Experiment set1IT045 for Pedobacter sp. GW460-11-11-14-LB5

R2A with Paraquat dichloride 0.003 mg/ml

Group: stress
Media: R2A + Paraquat dichloride (0.003 mg/ml)
Culturing: Pedo557_ML3, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
Growth: about 4.5 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: 1754 C2

Specific Phenotypes

For 48 genes in this experiment

For stress Paraquat dichloride in Pedobacter sp. GW460-11-11-14-LB5

For stress Paraquat dichloride across organisms

SEED Subsystems

Subsystem	#Specific
Predicted carbohydrate hydrolases	2
ATP-dependent RNA helicases, bacterial	1
Chitin and N-acetylglucosamine utilization	1
Conjugative transposon, Bacteroidales	1
Cysteine Biosynthesis	1
Entner-Doudoroff Pathway	1
Glycerol and Glycerol-3-phosphate Uptake and Utilization	1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	1
Glycolate, glyoxylate interconversions	1
Glycolysis and Gluconeogenesis	1
LMPTP YfkJ cluster	1
Methionine Biosynthesis	1
N-Acetyl-Galactosamine and Galactosamine Utilization	1
Phosphate metabolism	1
Photorespiration (oxidative C2 cycle)	1
Polysaccharide deacetylases	1
Thiamin biosynthesis	1
Ton and Tol transport systems	1
Transport of Zinc	1
tRNA processing	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Fatty acid biosynthesis
• Nucleotide sugars metabolism
• Glyoxylate and dicarboxylate metabolism
• Biosynthesis of unsaturated fatty acids
• Glycolysis / Gluconeogenesis
• Ubiquinone and menaquinone biosynthesis
• Pyrimidine metabolism
• Alanine and aspartate metabolism
• Cysteine metabolism
• Arginine and proline metabolism
• Selenoamino acid metabolism
• Cyanoamino acid metabolism
• Other glycan degradation
• Aminosugars metabolism
• Glycosaminoglycan degradation
• Glycerolipid metabolism
• Glycerophospholipid metabolism
• alpha-Linolenic acid metabolism
• Glycosphingolipid biosynthesis - globo series
• Glycosphingolipid biosynthesis - ganglio series
• Benzoate degradation via CoA ligation
• Thiamine metabolism
• Limonene and pinene degradation
• Nitrogen metabolism
• Sulfur metabolism
• Drug metabolism - other enzymes
• Biosynthesis of plant hormones

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
L-asparagine degradation I	1	1	1
cis-cyclopropane fatty acid (CFA) biosynthesis	1	1	1
pyrimidine ribonucleosides salvage I	3	3	2
L-cysteine biosynthesis I	2	2	1
thiamine diphosphate biosynthesis II (Bacillus)	2	2	1
thiamine diphosphate biosynthesis I (E. coli)	2	2	1
sterculate biosynthesis	2	1	1
oleate biosynthesis II (animals and fungi)	2	1	1
proline to cytochrome bo oxidase electron transfer	2	1	1
glycolate and glyoxylate degradation II	2	1	1
palmitoleate biosynthesis III (cyanobacteria)	2	1	1
palmitoleate biosynthesis IV (fungi and animals)	2	1	1
phospholipid remodeling (phosphatidate, yeast)	2	1	1
ephedrine biosynthesis	10	4	4
fatty acid biosynthesis initiation (type II)	3	3	1
L-asparagine degradation III (mammalian)	3	3	1
L-proline degradation I	3	3	1
thiamine diphosphate salvage V	3	2	1
oleate biosynthesis III (cyanobacteria)	3	2	1
chitin degradation II (Vibrio)	6	3	2
glycolate and glyoxylate degradation III	3	1	1
thiamine diphosphate biosynthesis III (Staphylococcus)	3	1	1
thiamine diphosphate biosynthesis IV (eukaryotes)	3	1	1
CDP-diacylglycerol biosynthesis II	4	4	1
CDP-diacylglycerol biosynthesis I	4	4	1
superpathway of L-aspartate and L-asparagine biosynthesis	4	2	1
glycolate and glyoxylate degradation I	4	2	1
superpathway of pyrimidine ribonucleosides salvage	10	9	2
thiamine diphosphate salvage II	5	4	1
superpathway of fatty acid biosynthesis initiation	5	4	1
CDP-diacylglycerol biosynthesis III	5	3	1
seleno-amino acid biosynthesis (plants)	5	3	1
phosphatidate biosynthesis (yeast)	5	3	1
N-(1-deoxy-D-fructos-1-yl)-L-asparagine degradation	5	2	1
peptidoglycan recycling II	10	3	2
phosphatidylglycerol biosynthesis I	6	6	1
phosphatidylglycerol biosynthesis II	6	6	1
cyanophycin metabolism	6	6	1
superpathway of phospholipid biosynthesis III (E. coli)	12	10	2
superpathway of stearidonate biosynthesis (cyanobacteria)	6	2	1
palmitoyl ethanolamide biosynthesis	6	2	1
(5R)-carbapenem carboxylate biosynthesis	6	1	1
peptidoglycan recycling I	14	8	2
thiamine diphosphate salvage IV (yeast)	7	4	1
L-Nδ-acetylornithine biosynthesis	7	4	1
superpathway of thiamine diphosphate biosynthesis III (eukaryotes)	7	3	1
superpathway of glycol metabolism and degradation	7	3	1
chitin degradation III (Serratia)	7	3	1
stigma estolide biosynthesis	7	2	1
diacylglycerol and triacylglycerol biosynthesis	7	2	1
L-citrulline biosynthesis	8	6	1
thiamine diphosphate formation from pyrithiamine and oxythiamine (yeast)	8	3	1
anandamide biosynthesis II	8	2	1
sorgoleone biosynthesis	8	2	1
superpathway of sulfate assimilation and cysteine biosynthesis	9	9	1
photorespiration III	9	5	1
photorespiration I	9	5	1
superpathway of thiamine diphosphate biosynthesis I	10	9	1
photorespiration II	10	5	1
nucleoside and nucleotide degradation (archaea)	10	4	1
superpathway of thiamine diphosphate biosynthesis II	11	9	1
superpathway of L-citrulline metabolism	12	8	1
anandamide biosynthesis I	12	3	1
superpathway of cardiolipin biosynthesis (bacteria)	13	8	1
superpathway of phospholipid biosynthesis II (plants)	28	10	2
superpathway of fatty acid biosynthesis I (E. coli)	16	14	1
plasmalogen biosynthesis I (aerobic)	16	2	1
superpathway of seleno-compound metabolism	19	6	1
streptorubin B biosynthesis	34	20	1
superpathway of fatty acid biosynthesis II (plant)	43	39	1
superpathway of fatty acids biosynthesis (E. coli)	53	48	1
mycolate biosynthesis	205	26	3
superpathway of mycolate biosynthesis	239	27	3