Experiment set19IT070 for Pseudomonas simiae WCS417

Chemotaxis:Motility:: Method=Plug_approach; Chemical=L-Tryptophan; Chemical_conc=5mM; Distance=2cm; Sample=outer; Collection=outgrowth_in_LBkan50

Group: motility_chemotaxis
Media: RCH2_defined_NO_ammonium_with_Glycerol
Culturing: fluoroDangl_ML3, soft agar plate, Aerobic, at 30 (C), shaken=0 rpm, (solid)
By: Peter Kim on 4-Oct-21
Media components: 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 30 mM PIPES sesquisodium salt, 2.2 mM Glycerol, 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 10 genes in this experiment

SEED Subsystems

Subsystem	#Specific
Aromatic amino acid degradation	2
Benzoate degradation	1
Branched-Chain Amino Acid Biosynthesis	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glycerol and Glycerol-3-phosphate Uptake and Utilization	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Histidine Biosynthesis	1
MLST	1
NAD and NADP cofactor biosynthesis global	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
• Histidine metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Fluorobenzoate degradation
• Tryptophan metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• Glycerolipid metabolism
• Carbazole degradation
• Benzoate degradation via CoA ligation
• 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
anthranilate degradation I (aerobic)	1	1	1
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
atromentin biosynthesis	2	1	1
benzoate degradation I (aerobic)	2	1	1
L-tyrosine degradation II	2	1	1
L-tryptophan degradation I (via anthranilate)	3	3	1
L-phenylalanine biosynthesis I	3	3	1
L-tyrosine biosynthesis I	3	3	1
glycerol degradation I	3	3	1
L-phenylalanine degradation II (anaerobic)	3	2	1
2-nitrobenzoate degradation II	3	1	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
glycerol and glycerophosphodiester degradation	4	4	1
L-tyrosine degradation III	4	2	1
L-phenylalanine degradation III	4	2	1
L-tyrosine degradation I	5	5	1
3-hydroxy-4-methyl-anthranilate biosynthesis II	5	3	1
L-tryptophan degradation to 2-amino-3-carboxymuconate semialdehyde	5	3	1
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
superpathway of aromatic amino acid biosynthesis	18	18	2
NAD de novo biosynthesis II (from tryptophan)	9	6	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	3	1
L-histidine biosynthesis	10	10	1
superpathway of L-tyrosine biosynthesis	10	10	1
superpathway of L-phenylalanine biosynthesis	10	10	1
meta cleavage pathway of aromatic compounds	10	3	1
rosmarinic acid biosynthesis I	10	2	1
(S)-reticuline biosynthesis I	11	1	1
L-tryptophan degradation XI (mammalian, via kynurenine)	23	7	2
superpathway of aromatic compound degradation via 3-oxoadipate	35	21	3
L-tryptophan degradation IX	12	4	1
L-tryptophan degradation XII (Geobacillus)	12	4	1
toluene degradation IV (aerobic) (via catechol)	13	4	1
superpathway of NAD biosynthesis in eukaryotes	14	9	1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate	42	15	3
superpathway of rosmarinic acid biosynthesis	14	3	1
L-tryptophan degradation III (eukaryotic)	15	6	1
mandelate degradation to acetyl-CoA	18	9	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	3	1
superpathway of chorismate metabolism	59	44	2
superpathway of aerobic toluene degradation	30	12	1
superpathway of histidine, purine, and pyrimidine biosynthesis	46	44	1