Experiment set1IT027 for Cupriavidus basilensis FW507-4G11

R2A with Doxycycline hyclate 0.0001 mg/ml

Group: stress
Media: R2A + Doxycycline hyclate (1e-04 mg/ml)
Culturing: cupriavidus_4G11_ML11, 48 well microplate; Tecan Infinite F200, Aerobic, at 25 (C), shaken=orbital
By: Mark on 3/3/2015
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
Growth plate: 1176 E5,E6

Specific Phenotypes

For 29 genes in this experiment

For stress Doxycycline hyclate in Cupriavidus basilensis FW507-4G11

For stress Doxycycline hyclate across organisms

SEED Subsystems

Subsystem	#Specific
Carotenoids	2
Biflavanoid biosynthesis	1
Conserved gene cluster associated with Met-tRNA formyltransferase	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Lipid A modifications	1
Methionine Biosynthesis	1
Methionine Degradation	1
Phosphate metabolism	1
Phosphonate metabolism	1
Purine conversions	1
Quorum Sensing: Autoinducer-2 Synthesis	1
Tannin biosynthesis	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Aminophosphonate metabolism
• Fatty acid biosynthesis
• Glycerophospholipid metabolism
• Carotenoid biosynthesis - General
• Biosynthesis of terpenoids and steroids
• Biosynthesis of plant hormones
• Biosynthesis of steroids
• Methionine metabolism
• Lysine degradation
• Histidine metabolism
• Tyrosine metabolism
• Benzoxazinone biosynthesis
• Diterpenoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Fatty acid metabolism
• Ubiquinone and menaquinone biosynthesis
• Purine metabolism
• Glycine, serine and threonine metabolism
• Lysine biosynthesis
• Arginine and proline metabolism
• Phenylalanine metabolism
• Tryptophan metabolism
• Selenoamino acid metabolism
• Nucleotide sugars metabolism
• Lipopolysaccharide biosynthesis
• Glycerolipid metabolism
• Ether lipid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• 1- and 2-Methylnaphthalene degradation
• Naphthalene and anthracene degradation
• Benzoate degradation via CoA ligation
• Ethylbenzene degradation
• Butanoate metabolism
• Porphyrin and chlorophyll metabolism
• Limonene and pinene degradation
• Caprolactam degradation
• Phenylpropanoid biosynthesis
• Alkaloid biosynthesis II
• Insect hormone biosynthesis
• Drug metabolism - other enzymes
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of type II polyketide backbone
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from shikimate pathway
• 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
2-aminoethylphosphonate biosynthesis	3	3	3
S-adenosyl-L-methionine biosynthesis	1	1	1
epoxysqualene biosynthesis	3	2	2
leucopelargonidin and leucocyanidin biosynthesis	4	2	2
methylphosphonate biosynthesis	4	2	2
2-aminoethylphosphonate degradation II	2	1	1
diploterol biosynthesis	2	1	1
palmitoleate biosynthesis III (cyanobacteria)	2	1	1
phospholipid remodeling (phosphatidate, yeast)	2	1	1
neurosporene biosynthesis	5	2	2
S-adenosyl-L-methionine salvage II	3	3	1
2-aminoethylphosphonate degradation I	3	2	1
oleate biosynthesis III (cyanobacteria)	3	2	1
L-methionine degradation I (to L-homocysteine)	3	2	1
trans-lycopene biosynthesis I	6	2	2
alkane biosynthesis I	3	1	1
heptadecane biosynthesis	3	1	1
ethene biosynthesis I (plants)	3	1	1
fosfomycin biosynthesis	7	2	2
CDP-diacylglycerol biosynthesis I	4	4	1
gondoate biosynthesis (anaerobic)	4	4	1
CDP-diacylglycerol biosynthesis II	4	4	1
guanosine ribonucleotides de novo biosynthesis	4	4	1
octanoyl-[acyl-carrier protein] biosynthesis (mitochondria, yeast)	12	9	3
inosine 5'-phosphate degradation	4	3	1
S-adenosyl-L-methionine salvage I	4	3	1
fatty acid biosynthesis initiation (mitochondria)	4	2	1
trans-lycopene biosynthesis II (oxygenic phototrophs and green sulfur bacteria)	8	3	2
β-carotene biosynthesis (engineered)	8	2	2
2'-deoxymugineic acid phytosiderophore biosynthesis	4	1	1
palmitoleate biosynthesis I (from (5Z)-dodec-5-enoate)	9	9	2
oleate biosynthesis IV (anaerobic)	14	13	3
palmitate biosynthesis III	29	21	6
cis-vaccenate biosynthesis	5	5	1
fatty acid elongation -- saturated	5	5	1
superpathway of unsaturated fatty acids biosynthesis (E. coli)	20	19	4
superpathway of fatty acid biosynthesis initiation	5	4	1
tetradecanoate biosynthesis (mitochondria)	25	17	5
phosphatidate biosynthesis (yeast)	5	3	1
CDP-diacylglycerol biosynthesis III	5	3	1
superpathway of L-cysteine biosynthesis (mammalian)	5	2	1
leucodelphinidin biosynthesis	5	1	1
palmitate biosynthesis II (type II fatty acid synthase)	31	29	6
superpathway of fatty acids biosynthesis (E. coli)	53	50	10
superpathway of fatty acid biosynthesis I (E. coli)	16	14	3
8-amino-7-oxononanoate biosynthesis I	11	9	2
phosphatidylglycerol biosynthesis II	6	6	1
superpathway of guanosine nucleotides de novo biosynthesis I	6	6	1
phosphatidylglycerol biosynthesis I	6	6	1
superpathway of phospholipid biosynthesis III (E. coli)	12	10	2
stearate biosynthesis II (bacteria and plants)	6	5	1
(5Z)-dodecenoate biosynthesis I	6	5	1
stearate biosynthesis IV	6	4	1
(5Z)-dodecenoate biosynthesis II	6	4	1
petroselinate biosynthesis	6	2	1
superpathway of stearidonate biosynthesis (cyanobacteria)	6	2	1
palmitoyl ethanolamide biosynthesis	6	2	1
rhizocticin A and B biosynthesis	12	2	2
superpathway of fatty acid biosynthesis II (plant)	43	38	7
dehydrophos biosynthesis	13	2	2
even iso-branched-chain fatty acid biosynthesis	34	24	5
odd iso-branched-chain fatty acid biosynthesis	34	24	5
anteiso-branched-chain fatty acid biosynthesis	34	24	5
ureide biosynthesis	7	5	1
L-cysteine biosynthesis VI (reverse transsulfuration)	7	3	1
diacylglycerol and triacylglycerol biosynthesis	7	3	1
hopanoid biosynthesis (bacteria)	14	4	2
stigma estolide biosynthesis	7	2	1
lycopadiene biosynthesis	7	1	1
biotin biosynthesis I	15	13	2
superpathway of guanosine nucleotides de novo biosynthesis II	8	7	1
adenosine nucleotides degradation I	8	5	1
anandamide biosynthesis II	8	2	1
cholesterol biosynthesis III (via desmosterol)	16	2	2
cholesterol biosynthesis II (via 24,25-dihydrolanosterol)	16	2	2
cholesterol biosynthesis I	16	2	2
streptorubin B biosynthesis	34	20	4
superpathway of S-adenosyl-L-methionine biosynthesis	9	7	1
staphyloxanthin biosynthesis	9	1	1
botryococcenes and methylated squalene biosynthesis	9	1	1
4,4'-diapolycopenedioate biosynthesis	9	1	1
FR-900098 and FR-33289 antibiotics biosynthesis	10	1	1
purine nucleotides degradation II (aerobic)	11	8	1
L-methionine salvage cycle III	11	3	1
mycobactin biosynthesis	11	2	1
L-methionine salvage cycle II (plants)	11	2	1
superpathway of carotenoid biosynthesis in plants	22	3	2
purine nucleotides degradation I (plants)	12	7	1
L-methionine salvage cycle I (bacteria and plants)	12	4	1
anandamide biosynthesis I	12	3	1
phosalacine biosynthesis	25	4	2
phosphinothricin tripeptide biosynthesis	25	4	2
superpathway of cardiolipin biosynthesis (bacteria)	13	9	1
superpathway of ergosterol biosynthesis II	26	11	2
superpathway of ergosterol biosynthesis I	26	5	2
superpathway of purine nucleotide salvage	14	12	1
superpathway of phospholipid biosynthesis II (plants)	28	10	2
superpathway of L-methionine salvage and degradation	16	7	1
plasmalogen biosynthesis I (aerobic)	16	3	1
superpathway of purines degradation in plants	18	11	1
superpathway of cholesterol biosynthesis	38	5	2
superpathway of purine nucleotides de novo biosynthesis I	21	21	1
aspartate superpathway	25	23	1
superpathway of purine nucleotides de novo biosynthesis II	26	24	1
superpathway of histidine, purine, and pyrimidine biosynthesis	46	44	1
mycolate biosynthesis	205	26	4
superpathway of mycolate biosynthesis	239	27	4