Experiment set2IT033 for Pedobacter sp. GW460-11-11-14-LB5

R2A with Vancomycin Hydrochloride Hydrate 0.06 mg/ml

Group: stress
Media: R2A + Vancomycin Hydrochloride Hydrate (0.06 mg/ml)
Culturing: Pedo557_ML3, 24-well transparent microplate; Multitron, Aerobic, at 30 (C), shaken=700 rpm
Growth: about 4.7 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: 1760 A2

Specific Phenotypes

For 103 genes in this experiment

For stress Vancomycin Hydrochloride Hydrate in Pedobacter sp. GW460-11-11-14-LB5

For stress Vancomycin Hydrochloride Hydrate across organisms

SEED Subsystems

Subsystem	#Specific
Multidrug Resistance Efflux Pumps	3
Conjugative transposon, Bacteroidales	2
Lactose and Galactose Uptake and Utilization	2
Maltose and Maltodextrin Utilization	2
Multidrug Resistance, Tripartite Systems Found in Gram Negative Bacteria	2
Predicted carbohydrate hydrolases	2
Ton and Tol transport systems	2
Alginate metabolism	1
Biogenesis of c-type cytochromes	1
Biotin biosynthesis	1
Cobalt-zinc-cadmium resistance	1
Cysteine Biosynthesis	1
ECF class transporters	1
Folate Biosynthesis	1
Galactosylceramide and Sulfatide metabolism	1
Glycerol and Glycerol-3-phosphate Uptake and Utilization	1
Iron acquisition in Vibrio	1
L-fucose utilization	1
L-fucose utilization temp	1
Lactose utilization	1
Mannose Metabolism	1
Methionine Biosynthesis	1
Multidrug efflux pump in Campylobacter jejuni (CmeABC operon)	1
Periplasmic disulfide interchange	1
Polysaccharide deacetylases	1
Pyruvate metabolism I: anaplerotic reactions, PEP	1
Serine-glyoxylate cycle	1
Transcription factors bacterial	1
Two cell division clusters relating to chromosome partitioning	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Galactose metabolism
• Nucleotide sugars metabolism
• Biosynthesis of plant hormones
• Glycolysis / Gluconeogenesis
• Other glycan degradation
• Citrate cycle (TCA cycle)
• Fructose and mannose metabolism
• Fatty acid biosynthesis
• Ubiquinone and menaquinone biosynthesis
• Cysteine metabolism
• Selenoamino acid metabolism
• Starch and sucrose metabolism
• N-Glycan biosynthesis
• Streptomycin biosynthesis
• Glycosaminoglycan degradation
• Peptidoglycan biosynthesis
• alpha-Linolenic acid metabolism
• Sphingolipid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• Pyruvate metabolism
• Benzoate degradation via CoA ligation
• Carbon fixation in photosynthetic organisms
• Limonene and pinene degradation
• Zeatin biosynthesis
• Sulfur metabolism
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of phenylpropanoids
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from shikimate pathway
• 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

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
lactose degradation III	1	1	1
xyloglucan degradation II (exoglucanase)	8	5	5
L-cysteine biosynthesis I	2	2	1
di-trans,poly-cis-undecaprenyl phosphate biosynthesis	2	2	1
trehalose degradation II (cytosolic)	2	1	1
trehalose degradation I (low osmolarity)	2	1	1
β-alanine degradation III	2	1	1
D-galactose detoxification	3	3	1
trehalose degradation IV	3	3	1
GDP-α-D-glucose biosynthesis	3	2	1
trehalose degradation V	3	2	1
stachyose degradation	7	6	2
sucrose degradation III (sucrose invertase)	4	3	1
D-galactose degradation I (Leloir pathway)	5	5	1
polyisoprenoid biosynthesis (E. coli)	5	5	1
uracil degradation III	5	3	1
glucose and glucose-1-phosphate degradation	5	3	1
seleno-amino acid biosynthesis (plants)	5	3	1
protein O-mannosylation III (mammals, core M3)	5	1	1
cis-zeatin biosynthesis	5	1	1
protein O-mannosylation II (mammals, core M1 and core M2)	5	1	1
glycogen degradation II	6	3	1
UDP-N-acetyl-D-glucosamine biosynthesis II	6	3	1
UDP-N-acetyl-D-galactosamine biosynthesis II	7	4	1
lipoprotein posttranslational modification (Gram-negative bacteria)	7	2	1
glycogen degradation I	8	3	1
sucrose biosynthesis II	8	3	1
protein O-mannosylation I (yeast)	8	1	1
superpathway of sulfate assimilation and cysteine biosynthesis	9	9	1
1,3-propanediol biosynthesis (engineered)	9	5	1
chitin biosynthesis	9	4	1
glycolysis III (from glucose)	11	10	1
protein N-glycosylation (Haloferax volcanii)	11	1	1
homolactic fermentation	12	10	1
gluconeogenesis I	13	12	1
3-hydroxypropanoate cycle	13	7	1
glyoxylate assimilation	13	4	1
superpathway of glyoxylate cycle and fatty acid degradation	14	10	1
C4 photosynthetic carbon assimilation cycle, PEPCK type	14	7	1
Bifidobacterium shunt	15	12	1
type I lipoteichoic acid biosynthesis (S. aureus)	17	5	1
heterolactic fermentation	18	13	1
3-hydroxypropanoate/4-hydroxybutanate cycle	18	10	1
superpathway of the 3-hydroxypropanoate cycle	18	7	1
superpathway of seleno-compound metabolism	19	6	1
protein N-glycosylation initial phase (eukaryotic)	19	1	1