Experiment set22IT040 for Pseudomonas fluorescens SBW25-INTG

L-Ornithine 10 mM carbon source

Group: carbon source
Media: MME_noNitrogen_noCarbon + L-Ornithine (10 mM) + Ammonium chloride (10 mM), pH=7
Culturing: PseudoSBW25_INTG_ML3, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C), shaken=1200 rpm
By: Joshua Elmore on 8-Mar-22
Media components: 9.1 mM Potassium phosphate dibasic trihydrate, 20 mM 3-(N-morpholino)propanesulfonic acid, 4.3 mM Sodium Chloride, 0.41 mM Magnesium Sulfate Heptahydrate, 0.07 mM Calcium chloride dihydrate, MME Trace Minerals (0.5 mg/L EDTA tetrasodium tetrahydrate salt, 2 mg/L Ferric chloride, 0.05 mg/L Boric Acid, 0.05 mg/L Zinc chloride, 0.03 mg/L copper (II) chloride dihydrate, 0.05 mg/L Manganese (II) chloride tetrahydrate, 0.05 mg/L Diammonium molybdate, 0.05 mg/L Cobalt chloride hexahydrate, 0.05 mg/L Nickel (II) chloride hexahydrate)

Specific Phenotypes

For 32 genes in this experiment

For carbon source L-Ornithine in Pseudomonas fluorescens SBW25-INTG

For carbon source L-Ornithine across organisms

SEED Subsystems

Subsystem	#Specific
Arginine and Ornithine Degradation	10
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	3
Cysteine Biosynthesis	2
Methionine Biosynthesis	2
Polyamine Metabolism	2
Arginine Deiminase Pathway	1
Choline and Betaine Uptake and Betaine Biosynthesis	1
Conserved gene cluster possibly involved in RNA metabolism	1
Entner-Doudoroff Pathway	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Methionine Salvage	1
Methylglyoxal Metabolism	1
Proline, 4-hydroxyproline uptake and utilization	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Respiratory dehydrogenases 1	1
Thiamin 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:

• Arginine and proline metabolism
• Urea cycle and metabolism of amino groups
• Cysteine metabolism
• Lysine biosynthesis
• Tryptophan metabolism
• Sulfur metabolism
• Glycolysis / Gluconeogenesis
• Ascorbate and aldarate metabolism
• Fatty acid metabolism
• Glutamate metabolism
• Methionine metabolism
• Valine, leucine and isoleucine degradation
• Lysine degradation
• Histidine metabolism
• Phenylalanine metabolism
• beta-Alanine metabolism
• Selenoamino acid metabolism
• Cyanoamino acid metabolism
• Glycerolipid metabolism
• Pyruvate metabolism
• 1,2-Dichloroethane degradation
• Benzoate degradation via CoA ligation
• Propanoate metabolism
• 3-Chloroacrylic acid degradation
• Styrene degradation
• Butanoate metabolism
• Limonene and pinene degradation
• 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-cysteine biosynthesis I	2	2	2
L-proline degradation I	3	3	2
putrescine biosynthesis II	3	3	2
L-arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway)	3	3	2
L-arginine degradation I (arginase pathway)	3	3	2
indole-3-acetate biosynthesis IV (bacteria)	2	2	1
L-lactaldehyde degradation (aerobic)	2	2	1
acrylonitrile degradation I	2	2	1
putrescine degradation V	2	2	1
indole-3-acetate biosynthesis III (bacteria)	2	2	1
ethylene glycol degradation	2	1	1
putrescine degradation I	2	1	1
L-arginine degradation II (AST pathway)	5	5	2
seleno-amino acid biosynthesis (plants)	5	3	2
ethanol degradation II	3	3	1
L-ornithine biosynthesis II	3	3	1
ethanol degradation IV	3	3	1
L-proline biosynthesis III (from L-ornithine)	3	3	1
putrescine degradation IV	3	2	1
superpathway of acrylonitrile degradation	3	2	1
L-arginine degradation X (arginine monooxygenase pathway)	3	2	1
ethanol degradation III	3	2	1
hypotaurine degradation	3	2	1
methylglyoxal degradation V	3	2	1
methylglyoxal degradation IV	3	2	1
histamine degradation	3	1	1
oxalate degradation II	3	1	1
5'-deoxyadenosine degradation I	3	1	1
L-Nδ-acetylornithine biosynthesis	7	6	2
L-citrulline biosynthesis	8	8	2
L-arginine degradation VI (arginase 2 pathway)	4	4	1
superpathway of polyamine biosynthesis II	8	6	2
phytol degradation	4	3	1
L-cysteine biosynthesis VII (from S-sulfo-L-cysteine)	4	3	1
putrescine degradation III	4	3	1
D-arabinose degradation II	4	2	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	2	1
fatty acid α-oxidation I (plants)	4	2	1
N-3-oxalyl-L-2,3-diaminopropanoate biosynthesis	4	1	1
5'-deoxyadenosine degradation II	4	1	1
ethene biosynthesis II (microbes)	4	1	1
superpathway of sulfate assimilation and cysteine biosynthesis	9	9	2
L-ornithine biosynthesis I	5	5	1
L-arginine degradation XIII (reductive Stickland reaction)	5	5	1
mitochondrial NADPH production (yeast)	5	4	1
octane oxidation	5	4	1
lactate biosynthesis (archaea)	5	3	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
dopamine degradation	5	2	1
S-methyl-5-thio-α-D-ribose 1-phosphate degradation III	5	2	1
S-methyl-5-thio-α-D-ribose 1-phosphate degradation II	5	2	1
superpathway of L-citrulline metabolism	12	10	2
thiazole component of thiamine diphosphate biosynthesis I	6	4	1
hydrogen sulfide biosynthesis II (mammalian)	6	4	1
3-methyl-branched fatty acid α-oxidation	6	3	1
D-cycloserine biosynthesis	6	1	1
(5R)-carbapenem carboxylate biosynthesis	6	1	1
alkane oxidation	6	1	1
noradrenaline and adrenaline degradation	13	8	2
thiazole component of thiamine diphosphate biosynthesis II	7	5	1
superpathway of glycol metabolism and degradation	7	5	1
serotonin degradation	7	4	1
L-cysteine biosynthesis VI (reverse transsulfuration)	7	3	1
S-methyl-5-thio-α-D-ribose 1-phosphate degradation I	7	2	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 methylglyoxal degradation	8	5	1
aromatic biogenic amine degradation (bacteria)	8	4	1
L-rhamnose degradation II	8	4	1
superpathway of ornithine degradation	8	4	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
L-arginine biosynthesis I (via L-ornithine)	9	9	1
L-lysine biosynthesis I	9	9	1
L-arginine biosynthesis III (via N-acetyl-L-citrulline)	9	8	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	6	1
superpathway of seleno-compound metabolism	19	8	2
L-arginine biosynthesis II (acetyl cycle)	10	10	1
superpathway of thiamine diphosphate biosynthesis I	10	8	1
superpathway of thiamine diphosphate biosynthesis II	11	9	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	7	1
L-methionine salvage cycle III	11	5	1
L-methionine salvage cycle II (plants)	11	3	1
indole-3-acetate biosynthesis II	12	5	1
superpathway of fucose and rhamnose degradation	12	5	1
L-methionine salvage cycle I (bacteria and plants)	12	4	1
superpathway of L-arginine and L-ornithine degradation	13	9	1
superpathway of arginine and polyamine biosynthesis	17	15	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	1
aspartate superpathway	25	22	1
superpathway of pentose and pentitol degradation	42	16	1