Experiment set10IT012 for Pseudomonas putida KT2440

L-Leucine carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + L-Leucine (10 mM)
Culturing: Putida_ML5_JBEI, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 4.3 generations
By: Mitchell Thompson on 10/1/18
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 31 genes in this experiment

For carbon source L-Leucine in Pseudomonas putida KT2440

For carbon source L-Leucine across organisms

SEED Subsystems

Subsystem	#Specific
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	9
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	2
Leucine Degradation and HMG-CoA Metabolism	2
Arginine and Ornithine Degradation	1
DNA-replication	1
DNA repair, bacterial	1
Glutamate dehydrogenases	1
Glycolysis and Gluconeogenesis	1
Glycolysis and Gluconeogenesis, including Archaeal enzymes	1
HMG CoA Synthesis	1
Homogentisate pathway of aromatic compound degradation	1
Isoleucine degradation	1
Proline, 4-hydroxyproline uptake and utilization	1
Protein chaperones	1
Proteolysis in bacteria, ATP-dependent	1
Pyruvate Alanine Serine Interconversions	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
Respiratory dehydrogenases 1	1
Serine-glyoxylate cycle	1
Threonine and Homoserine Biosynthesis	1
Transport of Zinc	1
Valine 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
• Arginine and proline metabolism
• Glutamate metabolism
• Alanine and aspartate metabolism
• Tyrosine metabolism
• Pyruvate metabolism
• Alkaloid biosynthesis I
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of plant hormones
• Glycolysis / Gluconeogenesis
• Citrate cycle (TCA cycle)
• Puromycin biosynthesis
• Glycine, serine and threonine metabolism
• Cysteine metabolism
• Phenylalanine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• beta-Alanine metabolism
• Nucleotide sugars metabolism
• alpha-Linolenic acid metabolism
• Trinitrotoluene degradation
• Propanoate metabolism
• Styrene degradation
• Carbon fixation in photosynthetic organisms
• Reductive carboxylate cycle (CO2 fixation)
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Nitrogen metabolism
• Alkaloid biosynthesis II
• Insect hormone biosynthesis
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• 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
L-aspartate degradation I	1	1	1
L-aspartate biosynthesis	1	1	1
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
L-glutamate degradation I	1	1	1
L-proline degradation I	3	3	2
L-glutamate degradation II	2	2	1
malate/L-aspartate shuttle pathway	2	2	1
β-alanine degradation II	2	2	1
L-tryptophan degradation IV (via indole-3-lactate)	2	1	1
L-tyrosine degradation II	2	1	1
atromentin biosynthesis	2	1	1
L-tyrosine degradation I	5	5	2
pyruvate decarboxylation to acetyl CoA I	3	3	1
L-alanine degradation II (to D-lactate)	3	3	1
glycine biosynthesis II	3	3	1
2-oxoglutarate decarboxylation to succinyl-CoA	3	3	1
L-tyrosine biosynthesis I	3	3	1
2-oxoisovalerate decarboxylation to isobutanoyl-CoA	3	3	1
L-phenylalanine biosynthesis I	3	3	1
glycine cleavage	3	3	1
L-leucine degradation I	6	5	2
L-arginine degradation I (arginase pathway)	3	2	1
L-phenylalanine degradation II (anaerobic)	3	2	1
L-asparagine degradation III (mammalian)	3	2	1
sulfolactate degradation III	3	1	1
ethene biosynthesis IV (engineered)	3	1	1
indole-3-acetate biosynthesis VI (bacteria)	3	1	1
(R)-cysteate degradation	3	1	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
Arg/N-end rule pathway (eukaryotic)	14	8	4
superpathway of L-aspartate and L-asparagine biosynthesis	4	3	1
L-tyrosine degradation III	4	2	1
L-phenylalanine degradation III	4	2	1
L-tryptophan degradation VIII (to tryptophol)	4	1	1
ethene biosynthesis II (microbes)	4	1	1
trans-4-hydroxy-L-proline degradation I	5	3	1
superpathway of plastoquinol biosynthesis	5	2	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	2	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
L-tryptophan degradation XIII (reductive Stickland reaction)	5	1	1
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	7	2
superpathway of L-threonine biosynthesis	6	6	1
TCA cycle VIII (Chlamydia)	6	5	1
β-alanine biosynthesis II	6	5	1
superpathway of sulfolactate degradation	6	2	1
(5R)-carbapenem carboxylate biosynthesis	6	1	1
coenzyme M biosynthesis II	6	1	1
anaerobic energy metabolism (invertebrates, cytosol)	7	5	1
L-Nδ-acetylornithine biosynthesis	7	5	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	8	2
L-glutamate degradation XI (reductive Stickland reaction)	7	2	1
4-aminobutanoate degradation V	7	2	1
L-citrulline biosynthesis	8	7	1
superpathway of aromatic amino acid biosynthesis	18	18	2
superpathway of L-methionine biosynthesis (transsulfuration)	9	7	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	6	1
superpathway of L-tyrosine biosynthesis	10	10	1
superpathway of L-phenylalanine biosynthesis	10	10	1
superpathway of coenzyme A biosynthesis II (plants)	10	9	1
glycolysis V (Pyrococcus)	10	7	1
L-glutamate degradation V (via hydroxyglutarate)	10	5	1
rosmarinic acid biosynthesis I	10	2	1
glycolysis II (from fructose 6-phosphate)	11	9	1
(S)-reticuline biosynthesis I	11	3	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	12	1
superpathway of L-citrulline metabolism	12	9	1
indole-3-acetate biosynthesis II	12	5	1
superpathway of L-isoleucine biosynthesis I	13	13	1
gluconeogenesis I	13	11	1
glycolysis I (from glucose 6-phosphate)	13	10	1
superpathway of rosmarinic acid biosynthesis	14	2	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	14	1
superpathway of anaerobic energy metabolism (invertebrates)	17	10	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	1
superpathway of hexitol degradation (bacteria)	18	13	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	14	1
superpathway of anaerobic sucrose degradation	19	13	1
methylaspartate cycle	19	10	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	18	1
superpathway of N-acetylneuraminate degradation	22	12	1
aspartate superpathway	25	22	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	22	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	4	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	21	2
superpathway of chorismate metabolism	59	42	2