Experiment set1IT025 for Pedobacter sp. GW460-11-11-14-LB5

R2A with Sisomicin sulfate salt 0.008 mg/ml

Group: stress
Media: R2A + Sisomicin sulfate salt (0.008 mg/ml)
Culturing: Pedo557_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: 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: 1755 B2

Specific Phenotypes

For 25 genes in this experiment

For stress Sisomicin sulfate salt in Pedobacter sp. GW460-11-11-14-LB5

For stress Sisomicin sulfate salt across organisms

SEED Subsystems

Subsystem	#Specific
Glycerol and Glycerol-3-phosphate Uptake and Utilization	2
LMPTP YfkJ cluster	2
tRNA processing	2
Chorismate: Intermediate for synthesis of PAPA antibiotics, PABA, anthranilate, 3-hydroxyanthranilate and more.	1
Copper homeostasis: copper tolerance	1
D-Tagatose and Galactitol Utilization	1
Folate Biosynthesis	1
Glycolysis and Gluconeogenesis	1
Glycolysis and Gluconeogenesis, including Archaeal enzymes	1
Heat shock dnaK gene cluster extended	1
Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria	1
N-Acetyl-Galactosamine and Galactosamine Utilization	1
Ribosome biogenesis bacterial	1
Ton and Tol transport systems	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Ubiquinone and menaquinone biosynthesis
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of phenylpropanoids
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of plant hormones
• Glycolysis / Gluconeogenesis
• Pentose phosphate pathway
• Fructose and mannose metabolism
• Galactose metabolism
• Ascorbate and aldarate metabolism
• Fatty acid biosynthesis
• Valine, leucine and isoleucine degradation
• Valine, leucine and isoleucine biosynthesis
• Histidine metabolism
• Tyrosine metabolism
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• Nucleotide sugars metabolism
• Glycosaminoglycan degradation
• alpha-Linolenic acid metabolism
• Naphthalene and anthracene degradation
• Benzoate degradation via CoA ligation
• Pantothenate and CoA biosynthesis
• Folate biosynthesis
• Porphyrin and chlorophyll metabolism
• Limonene and pinene degradation
• Carotenoid biosynthesis - General
• Phenylpropanoid biosynthesis
• Flavonoid biosynthesis
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Insect hormone biosynthesis
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Biosynthesis of alkaloids derived from terpenoid and polyketide

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
4-aminobenzoate biosynthesis I	2	2	1
sedoheptulose bisphosphate bypass	2	2	1
4-aminobenzoate biosynthesis II	2	1	1
L-alanine biosynthesis I	2	1	1
L-isoleucine biosynthesis V	3	2	1
L-isoleucine degradation II	3	2	1
L-valine degradation II	3	2	1
L-leucine degradation III	3	2	1
L-isoleucine degradation III (oxidative Stickland reaction)	3	1	1
L-valine degradation III (oxidative Stickland reaction)	3	1	1
L-leucine degradation V (oxidative Stickland reaction)	3	1	1
L-valine biosynthesis	4	4	1
superpathway of L-alanine biosynthesis	4	2	1
D-galactosamine and N-acetyl-D-galactosamine degradation	4	2	1
chondroitin sulfate degradation I (bacterial)	8	2	2
L-leucine degradation IV (reductive Stickland reaction)	5	2	1
galactitol degradation	5	2	1
N-acetyl-D-galactosamine degradation	5	2	1
lactose degradation I	5	1	1
superpathway of branched chain amino acid biosynthesis	17	17	3
L-leucine biosynthesis	6	6	1
L-isoleucine biosynthesis IV	6	4	1
L-leucine degradation I	6	4	1
L-isoleucine degradation I	6	4	1
L-isoleucine biosynthesis I (from threonine)	7	7	1
L-isoleucine biosynthesis III	7	4	1
L-isoleucine biosynthesis II	8	6	1
L-valine degradation I	8	3	1
formaldehyde assimilation II (assimilatory RuMP Cycle)	9	7	1
superpathway of hexitol degradation (bacteria)	18	12	2
1,3-propanediol biosynthesis (engineered)	9	5	1
glycolysis IV	10	8	1
superpathway of tetrahydrofolate biosynthesis	10	8	1
glycolysis II (from fructose 6-phosphate)	11	10	1
glycolysis III (from glucose)	11	10	1
superpathway of candicidin biosynthesis	11	4	1
homolactic fermentation	12	10	1
superpathway of tetrahydrofolate biosynthesis and salvage	12	10	1
superpathway of L-isoleucine biosynthesis I	13	13	1
glycolysis I (from glucose 6-phosphate)	13	11	1
superpathway of glycolysis and the Entner-Doudoroff pathway	17	14	1
superpathway of L-threonine metabolism	18	12	1
superpathway of anaerobic sucrose degradation	19	14	1
hexitol fermentation to lactate, formate, ethanol and acetate	19	13	1
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle	22	18	1
superpathway of N-acetylneuraminate degradation	22	16	1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass	26	21	1
anteiso-branched-chain fatty acid biosynthesis	34	24	1
odd iso-branched-chain fatty acid biosynthesis	34	24	1
even iso-branched-chain fatty acid biosynthesis	34	24	1
superpathway of chorismate metabolism	59	35	1