Experiment set16IT018 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 5.9 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 27 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)	7
Isoleucine degradation	4
Leucine Degradation and HMG-CoA Metabolism	4
Valine degradation	4
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	2
Arginine and Ornithine Degradation	1
DNA-replication	1
DNA repair, bacterial	1
Glutamate dehydrogenases	1
HMG CoA Synthesis	1
Proline, 4-hydroxyproline uptake and utilization	1
Protein chaperones	1
Pyruvate Alanine Serine Interconversions	1
Respiratory dehydrogenases 1	1
Serine-glyoxylate cycle	1
Threonine and Homoserine Biosynthesis	1
Transport of Zinc	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
• Cysteine metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• beta-Alanine metabolism
• Propanoate metabolism
• Carbon fixation in photosynthetic organisms
• Nitrogen metabolism
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-aspartate biosynthesis	1	1	1
L-aspartate degradation I	1	1	1
L-glutamate degradation I	1	1	1
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
L-proline degradation I	3	3	2
2-oxoisovalerate decarboxylation to isobutanoyl-CoA	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
atromentin biosynthesis	2	1	1
L-tyrosine degradation II	2	1	1
L-tryptophan degradation IV (via indole-3-lactate)	2	1	1
L-alanine degradation II (to D-lactate)	3	3	1
L-phenylalanine biosynthesis I	3	3	1
L-tyrosine biosynthesis I	3	3	1
L-leucine degradation I	6	5	2
L-asparagine degradation III (mammalian)	3	2	1
L-arginine degradation I (arginase pathway)	3	2	1
L-phenylalanine degradation II (anaerobic)	3	2	1
(R)-cysteate degradation	3	1	1
ethene biosynthesis IV (engineered)	3	1	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
sulfolactate degradation III	3	1	1
indole-3-acetate biosynthesis VI (bacteria)	3	1	1
Arg/N-end rule pathway (eukaryotic)	14	8	4
superpathway of L-aspartate and L-asparagine biosynthesis	4	3	1
L-phenylalanine degradation III	4	2	1
L-tyrosine degradation III	4	2	1
L-tryptophan degradation VIII (to tryptophol)	4	1	1
ethene biosynthesis II (microbes)	4	1	1
L-tyrosine degradation I	5	5	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
coenzyme M biosynthesis II	6	1	1
(5R)-carbapenem carboxylate biosynthesis	6	1	1
L-Nδ-acetylornithine biosynthesis	7	5	1
anaerobic energy metabolism (invertebrates, cytosol)	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-phenylalanine biosynthesis	10	10	1
superpathway of L-tyrosine biosynthesis	10	10	1
superpathway of coenzyme A biosynthesis II (plants)	10	9	1
L-glutamate degradation V (via hydroxyglutarate)	10	5	1
rosmarinic acid biosynthesis I	10	2	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
superpathway of rosmarinic acid biosynthesis	14	2	1
superpathway of anaerobic energy metabolism (invertebrates)	17	10	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	1
methylaspartate cycle	19	10	1
aspartate superpathway	25	22	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	4	1
superpathway of chorismate metabolism	59	42	2
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	21	1