Experiment set3IT065 for Dyella japonica UNC79MFTsu3.2

LB with Fusidic acid sodium salt 0.4 mg/ml

Group: stress
Media: LB + Fusidic acid sodium salt (0.4 mg/ml)
Culturing: Dyella79_ML3, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
Growth: about 4.9 generations
By: Adam on 17-May-17
Media components: 10 g/L Tryptone, 5 g/L Yeast Extract, 5 g/L Sodium Chloride
Growth plate: 1772 D3

Specific Phenotypes

For 29 genes in this experiment

For stress Fusidic acid sodium salt in Dyella japonica UNC79MFTsu3.2

For stress Fusidic acid sodium salt across organisms

SEED Subsystems

Subsystem	#Specific
Phosphate metabolism	3
Biogenesis of cytochrome c oxidases	2
High affinity phosphate transporter and control of PHO regulon	2
Arginine Deiminase Pathway	1
Arginine and Ornithine Degradation	1
Branched-Chain Amino Acid Biosynthesis	1
Heat shock dnaK gene cluster extended	1
Hfl operon	1
Leucine Degradation and HMG-CoA Metabolism	1
Multidrug Resistance Efflux Pumps	1
Oxidative stress	1
Polyamine Metabolism	1
Propionate-CoA to Succinate Module	1
Purine conversions	1
TCA Cycle	1
Universal GTPases	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Biosynthesis of alkaloids derived from shikimate pathway
• Citrate cycle (TCA cycle)
• Fatty acid biosynthesis
• Ubiquinone and menaquinone biosynthesis
• Oxidative phosphorylation
• Purine metabolism
• Valine, leucine and isoleucine degradation
• Valine, leucine and isoleucine biosynthesis
• Lysine degradation
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• Lipopolysaccharide biosynthesis
• Peptidoglycan biosynthesis
• Naphthalene and anthracene degradation
• Glyoxylate and dicarboxylate metabolism
• Reductive carboxylate cycle (CO2 fixation)
• Biotin metabolism
• Folate biosynthesis
• Porphyrin and chlorophyll metabolism
• Carotenoid biosynthesis - General
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of phenylpropanoids
• 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
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
polyphosphate metabolism	2	2	1
glyoxylate cycle	6	6	2
octanoyl-[acyl-carrier protein] biosynthesis (mitochondria, yeast)	12	12	3
gondoate biosynthesis (anaerobic)	4	4	1
nitrogen remobilization from senescing leaves	8	7	2
partial TCA cycle (obligate autotrophs)	8	7	2
palmitate biosynthesis III	29	28	7
tetradecanoate biosynthesis (mitochondria)	25	23	6
palmitate biosynthesis II (type II fatty acid synthase)	31	29	7
TCA cycle IV (2-oxoglutarate decarboxylase)	9	8	2
TCA cycle II (plants and fungi)	9	8	2
palmitoleate biosynthesis I (from (5Z)-dodec-5-enoate)	9	8	2
TCA cycle V (2-oxoglutarate synthase)	9	8	2
TCA cycle VI (Helicobacter)	9	6	2
TCA cycle VII (acetate-producers)	9	6	2
oleate biosynthesis IV (anaerobic)	14	13	3
superpathway of fatty acids biosynthesis (E. coli)	53	48	11
2-methylcitrate cycle I	5	5	1
fatty acid elongation -- saturated	5	5	1
TCA cycle III (animals)	10	9	2
superpathway of unsaturated fatty acids biosynthesis (E. coli)	20	17	4
TCA cycle I (prokaryotic)	10	8	2
cis-vaccenate biosynthesis	5	4	1
8-amino-7-oxononanoate biosynthesis IV	5	4	1
superpathway of fatty acid biosynthesis II (plant)	43	38	8
8-amino-7-oxononanoate biosynthesis I	11	10	2
reductive TCA cycle I	11	6	2
anteiso-branched-chain fatty acid biosynthesis	34	30	6
odd iso-branched-chain fatty acid biosynthesis	34	30	6
even iso-branched-chain fatty acid biosynthesis	34	30	6
superpathway of glyoxylate bypass and TCA	12	10	2
stearate biosynthesis II (bacteria and plants)	6	5	1
2-methylcitrate cycle II	6	5	1
(5Z)-dodecenoate biosynthesis I	6	5	1
(5Z)-dodecenoate biosynthesis II	6	4	1
stearate biosynthesis IV	6	4	1
reductive TCA cycle II	12	6	2
petroselinate biosynthesis	6	2	1
streptorubin B biosynthesis	34	20	5
superpathway of glyoxylate cycle and fatty acid degradation	14	11	2
biotin biosynthesis I	15	14	2
superpathway of fatty acid biosynthesis I (E. coli)	16	14	2
mixed acid fermentation	16	11	2
2-allylmalonyl-CoA biosynthesis	8	2	1
methylaspartate cycle	19	11	2
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	19	2
ethene biosynthesis V (engineered)	25	17	2
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	23	2
mycolate biosynthesis	205	25	5
superpathway of mycolate biosynthesis	239	26	5