation	4	3	2
ethanol degradation I	2	1	1
γ-linolenate biosynthesis II (animals)	2	1	1
pyruvate fermentation to ethanol II	2	1	1
linoleate biosynthesis II (animals)	2	1	1
octane oxidation	5	4	2
ketolysis	3	3	1
ethanol degradation II	3	3	1
L-ornithine biosynthesis II	3	3	1
L-leucine degradation I	6	5	2
methylglyoxal degradation VIII	3	2	1
L-isoleucine degradation II	3	2	1
methylglyoxal degradation I	3	2	1
L-leucine degradation III	3	2	1
L-valine degradation II	3	2	1
3-methyl-branched fatty acid α-oxidation	6	3	2
L-methionine degradation III	3	1	1
alkane biosynthesis II	3	1	1
pyruvate fermentation to ethanol I	3	1	1
oleate biosynthesis I (plants)	3	1	1
pyruvate fermentation to ethanol III	3	1	1
L-proline biosynthesis I (from L-glutamate)	4	4	1
salidroside biosynthesis	4	3	1
phospholipid remodeling (phosphatidylethanolamine, yeast)	4	2	1
L-tyrosine degradation III	4	2	1
L-phenylalanine degradation III	4	2	1
long chain fatty acid ester synthesis (engineered)	4	1	1
wax esters biosynthesis II	4	1	1
phosphatidylcholine acyl editing	4	1	1
sporopollenin precursors biosynthesis	18	4	4
pyruvate fermentation to isobutanol (engineered)	5	4	1
ethanolamine utilization	5	4	1
acetylene degradation (anaerobic)	5	3	1
phenylethanol biosynthesis	5	3	1
protein S-nitrosylation and denitrosylation	5	3	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
(S)-propane-1,2-diol degradation	5	2	1
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
superpathway of C1 compounds oxidation to CO2	12	5	2
stearate biosynthesis I (animals)	6	1	1
noradrenaline and adrenaline degradation	13	8	2
pyridoxal 5'-phosphate biosynthesis I	7	7	1
3-methylbutanol biosynthesis (engineered)	7	6	1
L-Nδ-acetylornithine biosynthesis	7	5	1
serotonin degradation	7	4	1
capsaicin biosynthesis	7	3	1
ceramide degradation by α-oxidation	7	2	1
icosapentaenoate biosynthesis III (8-desaturase, mammals)	7	1	1
arachidonate biosynthesis III (6-desaturase, mammals)	7	1	1
icosapentaenoate biosynthesis II (6-desaturase, mammals)	7	1	1
L-citrulline biosynthesis	8	7	1
superpathway of methylglyoxal degradation	8	5	1
2-deoxy-D-ribose degradation II	8	4	1
butanol and isobutanol biosynthesis (engineered)	8	3	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
Entner-Doudoroff pathway I	9	8	1
TCA cycle VI (Helicobacter)	9	7	1
sucrose biosynthesis I (from photosynthesis)	9	7	1
heterolactic fermentation	18	12	2
superpathway of fermentation (Chlamydomonas reinhardtii)	9	4	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	14	2
superpathway of anaerobic sucrose degradation	19	13	2
glycolysis IV	10	8	1
suberin monomers biosynthesis	20	4	2
superpathway of fatty acid biosynthesis II (plant)	43	38	4
glycolysis III (from glucose)	11	9	1
glycolysis II (from fructose 6-phosphate)	11	9	1
glycolysis VI (from fructose)	11	7	1
superpathway of N-acetylneuraminate degradation	22	12	2
superpathway of pyridoxal 5'-phosphate biosynthesis and salvage	12	11	1
formaldehyde assimilation III (dihydroxyacetone cycle)	12	10	1
gluconeogenesis III	12	9	1
superpathway of L-citrulline metabolism	12	9	1
homolactic fermentation	12	9	1
gluconeogenesis I	13	11	1
glycolysis I (from glucose 6-phosphate)	13	10	1
superpathway of Clostridium acetobutylicum solventogenic fermentation	13	4	1
L-tryptophan degradation V (side chain pathway)	13	1	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
mixed acid fermentation	16	12	1
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 Clostridium acetobutylicum acidogenic and solventogenic fermentation	17	6	1
superpathway of hexitol degradation (bacteria)	18	13	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	18	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