Experiment set1IT096 for Escherichia coli BW25113

Putrescine Dihydrochloride nitrogen source

Group: nitrogen source
Media: M9 minimal media_noNitrogen + Putrescine Dihydrochloride (20 mM)
Culturing: Keio_ML9, tube, Aerobic, at 37 (C), shaken=200 rpm
Growth: about 5.0 generations
By: Kelly on 6/19/2014
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 21 genes in this experiment

For nitrogen source Putrescine Dihydrochloride in Escherichia coli BW25113

For nitrogen source Putrescine Dihydrochloride across organisms

SEED Subsystems

Subsystem	#Specific
ATP-dependent RNA helicases, bacterial	1
Ammonia assimilation	1
Conserved gene cluster associated with Met-tRNA formyltransferase	1
Cyanophycin Metabolism	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glycerol and Glycerol-3-phosphate Uptake and Utilization	1
Glycogen metabolism	1
NAD and NADP cofactor biosynthesis global	1
NAD regulation	1
Nudix proteins (nucleoside triphosphate hydrolases)	1
PnuC-like transporters	1
Trehalose Biosynthesis	1
tRNA processing	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Urea cycle and metabolism of amino groups
• Arginine and proline metabolism
• Tryptophan metabolism
• Naphthalene and anthracene degradation
• Nicotinate and nicotinamide metabolism
• Ubiquinone and menaquinone biosynthesis
• Purine metabolism
• Pyrimidine metabolism
• Alanine and aspartate metabolism
• Geraniol degradation
• Lysine biosynthesis
• Histidine metabolism
• Tyrosine metabolism
• Benzoxazinone biosynthesis
• Starch and sucrose metabolism
• Lipopolysaccharide biosynthesis
• 1- and 2-Methylnaphthalene degradation
• Folate biosynthesis
• Porphyrin and chlorophyll metabolism
• Limonene and pinene degradation
• Carotenoid biosynthesis - General
• Nitrogen metabolism
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of alkaloids derived from shikimate pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
NAD salvage pathway IV (from nicotinamide riboside)	2	2	2
superpathway of L-asparagine biosynthesis	2	2	2
L-glutamine degradation I	1	1	1
L-asparagine biosynthesis II	1	1	1
L-asparagine biosynthesis I	1	1	1
putrescine degradation II	4	4	3
superpathway of ornithine degradation	8	8	4
pseudouridine degradation	2	2	1
L-glutamate biosynthesis I	2	2	1
putrescine degradation I	2	2	1
4-aminobutanoate degradation I	2	2	1
NAD biosynthesis from nicotinamide	2	1	1
putrescine degradation V	2	1	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	11	5
superpathway of L-arginine and L-ornithine degradation	13	13	5
superpathway of 4-aminobutanoate degradation	3	3	1
ammonia assimilation cycle III	3	3	1
putrescine degradation IV	3	2	1
N-methylpyrrolidone degradation	3	1	1
4-aminobutanoate degradation IV	3	1	1
glycogen biosynthesis I (from ADP-D-Glucose)	4	4	1
superpathway of L-aspartate and L-asparagine biosynthesis	4	4	1
GABA shunt II	4	3	1
GABA shunt I	4	3	1
L-asparagine biosynthesis III (tRNA-dependent)	4	1	1
glycogen biosynthesis II (from UDP-D-Glucose)	4	1	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	1	1
starch biosynthesis	10	6	2
L-glutamate and L-glutamine biosynthesis	7	5	1
superpathway of NAD biosynthesis in eukaryotes	14	7	2
L-citrulline biosynthesis	8	6	1
glycogen biosynthesis III (from α-maltose 1-phosphate)	8	3	1
superpathway of L-citrulline metabolism	12	8	1