Experiment set6IT068 for Klebsiella michiganensis M5al

Thymidine nitrogen source

Group: nitrogen source
Media: RCH2_defined_Glucose_noNitrogen + Thymidine (10 mM), pH=7
Culturing: Koxy_ML2, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
By: Adam on 27-Apr-17
Media components: 0.1 g/L Potassium Chloride, 0.6 g/L Sodium phosphate monobasic monohydrate, 20 mM D-Glucose, 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: 1811 C1

Specific Phenotypes

For 10 genes in this experiment

For nitrogen source Thymidine in Klebsiella michiganensis M5al

For nitrogen source Thymidine across organisms

SEED Subsystems

Subsystem	#Specific
Pyrimidine utilization	3
Nitrate and nitrite ammonification	2
Deoxyribose and Deoxynucleoside Catabolism	1
Nudix proteins (nucleoside triphosphate hydrolases)	1
Phosphate metabolism	1
Stringent Response, (p)ppGpp metabolism	1
Urea decomposition	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Purine metabolism
• Puromycin biosynthesis
• Pyrimidine metabolism
• Drug metabolism - other enzymes
• Nucleotide sugars metabolism
• Lipopolysaccharide biosynthesis
• Glycosylphosphatidylinositol(GPI)-anchor biosynthesis
• alpha-Linolenic acid metabolism
• Trinitrotoluene degradation
• Folate biosynthesis
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Alkaloid biosynthesis I
• Insect hormone biosynthesis

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
pyrimidine deoxyribonucleosides degradation	3	3	2
pyrimidine ribonucleosides degradation	2	2	1
β-alanine degradation III	2	1	1
uracil degradation III	5	5	2
superpathway of pyrimidine deoxyribonucleosides degradation	6	6	2
superpathway of pyrimidine ribonucleosides degradation	5	4	1
ppGpp metabolism	6	6	1
nucleoside and nucleotide degradation (archaea)	10	4	1
3-hydroxypropanoate cycle	13	7	1
glyoxylate assimilation	13	5	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	10	1
superpathway of the 3-hydroxypropanoate cycle	18	7	1