Experiment set2IT004 for Caulobacter crescentus NA1000

Putrescine Dihydrochloride nitrogen source

Group: nitrogen source
Media: M2_noNitrogen + Putrescine Dihydrochloride (20 mM)
Culturing: Caulo_ML2, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
Growth: about 3.8 generations
By: Jayashree on 22-Mar-17
Media components: 1.74 g/L Disodium phosphate, 1.06 g/L Potassium phosphate monobasic, 20 mM D-Glucose, 0.5 mM Magnesium sulfate, 0.5 mM Calcium chloride, 0.01 mM Iron (II) sulfate heptahydrate, 0.008 mM EDTA
Growth plate: 1527 A6

Specific Phenotypes

For 25 genes in this experiment

For nitrogen source Putrescine Dihydrochloride in Caulobacter crescentus NA1000

For nitrogen source Putrescine Dihydrochloride across organisms

SEED Subsystems

Subsystem	#Specific
Nitrate and nitrite ammonification	2
Entner-Doudoroff Pathway	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Methionine Biosynthesis	1
Methionine Degradation	1
Methylglyoxal Metabolism	1
Pyridoxin (Vitamin B6) Biosynthesis	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
YbbK	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
• Butanoate metabolism
• Limonene and pinene degradation
• Glycolysis / Gluconeogenesis
• Ascorbate and aldarate metabolism
• Fatty acid metabolism
• Glutamate metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Lysine biosynthesis
• Lysine degradation
• Histidine metabolism
• Tyrosine metabolism
• beta-Alanine metabolism
• Glycerolipid metabolism
• Pyruvate metabolism
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• 1,2-Dichloroethane degradation
• Propanoate metabolism
• 3-Chloroacrylic acid degradation
• Vitamin B6 metabolism
• Porphyrin and chlorophyll metabolism

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
putrescine degradation V	2	2	1
pyridoxal 5'-phosphate salvage I	6	5	3
putrescine degradation I	2	1	1
4-aminobutanoate degradation II	2	1	1
ethylene glycol degradation	2	1	1
4-aminobutanoate degradation III	2	1	1
ethanol degradation II	3	3	1
ethanol degradation IV	3	3	1
pyridoxal 5'-phosphate salvage II (plants)	9	8	3
ethanol degradation III	3	2	1
putrescine degradation IV	3	2	1
hypotaurine degradation	3	2	1
histamine degradation	3	1	1
superpathway of 4-aminobutanoate degradation	3	1	1
superpathway of pyridoxal 5'-phosphate biosynthesis and salvage	12	10	3
phytol degradation	4	3	1
4-amino-2-methyl-5-diphosphomethylpyrimidine biosynthesis II	8	4	2
L-tryptophan degradation X (mammalian, via tryptamine)	4	2	1
fatty acid α-oxidation I (plants)	4	2	1
putrescine degradation III	4	2	1
D-arabinose degradation II	4	1	1
mitochondrial NADPH production (yeast)	5	3	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
dopamine degradation	5	2	1
octane oxidation	5	2	1
L-lysine degradation IV	5	1	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	5	2
tetrapyrrole biosynthesis I (from glutamate)	6	5	1
3-methyl-branched fatty acid α-oxidation	6	3	1
L-lysine degradation X	6	3	1
L-lysine degradation III	6	1	1
alkane oxidation	6	1	1
noradrenaline and adrenaline degradation	13	8	2
superpathway of L-arginine and L-ornithine degradation	13	7	2
serotonin degradation	7	4	1
L-lysine degradation I	7	3	1
superpathway of glycol metabolism and degradation	7	3	1
ceramide degradation by α-oxidation	7	2	1
limonene degradation IV (anaerobic)	7	1	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	6	1
superpathway of ornithine degradation	8	5	1
aromatic biogenic amine degradation (bacteria)	8	3	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
4-hydroxyphenylacetate degradation	8	2	1
TCA cycle IV (2-oxoglutarate decarboxylase)	9	8	1
Entner-Doudoroff pathway II (non-phosphorylative)	9	4	1
superpathway of heme b biosynthesis from glutamate	10	8	1
nicotine degradation II (pyrrolidine pathway)	11	2	1
nicotine degradation I (pyridine pathway)	17	4	1
adenosylcobalamin biosynthesis II (aerobic)	33	15	1
adenosylcobalamin biosynthesis I (anaerobic)	36	14	1
superpathway of pentose and pentitol degradation	42	12	1
superpathway of L-lysine degradation	43	8	1