Experiment set5IT064 for Agrobacterium fabrum C58

R2A with Vancomycin Hydrochloride Hydrate 0.009 mM

Group: stress
Media: R2A + Vancomycin Hydrochloride Hydrate (0.009 mM)
Culturing: Agro_ML11, 96 deep-well microplate; 0.8 mL volume, Aerobic, at 28 (C), shaken=700 rpm
By: Hans Carlson and Mitchell Thompson on 22-Jun-21
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: 1B C9

Specific Phenotypes

For 134 genes in this experiment

For stress Vancomycin Hydrochloride Hydrate in Agrobacterium fabrum C58

For stress Vancomycin Hydrochloride Hydrate across organisms

SEED Subsystems

Subsystem	#Specific
Peptidoglycan Biosynthesis	6
Flagellum	4
Phosphate metabolism	4
Widespread colonization island	4
Copper homeostasis: copper tolerance	2
Deoxyribose and Deoxynucleoside Catabolism	2
Flagellar motility	2
Glycerolipid and Glycerophospholipid Metabolism in Bacteria	2
Heat shock dnaK gene cluster extended	2
Hfl operon	2
Histidine Degradation	2
Proteasome bacterial	2
Two cell division clusters relating to chromosome partitioning	2
2-phosphoglycolate salvage	1
Anaerobic respiratory reductases	1
Arginine Biosynthesis extended	1
Arsenic resistance	1
Bacterial Cell Division	1
Bacterial Cytoskeleton	1
Biotin biosynthesis	1
D-Galacturonate and D-Glucuronate Utilization	1
D-ribose utilization	1
Glutamate dehydrogenases	1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis	1
Glycolate, glyoxylate interconversions	1
Mannitol Utilization	1
Oxidative stress	1
Photorespiration (oxidative C2 cycle)	1
Potassium homeostasis	1
Proteolysis in bacteria, ATP-dependent	1
Pyruvate Alanine Serine Interconversions	1
Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization	1
Ribosomal protein S12p Asp methylthiotransferase	1
Sex pheromones in Enterococcus faecalis and other Firmicutes	1
Sodium Hydrogen Antiporter	1
Synechocystis experimental	1
Ton and Tol transport systems	1
Transport of Manganese	1
Transport of Zinc	1
Triacylglycerol metabolism	1
Type IV pilus	1
Xylose utilization	1
ZZ gjo need homes	1
n-Phenylalkanoic acid degradation	1
tRNA processing	1

Metabolic Maps

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

Maps containing gene(s) with specific phenotypes:

• Glycerophospholipid metabolism
• Lipopolysaccharide biosynthesis
• Arginine and proline metabolism
• Peptidoglycan biosynthesis
• Fructose and mannose metabolism
• Lysine degradation
• Histidine metabolism
• Nucleotide sugars metabolism
• Glycerolipid metabolism
• Glycosphingolipid biosynthesis - ganglio series
• Carotenoid biosynthesis - General
• Anthocyanin biosynthesis
• Alkaloid biosynthesis I
• Pentose phosphate pathway
• Ascorbate and aldarate metabolism
• Ubiquinone and menaquinone biosynthesis
• Urea cycle and metabolism of amino groups
• Purine metabolism
• Tyrosine metabolism
• Phenylalanine metabolism
• Aminosugars metabolism
• Glycosaminoglycan degradation
• Glycosphingolipid biosynthesis - globo series
• Benzoate degradation via CoA ligation
• Butanoate metabolism
• Flavonoid biosynthesis
• Insect hormone biosynthesis
• Biosynthesis of unsaturated fatty acids
• Biosynthesis of alkaloids derived from shikimate pathway
• Biosynthesis of alkaloids derived from ornithine, lysine and nicotinic acid
• Fatty acid biosynthesis
• Fatty acid metabolism
• C21-Steroid hormone metabolism
• Puromycin biosynthesis
• Glutamate metabolism
• Glycine, serine and threonine metabolism
• Bisphenol A degradation
• Tryptophan metabolism
• Benzoxazinone biosynthesis
• D-Arginine and D-ornithine metabolism
• D-Alanine metabolism
• N-Glycan biosynthesis
• Other glycan degradation
• O-Glycan biosynthesis
• High-mannose type N-glycan biosynthesis
• O-Mannosyl glycan biosynthesis
• Polyketide sugar unit biosynthesis
• Keratan sulfate biosynthesis
• Glycosylphosphatidylinositol(GPI)-anchor biosynthesis
• Ether lipid metabolism
• Linoleic acid metabolism
• Sphingolipid metabolism
• Glycosphingolipid biosynthesis - lacto and neolacto series
• 1- and 2-Methylnaphthalene degradation
• Tetrachloroethene degradation
• Naphthalene and anthracene degradation
• Glyoxylate and dicarboxylate metabolism
• Ethylbenzene degradation
• Nicotinate and nicotinamide metabolism
• Biotin metabolism
• Retinol metabolism
• Porphyrin and chlorophyll metabolism
• Limonene and pinene degradation
• Diterpenoid biosynthesis
• Zeatin biosynthesis
• Nitrogen metabolism
• Phenylpropanoid biosynthesis
• Flavone and flavonol biosynthesis
• Alkaloid biosynthesis II
• Biosynthesis of type II polyketide backbone
• Biosynthesis of type II polyketide products
• Biosynthesis of terpenoids and steroids
• Biosynthesis of alkaloids derived from histidine and purine
• Biosynthesis of plant hormones
• Phosphatidylinositol signaling system

MetaCyc Pathways

Pathways that contain genes with specific phenotypes:

Pathway	#Steps	#Present	#Specific
phosphatidylcholine biosynthesis V	3	3	3
L-glutamate degradation I	1	1	1
long-chain fatty acid activation	1	1	1
D-alanine degradation	1	1	1
cellulose and hemicellulose degradation (cellulolosome)	3	2	2
(1,4)-β-D-xylan degradation	2	1	1
linoleate biosynthesis II (animals)	2	1	1
phospholipid remodeling (phosphatidate, yeast)	2	1	1
γ-linolenate biosynthesis II (animals)	2	1	1
arsenate detoxification III	2	1	1
palmitoleate biosynthesis III (cyanobacteria)	2	1	1
phosphatidylcholine biosynthesis III	5	2	2
L-alanine degradation II (to D-lactate)	3	3	1
oleate biosynthesis III (cyanobacteria)	3	2	1
2-deoxy-α-D-ribose 1-phosphate degradation	3	2	1
3-methyl-branched fatty acid α-oxidation	6	3	2
chitin degradation II (Vibrio)	6	2	2
oleate biosynthesis I (plants)	3	1	1
alkane biosynthesis II	3	1	1
ethene biosynthesis IV (engineered)	3	1	1
diacylglycerol and triacylglycerol biosynthesis	7	3	2
CDP-diacylglycerol biosynthesis I	4	4	1
CDP-diacylglycerol biosynthesis II	4	4	1
phytol degradation	4	3	1
phospholipid remodeling (phosphatidylethanolamine, yeast)	4	2	1
arsenic detoxification (bacteria)	4	2	1
peptidoglycan maturation (meso-diaminopimelate containing)	12	3	3
long chain fatty acid ester synthesis (engineered)	4	1	1
wax esters biosynthesis II	4	1	1
phosphatidylcholine acyl editing	4	1	1
sporopollenin precursors biosynthesis	18	4	4
L-arginine biosynthesis II (acetyl cycle)	10	10	2
L-histidine degradation II	5	5	1
L-ornithine biosynthesis I	5	5	1
mannitol cycle	5	4	1
CDP-diacylglycerol biosynthesis III	5	4	1
phosphatidate biosynthesis (yeast)	5	3	1
sphingosine and sphingosine-1-phosphate metabolism	10	4	2
octane oxidation	5	2	1
phosphatidylcholine biosynthesis IV	5	1	1
phosphatidate metabolism, as a signaling molecule	5	1	1
peptidoglycan biosynthesis II (staphylococci)	17	12	3
peptidoglycan biosynthesis IV (Enterococcus faecium)	17	12	3
purine ribonucleosides degradation	6	6	1
phosphatidylglycerol biosynthesis II	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
fatty acid salvage	6	5	1
superpathway of pyrimidine deoxyribonucleosides degradation	6	5	1
stearate biosynthesis IV	6	4	1
arsenate detoxification I	6	3	1
palmitoyl ethanolamide biosynthesis	6	2	1
arsenic detoxification (plants)	6	2	1
superpathway of stearidonate biosynthesis (cyanobacteria)	6	2	1
6-gingerol analog biosynthesis (engineered)	6	2	1
superpathway of phosphatidylcholine biosynthesis	12	2	2
stearate biosynthesis I (animals)	6	1	1
superpathway of purine deoxyribonucleosides degradation	7	6	1
superpathway of phospholipid biosynthesis II (plants)	28	12	4
chitin degradation III (Serratia)	7	2	1
ceramide degradation by α-oxidation	7	2	1
4-aminobutanoate degradation V	7	2	1
stigma estolide biosynthesis	7	2	1
icosapentaenoate biosynthesis III (8-desaturase, mammals)	7	1	1
icosapentaenoate biosynthesis II (6-desaturase, mammals)	7	1	1
capsaicin biosynthesis	7	1	1
arachidonate biosynthesis III (6-desaturase, mammals)	7	1	1
L-glutamate degradation XI (reductive Stickland reaction)	7	1	1
ceramide and sphingolipid recycling and degradation (yeast)	16	4	2
2-deoxy-D-ribose degradation II	8	2	1
anandamide biosynthesis II	8	2	1
peptidoglycan biosynthesis V (β-lactam resistance)	17	11	2
L-arginine biosynthesis I (via L-ornithine)	9	9	1
L-arginine biosynthesis III (via N-acetyl-L-citrulline)	9	8	1
photorespiration I	9	6	1
photorespiration III	9	6	1
photorespiration II	10	6	1
L-glutamate degradation V (via hydroxyglutarate)	10	4	1
peptidoglycan recycling II	10	2	1
suberin monomers biosynthesis	20	3	2
superpathway of fatty acid biosynthesis II (plant)	43	38	4
peptidoglycan biosynthesis I (meso-diaminopimelate containing)	12	11	1
anandamide biosynthesis I	12	3	1
arsenic detoxification (yeast)	12	3	1
superpathway of cardiolipin biosynthesis (bacteria)	13	10	1
peptidoglycan recycling I	14	8	1
peptidoglycan biosynthesis III (mycobacteria)	15	11	1
palmitate biosynthesis II (type II fatty acid synthase)	31	29	2
plasmalogen biosynthesis I (aerobic)	16	1	1
cutin biosynthesis	16	1	1
superpathway of arginine and polyamine biosynthesis	17	14	1
type I lipoteichoic acid biosynthesis (S. aureus)	17	5	1
methylaspartate cycle	19	12	1
superpathway of fatty acids biosynthesis (E. coli)	53	49	2
palmitate biosynthesis III	29	28	1
oleate β-oxidation	35	27	1