Experiment set6IT083 for Cupriavidus basilensis FW507-4G11

R2A with Nickel (II) chloride hexahydrate 0.5 mM

Group: stress
Media: R2A + Nickel (II) chloride hexahydrate (0.5 mM)
Culturing: cupriavidus_4G11_ML11, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
Growth: about 3.1 generations
By: Mark on 5/20/2015
Media components: 0.5 g/L Bacto Peptone, 0.5 g/L casamino acids, 0.5 g/L Yeast Extract, 0.5 g/L D-Glucose, 0.5 g/L Starch, 0.3 g/L Potassium phosphate dibasic, 0.05 g/L Magnesium Sulfate Heptahydrate, 0.3 g/L Sodium pyruvate

Specific Phenotypes

For 36 genes in this experiment

For stress Nickel (II) chloride hexahydrate in Cupriavidus basilensis FW507-4G11

For stress Nickel (II) chloride hexahydrate across organisms

SEED Subsystems

Subsystem	#Specific
Phosphate metabolism	3
Flagellar motility	2
Hydantoin metabolism	2
Thiamin biosynthesis	2
Bacterial Cell Division	1
Bacterial Chemotaxis	1
Bacterial Cytoskeleton	1
Bacterial RNA-metabolizing Zn-dependent hydrolases	1
Biflavanoid biosynthesis	1
Chorismate Synthesis	1
Cobalt-zinc-cadmium resistance	1
Common Pathway For Synthesis of Aromatic Compounds (DAHP synthase to chorismate)	1
Flagellum	1
Folate Biosynthesis	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
High affinity phosphate transporter and control of PHO regulon	1
Histidine Biosynthesis	1
Histidine Degradation	1
Iron acquisition in Vibrio	1
LMPTP YfkJ cluster	1
Oxidative stress	1
Protein degradation	1
Purine conversions	1
Quinate degradation	1
Ribosome biogenesis bacterial	1
Tannin biosynthesis	1
Transport of Iron	1
Two-component regulatory systems in Campylobacter	1
tRNA processing	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Purine metabolism
• Biosynthesis of plant hormones
• Pyrimidine metabolism
• Tryptophan metabolism
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from histidine and purine
• Fatty acid metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Arginine and proline metabolism
• Phenylalanine, tyrosine and tryptophan biosynthesis
• Glutathione metabolism
• Glycerolipid metabolism
• Glycerophospholipid metabolism
• 1- and 2-Methylnaphthalene degradation
• Benzoate degradation via CoA ligation
• Nicotinate and nicotinamide metabolism
• Brassinosteroid biosynthesis
• Caprolactam degradation
• Flavonoid biosynthesis
• Aminoacyl-tRNA biosynthesis
• Biosynthesis of siderophore group nonribosomal peptides
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
leucopelargonidin and leucocyanidin biosynthesis	4	2	2
palmitoleate biosynthesis III (cyanobacteria)	2	1	1
pseudouridine degradation	2	1	1
phospholipid remodeling (phosphatidate, yeast)	2	1	1
adenosine nucleotides degradation II	5	4	2
purine nucleotides degradation II (aerobic)	11	8	4
gallate biosynthesis	3	2	1
oleate biosynthesis III (cyanobacteria)	3	2	1
NAD salvage pathway III (to nicotinamide riboside)	3	2	1
quinate degradation I	3	1	1
quinate degradation II	3	1	1
adenine and adenosine salvage V	3	1	1
purine deoxyribonucleosides degradation II	3	1	1
UTP and CTP dephosphorylation I	7	5	2
CDP-diacylglycerol biosynthesis II	4	4	1
CDP-diacylglycerol biosynthesis I	4	4	1
guanosine nucleotides degradation III	4	3	1
guanosine nucleotides degradation II	4	3	1
inosine 5'-phosphate degradation	4	3	1
adenosine nucleotides degradation I	8	5	2
purine nucleotides degradation I (plants)	12	7	3
adenine and adenosine salvage III	4	2	1
guanosine nucleotides degradation I	4	2	1
purine deoxyribonucleosides degradation I	4	1	1
adipate degradation	5	5	1
chorismate biosynthesis from 3-dehydroquinate	5	5	1
creatinine degradation II	5	3	1
CDP-diacylglycerol biosynthesis III	5	3	1
phosphatidate biosynthesis (yeast)	5	3	1
leucodelphinidin biosynthesis	5	1	1
phosphatidylglycerol biosynthesis I	6	6	1
phosphatidylglycerol biosynthesis II	6	6	1
superpathway of phospholipid biosynthesis III (E. coli)	12	10	2
fatty acid salvage	6	5	1
superpathway of purines degradation in plants	18	11	3
superpathway of guanosine nucleotides degradation (plants)	6	3	1
palmitoyl ethanolamide biosynthesis	6	2	1
superpathway of stearidonate biosynthesis (cyanobacteria)	6	2	1
purine ribonucleosides degradation	6	1	1
chorismate biosynthesis I	7	7	1
ureide biosynthesis	7	5	1
diacylglycerol and triacylglycerol biosynthesis	7	3	1
superpathway of purine deoxyribonucleosides degradation	7	2	1
stigma estolide biosynthesis	7	2	1
anandamide biosynthesis II	8	2	1
tunicamycin biosynthesis	9	1	1
L-histidine biosynthesis	10	10	1
superpathway of L-phenylalanine biosynthesis	10	10	1
superpathway of L-tyrosine biosynthesis	10	10	1
peptidoglycan recycling II	10	7	1
NAD salvage (plants)	11	6	1
oleate β-oxidation	35	29	3
chorismate biosynthesis II (archaea)	12	8	1
anandamide biosynthesis I	12	3	1
superpathway of L-tryptophan biosynthesis	13	13	1
superpathway of cardiolipin biosynthesis (bacteria)	13	9	1
peptidoglycan recycling I	14	10	1
2-methyl-branched fatty acid β-oxidation	14	10	1
superpathway of phospholipid biosynthesis II (plants)	28	10	2
plasmalogen biosynthesis I (aerobic)	16	3	1
superpathway of aromatic amino acid biosynthesis	18	18	1
tRNA charging	21	20	1
superpathway of aromatic compound degradation via 3-oxoadipate	35	25	1
superpathway of aromatic compound degradation via 2-hydroxypentadienoate	42	21	1
superpathway of histidine, purine, and pyrimidine biosynthesis	46	44	1
superpathway of chorismate metabolism	59	45	1