Experiment set10IT006 for Pseudomonas putida KT2440

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:

• Arginine and proline metabolism
• Urea cycle and metabolism of amino groups
• Butanoate metabolism
• Limonene and pinene degradation
• Valine, leucine and isoleucine biosynthesis
• Lysine degradation
• Histidine metabolism
• Tryptophan metabolism
• 1- and 2-Methylnaphthalene degradation
• Glycolysis / Gluconeogenesis
• Ascorbate and aldarate metabolism
• Fatty acid biosynthesis
• Fatty acid metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Lysine biosynthesis
• Tyrosine metabolism
• Phenylalanine metabolism
• beta-Alanine metabolism
• Lipopolysaccharide biosynthesis
• Glycerolipid metabolism
• Glycerophospholipid metabolism
• Ether lipid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• Pyruvate metabolism
• Naphthalene and anthracene degradation
• 1,2-Dichloroethane degradation
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• 3-Chloroacrylic acid degradation
• Ethylbenzene degradation
• C5-Branched dibasic acid metabolism
• Pantothenate and CoA biosynthesis
• Diterpenoid biosynthesis
• Carotenoid biosynthesis - General
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide backbone
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from histidine and purine

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-arginine degradation III (arginine decarboxylase/agmatinase pathway)	2	2	1
L-alanine biosynthesis I	2	2	1
putrescine degradation V	2	2	1
putrescine biosynthesis I	2	2	1
L-arginine degradation VIII (arginine oxidase pathway)	4	3	2
ethylene glycol degradation	2	1	1
putrescine degradation I	2	1	1
L-arginine degradation XI	2	1	1
pyruvate fermentation to (R)-acetoin II	2	1	1
ethanol degradation II	3	3	1
ethanol degradation IV	3	3	1
pyruvate fermentation to (S)-acetoin	3	2	1
ethanol degradation III	3	2	1
hypotaurine degradation	3	2	1
putrescine degradation IV	3	2	1
pyruvate fermentation to (R)-acetoin I	3	2	1
L-arginine degradation X (arginine monooxygenase pathway)	3	2	1
histamine degradation	3	1	1
L-valine biosynthesis	4	4	1
superpathway of L-alanine biosynthesis	4	4	1
phytol degradation	4	3	1
superpathway of putrescine biosynthesis	4	3	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	3	1
putrescine degradation III	4	3	1
D-arabinose degradation II	4	2	1
fatty acid α-oxidation I (plants)	4	2	1
L-arginine degradation XII	4	2	1
pyruvate fermentation to isobutanol (engineered)	5	4	1
mitochondrial NADPH production (yeast)	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
serotonin degradation	7	4	1
L-isoleucine biosynthesis III	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