Experiment set16IT019 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 5.5 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 30 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)	8
Isoleucine degradation	4
Leucine Degradation and HMG-CoA Metabolism	4
Valine degradation	4
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	2
ABC transporter dipeptide (TC 3.A.1.5.2)	1
Arginine and Ornithine Degradation	1
DNA-replication	1
DNA repair, bacterial	1
Glutamate dehydrogenases	1
HMG CoA Synthesis	1
Homogentisate pathway of aromatic compound degradation	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
• Alkaloid biosynthesis I
• Puromycin biosynthesis
• Cysteine metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• beta-Alanine metabolism
• Nucleotide sugars metabolism
• alpha-Linolenic acid metabolism
• Trinitrotoluene degradation
• Propanoate metabolism
• Carbon fixation in photosynthetic organisms
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Nitrogen metabolism
• Alkaloid biosynthesis II
• Insect hormone biosynthesis
• 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
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
L-glutamate degradation I	1	1	1
L-aspartate degradation I	1	1	1
L-aspartate biosynthesis	1	1	1
2-oxoisovalerate decarboxylation to isobutanoyl-CoA	3	3	2
L-proline degradation I	3	3	2
L-glutamate degradation II	2	2	1
β-alanine degradation II	2	2	1
malate/L-aspartate shuttle pathway	2	2	1
L-tyrosine degradation II	2	1	1
atromentin biosynthesis	2	1	1
L-tryptophan degradation IV (via indole-3-lactate)	2	1	1
L-tyrosine biosynthesis I	3	3	1
L-phenylalanine biosynthesis I	3	3	1
L-alanine degradation II (to D-lactate)	3	3	1
L-leucine degradation I	6	5	2
L-phenylalanine degradation II (anaerobic)	3	2	1
L-asparagine degradation III (mammalian)	3	2	1
L-arginine degradation I (arginase pathway)	3	2	1
(R)-cysteate degradation	3	1	1
indole-3-acetate biosynthesis VI (bacteria)	3	1	1
sulfolactate degradation III	3	1	1
ethene biosynthesis IV (engineered)	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
L-tyrosine degradation I	5	5	1
trans-4-hydroxy-L-proline degradation I	5	3	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	2	1
superpathway of plastoquinol biosynthesis	5	2	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
L-tryptophan degradation XIII (reductive Stickland reaction)	5	1	1
L-phenylalanine degradation VI (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
4-aminobutanoate degradation V	7	2	1
L-glutamate degradation XI (reductive Stickland reaction)	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