Experiment set1IT095 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 4.9 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 41 genes in this experiment

For nitrogen source Putrescine Dihydrochloride in Escherichia coli BW25113

For nitrogen source Putrescine Dihydrochloride across organisms

SEED Subsystems

Subsystem	#Specific
Trehalose Biosynthesis	2
ATP-dependent RNA helicases, bacterial	1
Ammonia assimilation	1
Arginine and Ornithine Degradation	1
Conserved gene cluster associated with Met-tRNA formyltransferase	1
Cyanophycin Metabolism	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glutathione: Non-redox reactions	1
Glycerol and Glycerol-3-phosphate Uptake and Utilization	1
Glycogen metabolism	1
Lactose utilization	1
Lysine Biosynthesis DAP Pathway	1
NAD and NADP cofactor biosynthesis global	1
NAD regulation	1
Nudix proteins (nucleoside triphosphate hydrolases)	1
Phenylalanine and Tyrosine Branches from Chorismate	1
PnuC-like transporters	1
Threonine and Homoserine Biosynthesis	1
Universal stress protein family	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
• Lysine biosynthesis
• Tyrosine metabolism
• Tryptophan metabolism
• Starch and sucrose metabolism
• Naphthalene and anthracene degradation
• Nicotinate and nicotinamide metabolism
• Alkaloid biosynthesis I
• Biosynthesis of alkaloids derived from shikimate pathway
• Ubiquinone and menaquinone biosynthesis
• Purine metabolism
• Pyrimidine metabolism
• Alanine and aspartate metabolism
• Glycine, serine and threonine metabolism
• Methionine metabolism
• Geraniol degradation
• Histidine metabolism
• Phenylalanine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Novobiocin biosynthesis
• Benzoxazinone biosynthesis
• 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 II
• Insect hormone biosynthesis
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
NAD salvage pathway IV (from nicotinamide riboside)	2	2	2
putrescine degradation I	2	2	2
superpathway of L-asparagine biosynthesis	2	2	2
L-asparagine biosynthesis II	1	1	1
3-(4-hydroxyphenyl)pyruvate biosynthesis	1	1	1
L-asparagine biosynthesis I	1	1	1
L-glutamine degradation I	1	1	1
putrescine degradation II	4	4	3
superpathway of ornithine degradation	8	8	5
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	11	6
pseudouridine degradation	2	2	1
4-aminobutanoate degradation I	2	2	1
trehalose biosynthesis I	2	2	1
L-phenylalanine biosynthesis III (cytosolic, plants)	2	2	1
L-glutamate biosynthesis I	2	2	1
NAD biosynthesis from nicotinamide	2	1	1
L-tyrosine degradation II	2	1	1
putrescine degradation V	2	1	1
atromentin biosynthesis	2	1	1
superpathway of L-arginine and L-ornithine degradation	13	13	6
ammonia assimilation cycle III	3	3	1
L-homoserine biosynthesis	3	3	1
superpathway of 4-aminobutanoate degradation	3	3	1
L-tyrosine biosynthesis I	3	3	1
L-phenylalanine biosynthesis I	3	3	1
L-leucine degradation III	3	2	1
putrescine degradation IV	3	2	1
L-phenylalanine degradation II (anaerobic)	3	2	1
N-methylpyrrolidone degradation	3	1	1
4-aminobutanoate degradation IV	3	1	1
L-leucine degradation V (oxidative Stickland reaction)	3	1	1
microcin B17 biosynthesis	3	1	1
L-tyrosine degradation IV (to 4-methylphenol)	3	1	1
superpathway of L-aspartate and L-asparagine biosynthesis	4	4	1
glycogen biosynthesis I (from ADP-D-Glucose)	4	4	1
GABA shunt II	4	3	1
L-tyrosine biosynthesis III	4	3	1
GABA shunt I	4	3	1
dipicolinate biosynthesis	4	3	1
L-phenylalanine biosynthesis II	4	2	1
L-phenylalanine degradation III	4	2	1
L-methionine biosynthesis IV	4	2	1
L-tyrosine biosynthesis II	4	2	1
spermidine biosynthesis II	4	2	1
L-tyrosine degradation III	4	2	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	1	1
glycogen biosynthesis II (from UDP-D-Glucose)	4	1	1
L-asparagine biosynthesis III (tRNA-dependent)	4	1	1
starch biosynthesis	10	6	2
superpathway of L-phenylalanine and L-tyrosine biosynthesis	5	2	1
ectoine biosynthesis	5	2	1
superpathway of plastoquinol biosynthesis	5	1	1
L-tyrosine degradation V (reductive Stickland reaction)	5	1	1
L-tyrosine degradation I	5	1	1
4-hydroxybenzoate biosynthesis I (eukaryotes)	5	1	1
L-phenylalanine degradation VI (reductive Stickland reaction)	5	1	1
L-leucine degradation IV (reductive Stickland reaction)	5	1	1
L-leucine biosynthesis	6	6	1
superpathway of L-threonine biosynthesis	6	6	1
L-lysine degradation X	6	5	1
norspermidine biosynthesis	6	2	1
L-leucine degradation I	6	2	1
L-lysine degradation I	7	7	1
L-lysine biosynthesis III	7	6	1
L-lysine biosynthesis VI	7	6	1
L-glutamate and L-glutamine biosynthesis	7	5	1
superpathway of NAD biosynthesis in eukaryotes	14	7	2
3-dehydroquinate biosynthesis II (archaea)	7	3	1
cremeomycin biosynthesis	7	2	1
superpathway of L-homoserine and L-methionine biosynthesis	8	8	1
L-citrulline biosynthesis	8	6	1
glycogen biosynthesis III (from α-maltose 1-phosphate)	8	3	1
grixazone biosynthesis	8	2	1
superpathway of polyamine biosynthesis III	8	2	1
superpathway of aromatic amino acid biosynthesis	18	18	2
L-lysine biosynthesis I	9	9	1
superpathway of S-adenosyl-L-methionine biosynthesis	9	9	1
superpathway of L-methionine biosynthesis (transsulfuration)	9	9	1
L-lysine biosynthesis II	9	6	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	4	1
superpathway of L-phenylalanine biosynthesis	10	10	1
superpathway of L-tyrosine biosynthesis	10	10	1
rosmarinic acid biosynthesis I	10	1	1
tropane alkaloids biosynthesis	11	1	1
(S)-reticuline biosynthesis I	11	1	1
superpathway of L-methionine biosynthesis (by sulfhydrylation)	12	10	1
chorismate biosynthesis II (archaea)	12	8	1
superpathway of L-citrulline metabolism	12	8	1
superpathway of L-isoleucine biosynthesis I	13	13	1
superpathway of rosmarinic acid biosynthesis	14	2	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis II	15	13	1
superpathway of hyoscyamine (atropine) and scopolamine biosynthesis	16	3	1
superpathway of branched chain amino acid biosynthesis	17	17	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	18	1
aspartate superpathway	25	24	1
platensimycin biosynthesis	26	6	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	3	1
superpathway of chorismate metabolism	59	54	2
odd iso-branched-chain fatty acid biosynthesis	34	24	1
superpathway of L-lysine degradation	43	14	1