Experiment set27S432 for Pseudomonas fluorescens SBW25-INTG

L-Ornithine carbon source

Group: carbon source
Media: MME_noCarbon + L-Ornithine (10 mM)
Culturing: PseudoSBW25_INTG_ML3, 96 deep-well microplate; 1.2 mL volume, Aerobic, at 30 (C)
By: Andrew Frank on 1/31/23
Media components: 9.1 mM Potassium phosphate dibasic trihydrate, 20 mM 3-(N-morpholino)propanesulfonic acid, 4.3 mM Sodium Chloride, 10 mM Ammonium 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 42 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	12
ABC transporter branched-chain amino acid (TC 3.A.1.4.1)	6
Polyamine Metabolism	3
Cysteine Biosynthesis	2
Fructose utilization	2
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	2
Methionine Biosynthesis	2
Acid resistance mechanisms	1
Arginine Deiminase Pathway	1
Branched-Chain Amino Acid Biosynthesis	1
Conserved gene cluster possibly involved in RNA metabolism	1
Entner-Doudoroff Pathway	1
Folate Biosynthesis	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Methionine Salvage	1
Methylglyoxal Metabolism	1
Pentose phosphate pathway	1
Proline, 4-hydroxyproline uptake and utilization	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Respiratory dehydrogenases 1	1
Thiamin biosynthesis	1
Threonine and Homoserine Biosynthesis	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
• Biosynthesis of plant hormones
• Glutamate metabolism
• Lysine biosynthesis
• Phenylalanine metabolism
• Tryptophan metabolism
• Sulfur metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Glycolysis / Gluconeogenesis
• Pentose phosphate pathway
• Ascorbate and aldarate metabolism
• Fatty acid metabolism
• Alanine and aspartate metabolism
• Glycine, serine and threonine metabolism
• Methionine metabolism
• Valine, leucine and isoleucine degradation
• Lysine degradation
• Histidine metabolism
• Tyrosine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• 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
• Carbon fixation in photosynthetic organisms
• Limonene and pinene degradation
• Alkaloid biosynthesis I
• Alkaloid biosynthesis II
• Biosynthesis of alkaloids derived from shikimate pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
putrescine biosynthesis II	3	3	3
L-arginine degradation IV (arginine decarboxylase/agmatine deiminase pathway)	3	3	3
L-cysteine biosynthesis I	2	2	2
arginine dependent acid resistance	1	1	1
L-aspartate biosynthesis	1	1	1
L-aspartate degradation I	1	1	1
L-ornithine degradation I (L-proline biosynthesis)	1	1	1
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
L-arginine degradation I (arginase pathway)	3	3	2
L-proline degradation I	3	3	2
glycine betaine biosynthesis IV (from glycine)	3	2	2
putrescine biosynthesis I	2	2	1
putrescine degradation V	2	2	1
L-arginine degradation VII (arginase 3 pathway)	2	2	1
indole-3-acetate biosynthesis IV (bacteria)	2	2	1
L-arginine degradation III (arginine decarboxylase/agmatinase pathway)	2	2	1
L-glutamate degradation II	2	2	1
acrylonitrile degradation I	2	2	1
indole-3-acetate biosynthesis III (bacteria)	2	2	1
L-lactaldehyde degradation (aerobic)	2	2	1
atromentin biosynthesis	2	1	1
malate/L-aspartate shuttle pathway	2	1	1
L-proline biosynthesis II (from arginine)	2	1	1
L-tryptophan degradation IV (via indole-3-lactate)	2	1	1
L-tyrosine degradation II	2	1	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
superpathway of polyamine biosynthesis II	8	6	3
L-proline biosynthesis III (from L-ornithine)	3	3	1
L-phenylalanine biosynthesis I	3	3	1
L-ornithine biosynthesis II	3	3	1
ethanol degradation II	3	3	1
ethanol degradation IV	3	3	1
L-tyrosine biosynthesis I	3	3	1
L-arginine degradation X (arginine monooxygenase pathway)	3	2	1
L-phenylalanine degradation II (anaerobic)	3	2	1
methylglyoxal degradation V	3	2	1
putrescine degradation IV	3	2	1
methylglyoxal degradation IV	3	2	1
ethanol degradation III	3	2	1
hypotaurine degradation	3	2	1
L-asparagine degradation III (mammalian)	3	2	1
superpathway of acrylonitrile degradation	3	2	1
histamine degradation	3	1	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
indole-3-acetate biosynthesis VI (bacteria)	3	1	1
5'-deoxyadenosine degradation I	3	1	1
sulfolactate degradation III	3	1	1
(R)-cysteate degradation	3	1	1
L-Nδ-acetylornithine biosynthesis	7	6	2
L-citrulline biosynthesis	8	8	2
superpathway of putrescine biosynthesis	4	4	1
L-arginine degradation VI (arginase 2 pathway)	4	4	1
L-cysteine biosynthesis VII (from S-sulfo-L-cysteine)	4	3	1
superpathway of L-aspartate and L-asparagine biosynthesis	4	3	1
phytol degradation	4	3	1
putrescine degradation III	4	3	1
L-tyrosine degradation III	4	2	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	2	1
fatty acid α-oxidation I (plants)	4	2	1
D-arabinose degradation II	4	2	1
L-phenylalanine degradation III	4	2	1
5'-deoxyadenosine degradation II	4	1	1
L-tryptophan degradation VIII (to tryptophol)	4	1	1
spermidine biosynthesis III	4	1	1
ethene biosynthesis II (microbes)	4	1	1
N-3-oxalyl-L-2,3-diaminopropanoate biosynthesis	4	1	1
superpathway of sulfate assimilation and cysteine biosynthesis	9	9	2
pentose phosphate pathway (non-oxidative branch) I	5	5	1
L-ornithine biosynthesis I	5	5	1
L-arginine degradation XIII (reductive Stickland reaction)	5	5	1
L-tyrosine degradation I	5	5	1
octane oxidation	5	4	1
mitochondrial NADPH production (yeast)	5	4	1
trans-4-hydroxy-L-proline degradation I	5	3	1
lactate biosynthesis (archaea)	5	3	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
superpathway of plastoquinol biosynthesis	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
dopamine degradation	5	2	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
L-tryptophan degradation XIII (reductive Stickland reaction)	5	1	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	7	2
C4 photosynthetic carbon assimilation cycle, NAD-ME type	11	6	2
superpathway of L-threonine biosynthesis	6	6	1
superpathway of L-citrulline metabolism	12	10	2
TCA cycle VIII (Chlamydia)	6	5	1
hydrogen sulfide biosynthesis II (mammalian)	6	4	1
thiazole component of thiamine diphosphate biosynthesis I	6	4	1
3-methyl-branched fatty acid α-oxidation	6	3	1
indole-3-acetate biosynthesis II	12	5	2
superpathway of sulfolactate degradation	6	2	1
alkane oxidation	6	1	1
coenzyme M biosynthesis II	6	1	1
D-cycloserine biosynthesis	6	1	1
(5R)-carbapenem carboxylate biosynthesis	6	1	1
superpathway of L-arginine and L-ornithine degradation	13	9	2
noradrenaline and adrenaline degradation	13	8	2
superpathway of glycol metabolism and degradation	7	5	1
thiazole component of thiamine diphosphate biosynthesis II	7	5	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	9	2
serotonin degradation	7	4	1
anaerobic energy metabolism (invertebrates, cytosol)	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
pentose phosphate pathway	8	8	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	7	1
superpathway of polyamine biosynthesis I	8	6	1
superpathway of methylglyoxal degradation	8	5	1
superpathway of ornithine degradation	8	4	1
L-rhamnose degradation II	8	4	1
aromatic biogenic amine degradation (bacteria)	8	4	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
superpathway of arginine and polyamine biosynthesis	17	15	2
superpathway of aromatic amino acid biosynthesis	18	18	2
L-lysine biosynthesis I	9	9	1
L-arginine biosynthesis I (via L-ornithine)	9	9	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	2
L-arginine biosynthesis III (via N-acetyl-L-citrulline)	9	8	1
superpathway of L-methionine biosynthesis (transsulfuration)	9	7	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	6	1
formaldehyde assimilation II (assimilatory RuMP Cycle)	9	6	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	5	1
superpathway of seleno-compound metabolism	19	8	2
superpathway of L-phenylalanine biosynthesis	10	10	1
superpathway of L-tyrosine biosynthesis	10	10	1
L-arginine biosynthesis II (acetyl cycle)	10	10	1
Rubisco shunt	10	8	1
superpathway of thiamine diphosphate biosynthesis I	10	8	1
rosmarinic acid biosynthesis I	10	1	1
superpathway of thiamine diphosphate biosynthesis II	11	9	1
L-methionine salvage cycle III	11	5	1
L-methionine salvage cycle II (plants)	11	3	1
(S)-reticuline biosynthesis I	11	1	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	12	1
formaldehyde assimilation III (dihydroxyacetone cycle)	12	10	1
superpathway of fucose and rhamnose degradation	12	5	1
L-methionine salvage cycle I (bacteria and plants)	12	4	1
aspartate superpathway	25	22	2
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of rosmarinic acid biosynthesis	14	1	1
Bifidobacterium shunt	15	12	1
superpathway of glucose and xylose degradation	17	16	1
superpathway of anaerobic energy metabolism (invertebrates)	17	8	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	4	1
superpathway of chorismate metabolism	59	42	2
superpathway of pentose and pentitol degradation	42	16	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	20	1