Experiment set6IT084 for Cupriavidus basilensis FW507-4G11

R2A with Cobalt chloride hexahydrate 0.3 mM

Group: stress
Media: R2A + Cobalt chloride hexahydrate (0.3 mM)
Culturing: cupriavidus_4G11_ML11, 24 deep-well microplate; Multitron, Aerobic, at 30 (C), shaken=750 rpm
Growth: about 2.7 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 22 genes in this experiment

For stress Cobalt chloride hexahydrate in Cupriavidus basilensis FW507-4G11

For stress Cobalt chloride hexahydrate across organisms

SEED Subsystems

Subsystem	#Specific
Iron acquisition in Vibrio	2
Transport of Iron	2
Bacterial Chemotaxis	1
Bacterial RNA-metabolizing Zn-dependent hydrolases	1
Branched-Chain Amino Acid Biosynthesis	1
Carotenoids	1
Flagellar motility	1
Folate Biosynthesis	1
Glycine and Serine Utilization	1
HMG CoA Synthesis	1
Leucine Biosynthesis	1
Leucine Degradation and HMG-CoA Metabolism	1
Lysine Biosynthesis DAP Pathway	1
Oxidative stress	1
Pyridoxin (Vitamin B6) Biosynthesis	1
Pyruvate metabolism II: acetyl-CoA, acetogenesis from pyruvate	1
Redox-dependent regulation of nucleus processes	1
Serine Biosynthesis	1
Ton and Tol transport systems	1
Two-component regulatory systems in Campylobacter	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Biosynthesis of terpenoids and steroids
• Biosynthesis of plant hormones
• Fatty acid metabolism
• Valine, leucine and isoleucine biosynthesis
• Lysine biosynthesis
• Lipopolysaccharide biosynthesis
• Caprolactam degradation
• Biosynthesis of steroids
• Glycine, serine and threonine metabolism
• Valine, leucine and isoleucine degradation
• Geraniol degradation
• Glutathione metabolism
• Nucleotide sugars metabolism
• Sphingolipid metabolism
• 1- and 2-Methylnaphthalene degradation
• 1,4-Dichlorobenzene degradation
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• C5-Branched dibasic acid metabolism
• Nicotinate and nicotinamide metabolism
• Brassinosteroid biosynthesis
• Carotenoid biosynthesis - General
• 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
long-chain fatty acid activation	1	1	1
epoxysqualene biosynthesis	3	2	2
linoleate biosynthesis II (animals)	2	1	1
γ-linolenate biosynthesis II (animals)	2	1	1
neurosporene biosynthesis	5	2	2
L-leucine biosynthesis	6	6	2
L-serine biosynthesis I	3	3	1
fatty acid salvage	6	5	2
L-cysteine biosynthesis IX (Trichomonas vaginalis)	3	2	1
3-methyl-branched fatty acid α-oxidation	6	3	2
trans-lycopene biosynthesis I	6	2	2
alkane biosynthesis II	3	1	1
oleate biosynthesis I (plants)	3	1	1
3-methylbutanol biosynthesis (engineered)	7	6	2
superpathway of L-serine and glycine biosynthesis I	4	4	1
phytol degradation	4	3	1
trans-lycopene biosynthesis II (oxygenic phototrophs and green sulfur bacteria)	8	3	2
β-carotene biosynthesis (engineered)	8	2	2
phosphatidylcholine acyl editing	4	1	1
wax esters biosynthesis II	4	1	1
long chain fatty acid ester synthesis (engineered)	4	1	1
sporopollenin precursors biosynthesis	18	8	4
adipate degradation	5	5	1
octane oxidation	5	4	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
stearate biosynthesis II (bacteria and plants)	6	5	1
stearate biosynthesis IV	6	4	1
6-gingerol analog biosynthesis (engineered)	6	3	1
stearate biosynthesis I (animals)	6	2	1
L-glutamate degradation XI (reductive Stickland reaction)	7	4	1
ceramide degradation by α-oxidation	7	2	1
icosapentaenoate biosynthesis II (6-desaturase, mammals)	7	1	1
lycopadiene biosynthesis	7	1	1
capsaicin biosynthesis	7	1	1
arachidonate biosynthesis III (6-desaturase, mammals)	7	1	1
icosapentaenoate biosynthesis III (8-desaturase, mammals)	7	1	1
L-isoleucine biosynthesis II	8	6	1
2-deoxy-D-ribose degradation II	8	5	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
cholesterol biosynthesis I	16	2	2
cholesterol biosynthesis III (via desmosterol)	16	2	2
cholesterol biosynthesis II (via 24,25-dihydrolanosterol)	16	2	2
superpathway of branched chain amino acid biosynthesis	17	17	2
oleate β-oxidation	35	29	4
L-lysine biosynthesis I	9	9	1
superpathway of sulfate assimilation and cysteine biosynthesis	9	9	1
staphyloxanthin biosynthesis	9	1	1
botryococcenes and methylated squalene biosynthesis	9	1	1
4,4'-diapolycopenedioate biosynthesis	9	1	1
L-glutamate degradation V (via hydroxyglutarate)	10	7	1
suberin monomers biosynthesis	20	5	2
superpathway of fatty acid biosynthesis II (plant)	43	38	4
superpathway of carotenoid biosynthesis in plants	22	3	2
superpathway of ergosterol biosynthesis II	26	11	2
2,5-xylenol and 3,5-xylenol degradation	13	5	1
superpathway of ergosterol biosynthesis I	26	5	2
2-methyl-branched fatty acid β-oxidation	14	10	1
hopanoid biosynthesis (bacteria)	14	4	1
palmitate biosynthesis II (type II fatty acid synthase)	31	29	2
cutin biosynthesis	16	3	1
superpathway of L-lysine, L-threonine and L-methionine biosynthesis I	18	16	1
superpathway of cholesterol biosynthesis	38	5	2
aspartate superpathway	25	23	1
superpathway of fatty acids biosynthesis (E. coli)	53	50	2
palmitate biosynthesis III	29	21	1