Experiment set4IT064 for Agrobacterium fabrum C58

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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: 1 C9

Specific Phenotypes

For 144 genes in this experiment

For stress Vancomycin Hydrochloride Hydrate in Agrobacterium fabrum C58

For stress Vancomycin Hydrochloride Hydrate across organisms

SEED Subsystems

Subsystem #Specific
Flagellum 5
Peptidoglycan Biosynthesis 5
Widespread colonization island 5
D-ribose utilization 3
Deoxyribose and Deoxynucleoside Catabolism 3
Histidine Degradation 3
Phosphate metabolism 3
Choline and Betaine Uptake and Betaine Biosynthesis 2
Copper homeostasis: copper tolerance 2
Flagellar motility 2
Hfl operon 2
Proteasome bacterial 2
Two cell division clusters relating to chromosome partitioning 2
2-phosphoglycolate salvage 1
Acetoin, butanediol metabolism 1
Anaerobic respiratory reductases 1
Arginine Biosynthesis extended 1
Arsenic resistance 1
Bacterial Cell Division 1
Bacterial Cytoskeleton 1
Bacterial RNA-metabolizing Zn-dependent hydrolases 1
Biotin biosynthesis 1
Branched-Chain Amino Acid Biosynthesis 1
Conserved gene cluster associated with Met-tRNA formyltransferase 1
D-Galacturonate and D-Glucuronate Utilization 1
DNA repair, bacterial MutL-MutS system 1
Glutamate dehydrogenases 1
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis 1
Glycerolipid and Glycerophospholipid Metabolism in Bacteria 1
Glycolate, glyoxylate interconversions 1
Heat shock dnaK gene cluster extended 1
Mannitol Utilization 1
Multidrug Resistance Efflux Pumps 1
Multidrug efflux pump in Campylobacter jejuni (CmeABC operon) 1
Oxidative stress 1
Photorespiration (oxidative C2 cycle) 1
Propionate-CoA to Succinate Module 1
Propionyl-CoA to Succinyl-CoA Module 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
Ribosome biogenesis bacterial 1
Serine-glyoxylate cycle 1
Sex pheromones in Enterococcus faecalis and other Firmicutes 1
Sodium Hydrogen Antiporter 1
Synechocystis experimental 1
TCA Cycle 1
Thioredoxin-disulfide reductase 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:

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
D-alanine degradation 1 1 1
long-chain fatty acid activation 1 1 1
cellulose and hemicellulose degradation (cellulolosome) 3 2 2
pyruvate fermentation to (R)-acetoin II 2 1 1
γ-linolenate biosynthesis II (animals) 2 1 1
linoleate biosynthesis II (animals) 2 1 1
arsenate detoxification III 2 1 1
(1,4)-β-D-xylan degradation 2 1 1
L-histidine degradation II 5 5 2
phosphatidylcholine biosynthesis III 5 2 2
glyoxylate cycle 6 6 2
urea degradation I 3 3 1
L-alanine degradation II (to D-lactate) 3 3 1
pyruvate fermentation to (R)-acetoin I 3 3 1
propanoyl CoA degradation I 3 3 1
pyruvate fermentation to (S)-acetoin 3 2 1
3-methyl-branched fatty acid α-oxidation 6 3 2
chitin degradation II (Vibrio) 6 2 2
alkane biosynthesis II 3 1 1
ethene biosynthesis IV (engineered) 3 1 1
oleate biosynthesis I (plants) 3 1 1
starch degradation I 3 1 1
conversion of succinate to propanoate 3 1 1
L-histidine degradation I 4 4 1
biotin-carboxyl carrier protein assembly 4 4 1
L-valine biosynthesis 4 4 1
partial TCA cycle (obligate autotrophs) 8 7 2
2-oxobutanoate degradation I 4 3 1
phytol degradation 4 3 1
nitrogen remobilization from senescing leaves 8 5 2
phospholipid remodeling (phosphatidylethanolamine, yeast) 4 2 1
arsenic detoxification (bacteria) 4 2 1
peptidoglycan maturation (meso-diaminopimelate containing) 12 3 3
phosphatidylcholine acyl editing 4 1 1
long chain fatty acid ester synthesis (engineered) 4 1 1
wax esters biosynthesis II 4 1 1
TCA cycle VII (acetate-producers) 9 8 2
TCA cycle V (2-oxoglutarate synthase) 9 8 2
TCA cycle IV (2-oxoglutarate decarboxylase) 9 8 2
TCA cycle II (plants and fungi) 9 8 2
TCA cycle VI (Helicobacter) 9 6 2
sporopollenin precursors biosynthesis 18 4 4
methylaspartate cycle 19 12 4
TCA cycle I (prokaryotic) 10 10 2
L-arginine biosynthesis II (acetyl cycle) 10 10 2
L-ornithine biosynthesis I 5 5 1
TCA cycle III (animals) 10 9 2
mannitol cycle 5 4 1
superpathway of (R,R)-butanediol biosynthesis 5 4 1
pyruvate fermentation to isobutanol (engineered) 5 4 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
reductive TCA cycle I 11 7 2
peptidoglycan biosynthesis IV (Enterococcus faecium) 17 12 3
peptidoglycan biosynthesis II (staphylococci) 17 12 3
superpathway of glyoxylate bypass and TCA 12 12 2
stearate biosynthesis II (bacteria and plants) 6 5 1
fatty acid salvage 6 5 1
L-histidine degradation III 6 4 1
stearate biosynthesis IV 6 4 1
reductive TCA cycle II 12 6 2
superpathway of allantoin degradation in yeast 6 3 1
L-isoleucine biosynthesis IV 6 3 1
arsenate detoxification I 6 3 1
arsenic detoxification (plants) 6 2 1
6-gingerol analog biosynthesis (engineered) 6 2 1
superpathway of 2,3-butanediol biosynthesis 6 2 1
superpathway of phosphatidylcholine biosynthesis 12 2 2
stearate biosynthesis I (animals) 6 1 1
3-hydroxypropanoate cycle 13 8 2
L-isoleucine biosynthesis I (from threonine) 7 7 1
superpathway of glyoxylate cycle and fatty acid degradation 14 12 2
L-isoleucine biosynthesis III 7 4 1
pyruvate fermentation to propanoate I 7 4 1
diacylglycerol and triacylglycerol biosynthesis 7 3 1
chitin degradation III (Serratia) 7 2 1
ceramide degradation by α-oxidation 7 2 1
4-aminobutanoate degradation V 7 2 1
arachidonate biosynthesis III (6-desaturase, mammals) 7 1 1
icosapentaenoate biosynthesis II (6-desaturase, mammals) 7 1 1
icosapentaenoate biosynthesis III (8-desaturase, mammals) 7 1 1
L-glutamate degradation XI (reductive Stickland reaction) 7 1 1
capsaicin biosynthesis 7 1 1
L-histidine degradation VI 8 7 1
glycogen degradation I 8 6 1
L-isoleucine biosynthesis II 8 5 1
mixed acid fermentation 16 9 2
ceramide and sphingolipid recycling and degradation (yeast) 16 4 2
2-deoxy-D-ribose degradation II 8 2 1
superpathway of branched chain amino acid biosynthesis 17 17 2
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 III 9 6 1
photorespiration I 9 6 1
3-hydroxypropanoate/4-hydroxybutanate cycle 18 11 2
superpathway of the 3-hydroxypropanoate cycle 18 8 2
anaerobic energy metabolism (invertebrates, mitochondrial) 10 8 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
superpathway of cytosolic glycolysis (plants), pyruvate dehydrogenase and TCA cycle 22 20 2
L-glutamate degradation VIII (to propanoate) 11 4 1
peptidoglycan biosynthesis I (meso-diaminopimelate containing) 12 11 1
arsenic detoxification (yeast) 12 3 1
ethene biosynthesis V (engineered) 25 16 2
superpathway of L-isoleucine biosynthesis I 13 13 1
superpathway of glycolysis, pyruvate dehydrogenase, TCA, and glyoxylate bypass 26 22 2
glyoxylate assimilation 13 5 1
(S)-lactate fermentation to propanoate, acetate and hydrogen 13 5 1
peptidoglycan recycling I 14 8 1
superpathway of phospholipid biosynthesis II (plants) 28 12 2
crotonyl-CoA/ethylmalonyl-CoA/hydroxybutyryl-CoA cycle (engineered) 14 3 1
peptidoglycan biosynthesis III (mycobacteria) 15 11 1
palmitate biosynthesis II (type II fatty acid synthase) 31 29 2
superpathway of L-methionine salvage and degradation 16 8 1
cutin biosynthesis 16 1 1
superpathway of arginine and polyamine biosynthesis 17 14 1
superpathway of anaerobic energy metabolism (invertebrates) 17 13 1
type I lipoteichoic acid biosynthesis (S. aureus) 17 5 1
superpathway of L-threonine metabolism 18 11 1
superpathway of fatty acids biosynthesis (E. coli) 53 49 2
palmitate biosynthesis III 29 28 1
oleate β-oxidation 35 27 1