Experiment set55S342 for Pseudomonas putida KT2440

Ammonium chloride and TNT nitrogen source

Group: nitrogen source
Media: M9 minimal media_noNitrogen + Ammonium chloride (100 mM) + Trinitrotoluene (0.44 mM)
Culturing: Putida_ML5_JBEI
By: Alex Rivier on 2/2/24
Media components: 4 g/L D-Glucose, 2 mM Magnesium sulfate, 0.1 mM Calcium chloride, 12.8 g/L Sodium phosphate dibasic heptahydrate, 3 g/L Potassium phosphate monobasic, 0.5 g/L Sodium Chloride

Specific Phenotypes

For 11 genes in this experiment

For nitrogen source Ammonium chloride in Pseudomonas putida KT2440

For nitrogen source Ammonium chloride across organisms

SEED Subsystems

Subsystem	#Specific
D-gluconate and ketogluconates metabolism	2
Fructose utilization	2
ABC transporter oligopeptide (TC 3.A.1.5.1)	1
Ammonia assimilation	1
Coenzyme PQQ synthesis	1
Copper homeostasis	1
Entner-Doudoroff Pathway	1
Fructose and Mannose Inducible PTS	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glutathione: Redox cycle	1
Mannitol Utilization	1
Pyrroloquinoline Quinone biosynthesis	1
Respiratory dehydrogenases 1	1

Metabolic Maps

Color code by fitness: see overview map or list of maps.

Maps containing gene(s) with specific phenotypes:

• Glycolysis / Gluconeogenesis
• Pentose phosphate pathway
• Fructose and mannose metabolism
• Galactose metabolism
• Ascorbate and aldarate metabolism
• Glutamate metabolism
• gamma-Hexachlorocyclohexane degradation
• Bisphenol A degradation
• Glutathione metabolism
• Starch and sucrose metabolism
• Nucleotide sugars metabolism
• Aminosugars metabolism
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Benzoate degradation via CoA ligation
• Ethylbenzene degradation
• Retinol metabolism
• Limonene and pinene degradation
• Nitrogen metabolism
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-glutamate biosynthesis I	2	2	2
L-glutamine degradation I	1	1	1
L-glutamine degradation II	1	1	1
ammonia assimilation cycle III	3	3	2
glutathione-peroxide redox reactions	3	2	1
L-glutamate and L-glutamine biosynthesis	7	6	2
L-asparagine biosynthesis III (tRNA-dependent)	4	4	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	3	1
glucose degradation (oxidative)	5	5	1
glucose and glucose-1-phosphate degradation	5	4	1
L-ascorbate biosynthesis VIII (engineered pathway)	7	5	1
L-citrulline biosynthesis	8	7	1
superpathway of L-citrulline metabolism	12	9	1