Experiment set2IT074 for Pseudomonas fluorescens GW456-L13

L-Tryptophan carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + L-Tryptophan (12.5 mM), pH=7
Culturing: pseudo13_ML2, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
By: Mark on 3/10/2015
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 30 mM PIPES sesquisodium salt, Wolfe's mineral mix (0.03 g/L Magnesium Sulfate Heptahydrate, 0.015 g/L Nitrilotriacetic acid, 0.01 g/L Sodium Chloride, 0.005 g/L Manganese (II) sulfate monohydrate, 0.001 g/L Cobalt chloride hexahydrate, 0.001 g/L Zinc sulfate heptahydrate, 0.001 g/L Calcium chloride dihydrate, 0.001 g/L Iron (II) sulfate heptahydrate, 0.00025 g/L Nickel (II) chloride hexahydrate, 0.0002 g/L Aluminum potassium sulfate dodecahydrate, 0.0001 g/L Copper (II) sulfate pentahydrate, 0.0001 g/L Boric Acid, 0.0001 g/L Sodium Molybdate Dihydrate, 0.003 mg/L Sodium selenite pentahydrate), Wolfe's vitamin mix (0.1 mg/L Pyridoxine HCl, 0.05 mg/L 4-Aminobenzoic acid, 0.05 mg/L Lipoic acid, 0.05 mg/L Nicotinic Acid, 0.05 mg/L Riboflavin, 0.05 mg/L Thiamine HCl, 0.05 mg/L calcium pantothenate, 0.02 mg/L biotin, 0.02 mg/L Folic Acid, 0.001 mg/L Cyanocobalamin)

Specific Phenotypes

For 19 genes in this experiment

For carbon source L-Tryptophan in Pseudomonas fluorescens GW456-L13

For carbon source L-Tryptophan across organisms

SEED Subsystems

Subsystem	#Specific
Aromatic amino acid degradation	2
Benzoate degradation	2
Catechol branch of beta-ketoadipate pathway	2
NAD and NADP cofactor biosynthesis global	2
Arginine and Ornithine Degradation	1
Branched-Chain Amino Acid Biosynthesis	1
Formate hydrogenase	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glycine and Serine Utilization	1
Glycine cleavage system	1
Molybdenum cofactor biosynthesis	1
Multidrug Resistance Efflux Pumps	1
Photorespiration (oxidative C2 cycle)	1
Protocatechuate branch of beta-ketoadipate pathway	1
Sialic Acid Metabolism	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:

• Benzoate degradation via hydroxylation
• Lysine biosynthesis
• Arginine and proline metabolism
• Fluorobenzoate degradation
• Tryptophan metabolism
• Carbazole degradation
• Glyoxylate and dicarboxylate metabolism
• Nitrogen metabolism
• Urea cycle and metabolism of amino groups
• Glycine, serine and threonine metabolism
• gamma-Hexachlorocyclohexane degradation
• Toluene and xylene degradation
• 1,4-Dichlorobenzene degradation
• Benzoate degradation via CoA ligation
• Styrene degradation
• Butanoate metabolism
• One carbon pool by folate
• Methane metabolism
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
anthranilate degradation I (aerobic)	1	1	1
formate oxidation to CO2	1	1	1
L-tryptophan degradation I (via anthranilate)	3	3	2
catechol degradation III (ortho-cleavage pathway)	6	6	3
catechol degradation to β-ketoadipate	4	4	2
benzoate degradation I (aerobic)	2	2	1
3-oxoadipate degradation	2	2	1
superpathway of salicylate degradation	7	6	3
3-hydroxy-4-methyl-anthranilate biosynthesis II	5	3	2
L-tryptophan degradation to 2-amino-3-carboxymuconate semialdehyde	5	3	2
aromatic compounds degradation via β-ketoadipate	9	9	3
glycine biosynthesis II	3	3	1
L-ornithine biosynthesis II	3	3	1
glycine cleavage	3	3	1
L-proline biosynthesis III (from L-ornithine)	3	3	1
glycine degradation	3	3	1
L-arginine degradation I (arginase pathway)	3	2	1
2-nitrobenzoate degradation II	3	2	1
4-methylcatechol degradation (ortho cleavage)	7	4	2
L-arginine degradation VI (arginase 2 pathway)	4	3	1
oxalate degradation VI	4	1	1
NAD de novo biosynthesis II (from tryptophan)	9	6	2
mandelate degradation to acetyl-CoA	18	10	4
L-arginine degradation II (AST pathway)	5	5	1
L-ornithine biosynthesis I	5	5	1
L-arginine degradation XIII (reductive Stickland reaction)	5	5	1
superpathway of aromatic compound degradation via 3-oxoadipate	35	21	7
oxalate degradation III	5	1	1
L-tryptophan degradation IX	12	7	2
L-tryptophan degradation XII (Geobacillus)	12	7	2
3-hydroxy-4-methyl-anthranilate biosynthesis I	6	2	1
L-Nδ-acetylornithine biosynthesis	7	5	1
superpathway of NAD biosynthesis in eukaryotes	14	9	2
L-glutamate degradation XI (reductive Stickland reaction)	7	3	1
L-tryptophan degradation III (eukaryotic)	15	7	2
L-tryptophan degradation XI (mammalian, via kynurenine)	23	8	3
L-citrulline biosynthesis	8	7	1
3-hydroxyquinaldate biosynthesis	8	2	1
L-arginine biosynthesis I (via L-ornithine)	9	9	1
L-lysine biosynthesis I	9	9	1
folate transformations III (E. coli)	9	9	1
L-arginine biosynthesis III (via N-acetyl-L-citrulline)	9	8	1
photorespiration I	9	6	1
photorespiration III	9	5	1
reductive glycine pathway of autotrophic CO2 fixation	9	5	1
L-arginine biosynthesis II (acetyl cycle)	10	10	1
photorespiration II	10	6	1
L-glutamate degradation V (via hydroxyglutarate)	10	6	1
meta cleavage pathway of aromatic compounds	10	6	1
quinoxaline-2-carboxylate biosynthesis	10	4	1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate	42	15	4
folate transformations II (plants)	11	10	1
toluene degradation III (aerobic) (via p-cresol)	11	7	1
superpathway of L-citrulline metabolism	12	9	1
superpathway of C1 compounds oxidation to CO2	12	6	1
folate transformations I	13	9	1
toluene degradation IV (aerobic) (via catechol)	13	6	1
superpathway of aerobic toluene degradation	30	13	2
purine nucleobases degradation I (anaerobic)	15	6	1
superpathway of arginine and polyamine biosynthesis	17	16	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	1
purine nucleobases degradation II (anaerobic)	24	16	1
aspartate superpathway	25	22	1