Experiment set11IT074 for Klebsiella michiganensis M5al

2'-Deoxycytidine 10 mM carbon source

Group: carbon source
Media: RCH2_defined_noCarbon + 2'-Deoxycytidine (10 mM), pH=7
Culturing: Koxy_ML2, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
By: Adam on 5/2/18
Media components: 0.25 g/L Ammonium chloride, 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 30 mM PIPES sesquisodium salt, 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)
Growth plate: Koxy_deoxyribosePlus_plate C4

Specific Phenotypes

For 23 genes in this experiment

For carbon source 2'-Deoxycytidine in Klebsiella michiganensis M5al

For carbon source 2'-Deoxycytidine across organisms

SEED Subsystems

Subsystem	#Specific
Deoxyribose and Deoxynucleoside Catabolism	3
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	2
CytR regulation	1
Entner-Doudoroff Pathway	1
Formate hydrogenase	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Ketoisovalerate oxidoreductase	1
Methylglyoxal Metabolism	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
• Pyrimidine metabolism
• Pyruvate metabolism
• Propanoate metabolism
• Ascorbate and aldarate metabolism
• Fatty acid metabolism
• Urea cycle and metabolism of amino groups
• Purine metabolism
• Valine, leucine and isoleucine degradation
• Lysine degradation
• Arginine and proline metabolism
• Histidine metabolism
• Tryptophan metabolism
• beta-Alanine metabolism
• Glycerolipid metabolism
• 1,2-Dichloroethane degradation
• 3-Chloroacrylic acid degradation
• Butanoate metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Limonene and pinene degradation
• Drug metabolism - other enzymes

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
acetate conversion to acetyl-CoA	1	1	1
acetate and ATP formation from acetyl-CoA III	1	1	1
superpathway of pyrimidine deoxyribonucleosides degradation	6	6	4
ethanol degradation II	3	3	2
ethanol degradation IV	3	3	2
pyrimidine deoxyribonucleosides degradation	3	3	2
2-deoxy-α-D-ribose 1-phosphate degradation	3	3	2
ethanol degradation III	3	2	2
putrescine degradation I	2	2	1
phenylethylamine degradation I	2	2	1
ethylene glycol degradation	2	2	1
pyrimidine ribonucleosides degradation	2	2	1
phenylethanol degradation	2	1	1
putrescine degradation V	2	1	1
phenylethylamine degradation II	2	1	1
2-deoxy-D-ribose degradation I	3	3	1
superpathway of acetate utilization and formation	3	3	1
putrescine degradation IV	3	2	1
L-isoleucine biosynthesis V	3	2	1
hypotaurine degradation	3	2	1
L-phenylalanine degradation II (anaerobic)	3	2	1
styrene degradation	3	1	1
histamine degradation	3	1	1
superpathway of purine deoxyribonucleosides degradation	7	7	2
D-arabinose degradation II	4	4	1
phytol degradation	4	3	1
chitin deacetylation	4	3	1
putrescine degradation III	4	2	1
fatty acid α-oxidation I (plants)	4	2	1
L-tryptophan degradation X (mammalian, via tryptamine)	4	1	1
superpathway of pyrimidine ribonucleosides degradation	5	4	1
mitochondrial NADPH production (yeast)	5	3	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
2-methylcitrate cycle I	5	2	1
octane oxidation	5	2	1
dopamine degradation	5	1	1
purine ribonucleosides degradation	6	6	1
L-isoleucine biosynthesis IV	6	4	1
3-methyl-branched fatty acid α-oxidation	6	3	1
2-methylcitrate cycle II	6	2	1
superpathway of bitter acids biosynthesis	18	3	3
lupulone and humulone biosynthesis	6	1	1
β-alanine biosynthesis II	6	1	1
alkane oxidation	6	1	1
adlupulone and adhumulone biosynthesis	6	1	1
colupulone and cohumulone biosynthesis	6	1	1
noradrenaline and adrenaline degradation	13	4	2
superpathway of glycol metabolism and degradation	7	7	1
serotonin degradation	7	3	1
ceramide degradation by α-oxidation	7	2	1
limonene degradation IV (anaerobic)	7	1	1
superpathway of ornithine degradation	8	8	1
superpathway of NAD/NADP - NADH/NADPH interconversion (yeast)	8	5	1
aromatic biogenic amine degradation (bacteria)	8	3	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
Entner-Doudoroff pathway II (non-phosphorylative)	9	7	1
reductive glycine pathway of autotrophic CO2 fixation	9	6	1
L-phenylalanine degradation IV (mammalian, via side chain)	9	5	1
cis-geranyl-CoA degradation	9	1	1
superpathway of coenzyme A biosynthesis II (plants)	10	5	1
nucleoside and nucleotide degradation (archaea)	10	4	1
superpathway of L-arginine, putrescine, and 4-aminobutanoate degradation	11	11	1
superpathway of phenylethylamine degradation	11	11	1
superpathway of L-arginine and L-ornithine degradation	13	13	1
anaerobic aromatic compound degradation (Thauera aromatica)	27	3	1
superpathway of pentose and pentitol degradation	42	21	1