Experiment set10IT006 for Pseudomonas putida KT2440

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L-Arginine carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + L-Arginine (10 mM)
Culturing: Putida_ML5_JBEI, tube, Aerobic, at 30 (C), shaken=200 rpm
Growth: about 3.9 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 18 genes in this experiment

For carbon source L-Arginine in Pseudomonas putida KT2440

For carbon source L-Arginine across organisms

SEED Subsystems

Subsystem #Specific
Arginine and Ornithine Degradation 9
Alanine biosynthesis 1
Branched-Chain Amino Acid Biosynthesis 1
DNA-binding regulatory proteins, strays 1
Entner-Doudoroff Pathway 1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria 1
Methylglyoxal Metabolism 1
Orphan regulatory proteins 1
Polyamine Metabolism 1
Pyruvate Alanine Serine Interconversions 1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate 1
Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization 1

Metabolic Maps

Color code by fitness: see overview map or list of maps.

Maps containing gene(s) with specific phenotypes:

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway #Steps #Present #Specific
L-arginine degradation IX (arginine:pyruvate transaminase pathway) 4 4 3
L-arginine degradation II (AST pathway) 5 5 3
L-alanine biosynthesis I 2 2 1
putrescine biosynthesis I 2 2 1
L-arginine degradation III (arginine decarboxylase/agmatinase pathway) 2 2 1
putrescine degradation V 2 2 1
L-arginine degradation VIII (arginine oxidase pathway) 4 3 2
putrescine degradation I 2 1 1
pyruvate fermentation to (R)-acetoin II 2 1 1
ethylene glycol degradation 2 1 1
L-arginine degradation XI 2 1 1
ethanol degradation IV 3 3 1
ethanol degradation II 3 3 1
putrescine degradation IV 3 2 1
hypotaurine degradation 3 2 1
L-arginine degradation X (arginine monooxygenase pathway) 3 2 1
pyruvate fermentation to (S)-acetoin 3 2 1
ethanol degradation III 3 2 1
pyruvate fermentation to (R)-acetoin I 3 2 1
histamine degradation 3 1 1
superpathway of L-alanine biosynthesis 4 4 1
L-valine biosynthesis 4 4 1
putrescine degradation III 4 3 1
L-tryptophan degradation X (mammalian, via tryptamine) 4 3 1
phytol degradation 4 3 1
superpathway of putrescine biosynthesis 4 3 1
L-arginine degradation XII 4 2 1
D-arabinose degradation II 4 2 1
fatty acid α-oxidation I (plants) 4 2 1
mitochondrial NADPH production (yeast) 5 4 1
pyruvate fermentation to isobutanol (engineered) 5 4 1
octane oxidation 5 4 1
superpathway of (R,R)-butanediol biosynthesis 5 3 1
sphingosine and sphingosine-1-phosphate metabolism 10 4 2
dopamine degradation 5 2 1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation 11 9 2
L-isoleucine biosynthesis IV 6 4 1
3-methyl-branched fatty acid α-oxidation 6 3 1
superpathway of 2,3-butanediol biosynthesis 6 2 1
alkane oxidation 6 1 1
superpathway of L-arginine and L-ornithine degradation 13 11 2
noradrenaline and adrenaline degradation 13 8 2
L-isoleucine biosynthesis I (from threonine) 7 7 1
superpathway of glycol metabolism and degradation 7 6 1
L-isoleucine biosynthesis III 7 4 1
serotonin degradation 7 4 1
ceramide degradation by α-oxidation 7 2 1
limonene degradation IV (anaerobic) 7 1 1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast) 8 7 1
superpathway of ornithine degradation 8 6 1
L-isoleucine biosynthesis II 8 5 1
superpathway of polyamine biosynthesis I 8 5 1
aromatic biogenic amine degradation (bacteria) 8 3 1
ceramide and sphingolipid recycling and degradation (yeast) 16 4 2
superpathway of branched chain amino acid biosynthesis 17 17 2
Entner-Doudoroff pathway II (non-phosphorylative) 9 5 1
superpathway of L-isoleucine biosynthesis I 13 13 1
superpathway of arginine and polyamine biosynthesis 17 14 1
superpathway of L-threonine metabolism 18 12 1
superpathway of pentose and pentitol degradation 42 10 1