Experiment set7IT041 for Klebsiella michiganensis M5al

LB with Nickel (II) chloride hexahydrate 1.5 mM

Group: stress
Media: LB + Nickel (II) chloride hexahydrate (1.5 mM)
Culturing: Koxy_ML2, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
By: Adam on 27-Apr-17
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride
Growth plate: 1801 A3

Specific Phenotypes

For 29 genes in this experiment

For stress Nickel (II) chloride hexahydrate in Klebsiella michiganensis M5al

For stress Nickel (II) chloride hexahydrate across organisms

SEED Subsystems

Subsystem	#Specific
Polyamine Metabolism	2
Ribonucleotide reduction	2
Calvin-Benson cycle	1
Campylobacter Iron Metabolism	1
Chorismate Synthesis	1
Cobalt-zinc-cadmium resistance	1
Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate)	1
Copper homeostasis: copper tolerance	1
Cysteine Biosynthesis	1
Glycolysis and Gluconeogenesis	1
Phosphate metabolism	1
Protein degradation	1
Rhamnose containing glycans	1
Teichoic and lipoteichoic acids biosynthesis	1
Thioredoxin-disulfide reductase	1
tRNA processing	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glutathione metabolism
• Pyrimidine metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of plant hormones
• Glycolysis / Gluconeogenesis
• Pentose phosphate pathway
• Fructose and mannose metabolism
• Purine metabolism
• Puromycin biosynthesis
• Methionine metabolism
• Cysteine metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Selenoamino acid metabolism
• Nucleotide sugars metabolism
• alpha-Linolenic acid metabolism
• Trinitrotoluene degradation
• Carbon fixation in photosynthetic organisms
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Sulfur metabolism
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of alkaloids derived from terpenoid and polyketide

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
guanosine deoxyribonucleotides de novo biosynthesis II	4	4	2
adenosine deoxyribonucleotides de novo biosynthesis II	4	4	2
pseudouridine degradation	2	2	1
glutathione degradation (DUG pathway)	2	2	1
sedoheptulose bisphosphate bypass	2	2	1
adenosine deoxyribonucleotides de novo biosynthesis I	2	2	1
L-cysteine biosynthesis I	2	2	1
3-dehydroquinate biosynthesis I	2	2	1
guanosine deoxyribonucleotides de novo biosynthesis I	2	2	1
superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis (E. coli)	14	14	4
superpathway of adenosine nucleotides de novo biosynthesis II	7	7	2
Ac/N-end rule pathway	21	6	6
superpathway of guanosine nucleotides de novo biosynthesis II	8	8	2
queuosine biosynthesis I (de novo)	4	4	1
pyrimidine deoxyribonucleotides de novo biosynthesis I	9	9	2
pyrimidine deoxyribonucleotides de novo biosynthesis III	9	8	2
superpathway of adenosine nucleotides de novo biosynthesis I	5	5	1
enterobacterial common antigen biosynthesis	5	4	1
seleno-amino acid biosynthesis (plants)	5	3	1
sucrose degradation V (sucrose α-glucosidase)	5	3	1
queuosine biosynthesis III (queuosine salvage)	5	3	1
superpathway of guanosine nucleotides de novo biosynthesis I	6	6	1
pentose phosphate pathway (non-oxidative branch) II	6	5	1
γ-glutamyl cycle	6	5	1
superpathway of purine nucleotides de novo biosynthesis II	26	26	4
Calvin-Benson-Bassham cycle	13	10	2
chorismate biosynthesis I	7	7	1
pyrimidine deoxyribonucleotides de novo biosynthesis IV	7	6	1
pyrimidine deoxyribonucleotides biosynthesis from CTP	8	6	1
oxygenic photosynthesis	17	11	2
superpathway of pyrimidine deoxyribonucleotides de novo biosynthesis	18	18	2
superpathway of sulfate assimilation and cysteine biosynthesis	9	9	1
1,3-propanediol biosynthesis (engineered)	9	7	1
sucrose biosynthesis I (from photosynthesis)	9	7	1
formaldehyde assimilation II (assimilatory RuMP Cycle)	9	7	1
superpathway of L-tyrosine biosynthesis	10	10	1
superpathway of L-phenylalanine biosynthesis	10	10	1
superpathway of enterobacterial common antigen biosynthesis	10	9	1
glycolysis IV	10	8	1
glycolysis V (Pyrococcus)	10	7	1
superpathway of purine nucleotides de novo biosynthesis I	21	21	2
glycolysis III (from glucose)	11	11	1
glycolysis II (from fructose 6-phosphate)	11	11	1
glycolysis VI (from fructose)	11	8	1
superpathway of histidine, purine, and pyrimidine biosynthesis	46	46	4
homolactic fermentation	12	12	1
formaldehyde assimilation III (dihydroxyacetone cycle)	12	11	1
gluconeogenesis III	12	9	1
ethene biosynthesis V (engineered)	25	18	2
superpathway of L-tryptophan biosynthesis	13	13	1
gluconeogenesis I	13	13	1
glycolysis I (from glucose 6-phosphate)	13	13	1
photosynthetic 3-hydroxybutanoate biosynthesis (engineered)	26	19	2
1-butanol autotrophic biosynthesis (engineered)	27	19	2
superpathway of purine nucleotide salvage	14	13	1
Arg/N-end rule pathway (eukaryotic)	14	4	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	17	1
superpathway of hexitol degradation (bacteria)	18	18	1
superpathway of aromatic amino acid biosynthesis	18	18	1
gluconeogenesis II (Methanobacterium thermoautotrophicum)	18	9	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	19	1
superpathway of anaerobic sucrose degradation	19	18	1
superpathway of seleno-compound metabolism	19	6	1
superpathway of N-acetylneuraminate degradation	22	22	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	18	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	25	1
Methanobacterium thermoautotrophicum biosynthetic metabolism	56	23	1
superpathway of chorismate metabolism	59	54	1