Experiment set3IT009 for Pseudomonas simiae WCS417

L-Tryptophan carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + L-Tryptophan (12.5 mM), pH=7
Culturing: fluoroDangl_ML3, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
By: Mark on 2/18/2015
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 17 genes in this experiment

For carbon source L-Tryptophan in Pseudomonas simiae WCS417

For carbon source L-Tryptophan across organisms

SEED Subsystems

Subsystem	#Specific
Aromatic amino acid degradation	3
Catechol branch of beta-ketoadipate pathway	3
NAD and NADP cofactor biosynthesis global	3
Benzoate degradation	2
Branched-Chain Amino Acid Biosynthesis	2
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	2
DNA-binding regulatory proteins, strays	1
Histidine Biosynthesis	1
Muconate lactonizing enzyme family	1
Protocatechuate branch of beta-ketoadipate pathway	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
• Fluorobenzoate degradation
• Tryptophan metabolism
• Toluene and xylene degradation
• 1,4-Dichlorobenzene degradation
• Carbazole degradation
• Benzoate degradation via CoA ligation
• Histidine metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• gamma-Hexachlorocyclohexane degradation
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• 2,4-Dichlorobenzoate degradation
• Glyoxylate and dicarboxylate metabolism
• Styrene degradation
• Butanoate metabolism
• Nitrogen metabolism
• Alkaloid biosynthesis II
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-tryptophan degradation I (via anthranilate)	3	3	3
anthranilate degradation I (aerobic)	1	1	1
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
catechol degradation to β-ketoadipate	4	4	3
catechol degradation III (ortho-cleavage pathway)	6	6	4
L-tryptophan degradation to 2-amino-3-carboxymuconate semialdehyde	5	3	3
3-hydroxy-4-methyl-anthranilate biosynthesis II	5	3	3
superpathway of salicylate degradation	7	7	4
3-oxoadipate degradation	2	2	1
atromentin biosynthesis	2	1	1
L-tyrosine degradation II	2	1	1
benzoate degradation I (aerobic)	2	1	1
aromatic compounds degradation via β-ketoadipate	9	9	4
L-phenylalanine biosynthesis I	3	3	1
L-tyrosine biosynthesis I	3	3	1
NAD de novo biosynthesis II (from tryptophan)	9	6	3
L-phenylalanine degradation II (anaerobic)	3	2	1
3-hydroxy-4-methyl-anthranilate biosynthesis I	6	2	2
2-nitrobenzoate degradation II	3	1	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
4-methylcatechol degradation (ortho cleavage)	7	4	2
mandelate degradation to acetyl-CoA	18	9	5
superpathway of aromatic compound degradation via 3-oxoadipate	35	21	9
L-phenylalanine degradation III	4	2	1
L-tyrosine degradation III	4	2	1
L-tryptophan degradation XII (Geobacillus)	12	4	3
L-tryptophan degradation IX	12	4	3
superpathway of NAD biosynthesis in eukaryotes	14	9	3
L-tyrosine degradation I	5	5	1
L-tryptophan degradation III (eukaryotic)	15	6	3
superpathway of plastoquinol biosynthesis	5	2	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
L-tryptophan degradation XI (mammalian, via kynurenine)	23	7	4
L-glutamate degradation XI (reductive Stickland reaction)	7	3	1
3-hydroxyquinaldate biosynthesis	8	2	1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate	42	15	5
superpathway of aromatic amino acid biosynthesis	18	18	2
L-phenylalanine degradation IV (mammalian, via side chain)	9	3	1
superpathway of L-phenylalanine biosynthesis	10	10	1
L-histidine biosynthesis	10	10	1
superpathway of L-tyrosine biosynthesis	10	10	1
L-glutamate degradation V (via hydroxyglutarate)	10	6	1
quinoxaline-2-carboxylate biosynthesis	10	4	1
meta cleavage pathway of aromatic compounds	10	3	1
rosmarinic acid biosynthesis I	10	2	1
toluene degradation III (aerobic) (via p-cresol)	11	8	1
(S)-reticuline biosynthesis I	11	1	1
toluene degradation IV (aerobic) (via catechol)	13	4	1
superpathway of rosmarinic acid biosynthesis	14	3	1
superpathway of aerobic toluene degradation	30	12	2
anaerobic aromatic compound degradation (Thauera aromatica)	27	3	1
superpathway of chorismate metabolism	59	44	2
superpathway of histidine, purine, and pyrimidine biosynthesis	46	44	1