Experiment set8IT059 for Phaeobacter inhibens DSM 17395

Putrescine Dihydrochloride nitrogen source

Group: nitrogen source
Media: DinoMM_noNitrogen_HighNutrient_SucroseC + Putrescine Dihydrochloride (5 mM), pH=7.2
Culturing: Phaeo_ML1, tube, Aerobic, at 25 (C), shaken=200 rpm
By: Mark on 1/20/2015
Media components: 20 g/L Sea salts, 0.1 g/L Potassium phosphate monobasic, 20 mM Sucrose, 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 17 genes in this experiment

For nitrogen source Putrescine Dihydrochloride in Phaeobacter inhibens DSM 17395

For nitrogen source Putrescine Dihydrochloride across organisms

SEED Subsystems

Subsystem	#Specific
Allantoin Utilization	1
Ammonia assimilation	1
Biotin biosynthesis	1
Choline and Betaine Uptake and Betaine Biosynthesis	1
D-ribose utilization	1
Deoxyribose and Deoxynucleoside Catabolism	1
ECF class transporters	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Maltose and Maltodextrin Utilization	1
Proline, 4-hydroxyproline uptake and utilization	1
Protein degradation	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Purine metabolism
• Glutamate metabolism
• Arginine and proline metabolism
• Glycolysis / Gluconeogenesis
• Pentose phosphate pathway
• Ascorbate and aldarate metabolism
• Fatty acid metabolism
• Urea cycle and metabolism of amino groups
• Glycine, serine and threonine metabolism
• Valine, leucine and isoleucine degradation
• Lysine degradation
• Histidine metabolism
• Tryptophan metabolism
• beta-Alanine metabolism
• Glycerolipid metabolism
• Pyruvate metabolism
• 1,2-Dichloroethane degradation
• Propanoate metabolism
• 3-Chloroacrylic acid degradation
• Butanoate metabolism
• Limonene and pinene degradation
• Nitrogen metabolism
• Drug metabolism - other enzymes
• Biosynthesis of alkaloids derived from histidine and purine

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-glutamine degradation I	1	1	1
L-glutamine biosynthesis I	1	1	1
ammonia assimilation cycle III	3	3	2
L-glutamate biosynthesis I	2	2	1
ammonia assimilation cycle II	2	2	1
ammonia assimilation cycle I	2	2	1
ribose phosphorylation	2	1	1
2-deoxy-D-ribose degradation I	3	3	1
ethanol degradation IV	3	3	1
hypotaurine degradation	3	3	1
superpathway of ammonia assimilation (plants)	3	3	1
ethanol degradation II	3	3	1
ethanol degradation III	3	2	1
histamine degradation	3	1	1
L-aspartate degradation III (anaerobic)	3	1	1
L-aspartate degradation II (aerobic)	3	1	1
L-glutamate and L-glutamine biosynthesis	7	7	2
L-asparagine biosynthesis III (tRNA-dependent)	4	4	1
glutaminyl-tRNAgln biosynthesis via transamidation	4	4	1
guanosine ribonucleotides de novo biosynthesis	4	4	1
phytol degradation	4	3	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	2	1
creatinine degradation I	4	2	1
fatty acid α-oxidation I (plants)	4	2	1
putrescine degradation III	4	1	1
octane oxidation	5	3	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
mitochondrial NADPH production (yeast)	5	2	1
dopamine degradation	5	1	1
creatinine degradation II	5	1	1
allantoin degradation to glyoxylate II	5	1	1
superpathway of guanosine nucleotides de novo biosynthesis I	6	6	1
3-methyl-branched fatty acid α-oxidation	6	3	1
alkane oxidation	6	1	1
noradrenaline and adrenaline degradation	13	4	2
serotonin degradation	7	3	1
ceramide degradation by α-oxidation	7	2	1
limonene degradation IV (anaerobic)	7	1	1
L-citrulline biosynthesis	8	8	1
superpathway of guanosine nucleotides de novo biosynthesis II	8	7	1
glycine betaine degradation I	8	7	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	4	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
superpathway of allantoin degradation in plants	8	1	1
aromatic biogenic amine degradation (bacteria)	8	1	1
L-arginine biosynthesis II (acetyl cycle)	10	10	1
superpathway of L-citrulline metabolism	12	10	1
superpathway of purine nucleotide salvage	14	13	1
superpathway of purine nucleotides de novo biosynthesis I	21	21	1
superpathway of purine nucleotides de novo biosynthesis II	26	23	1
superpathway of histidine, purine, and pyrimidine biosynthesis	46	42	1