Experiment set4IT041 for Agrobacterium fabrum C58

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R2A with Sodium m-arsenite 0.8 mM

Group: stress
Media: R2A + Sodium m-arsenite (0.8 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 A6

Specific Phenotypes

For 77 genes in this experiment

For stress Sodium m-arsenite in Agrobacterium fabrum C58

For stress Sodium m-arsenite across organisms

SEED Subsystems

Subsystem #Specific
Glutamine, Glutamate, Aspartate and Asparagine Biosynthesis 3
Heat shock dnaK gene cluster extended 3
Terminal cytochrome C oxidases 3
ABC transporter dipeptide (TC 3.A.1.5.2) 2
Arsenic resistance 2
Biogenesis of cbb3-type cytochrome c oxidases 2
Glycogen metabolism 2
Peptidoglycan Biosynthesis 2
Polyamine Metabolism 2
Proline, 4-hydroxyproline uptake and utilization 2
Thiamin biosynthesis 2
Transport of Manganese 2
Transport of Zinc 2
Bacterial Chemotaxis 1
Bacterial RNA-metabolizing Zn-dependent hydrolases 1
Biotin biosynthesis 1
Cobalt-zinc-cadmium resistance 1
CytR regulation 1
D-Galacturonate and D-Glucuronate Utilization 1
D-Sorbitol(D-Glucitol) and L-Sorbose Utilization 1
Experimental tye 1
Glutamate dehydrogenases 1
Heme and Siroheme Biosynthesis 1
Histidine Degradation 1
L-Arabinose utilization 1
Maltose and Maltodextrin Utilization 1
Methionine Biosynthesis 1
Multidrug Resistance Efflux Pumps 1
Multidrug efflux pump in Campylobacter jejuni (CmeABC operon) 1
NAD and NADP cofactor biosynthesis global 1
NAD regulation 1
One-carbon metabolism by tetrahydropterines 1
Pentose phosphate pathway 1
Peptidyl-prolyl cis-trans isomerase 1
Polyhydroxybutyrate metabolism 1
Proteasome bacterial 1
Proteolysis in bacteria, ATP-dependent 1
Purine conversions 1
Redox-dependent regulation of nucleus processes 1
Respiratory dehydrogenases 1 1
Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization 1
Serine-glyoxylate cycle 1
Sex pheromones in Enterococcus faecalis and other Firmicutes 1
Trehalose Biosynthesis 1
Two cell division clusters relating to chromosome partitioning 1
ZZ gjo need homes 1
cAMP signaling in bacteria 1
n-Phenylalkanoic acid degradation 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
L-asparagine degradation I 1 1 1
long-chain fatty acid activation 1 1 1
L-glutamate degradation I 1 1 1
cis-cyclopropane fatty acid (CFA) biosynthesis 1 1 1
L-proline degradation I 3 3 2
proline to cytochrome bo oxidase electron transfer 2 2 1
glycogen degradation I 8 6 4
trehalose degradation VI (periplasmic) 2 1 1
pseudouridine degradation 2 1 1
γ-linolenate biosynthesis II (animals) 2 1 1
arsenite to oxygen electron transfer 2 1 1
sterculate biosynthesis 2 1 1
linoleate biosynthesis II (animals) 2 1 1
arsenate detoxification III 2 1 1
D-glucarate degradation II 3 3 1
D-galactarate degradation II 3 3 1
pentose phosphate pathway (oxidative branch) I 3 3 1
L-alanine degradation II (to D-lactate) 3 3 1
adenine salvage 3 3 1
glycogen degradation II 6 5 2
L-asparagine degradation III (mammalian) 3 2 1
L-arginine degradation I (arginase pathway) 3 2 1
3-methyl-branched fatty acid α-oxidation 6 3 2
L-lyxonate degradation 3 1 1
ethene biosynthesis IV (engineered) 3 1 1
arsenite to oxygen electron transfer (via azurin) 3 1 1
starch degradation I 3 1 1
alkane biosynthesis II 3 1 1
oleate biosynthesis I (plants) 3 1 1
glycogen biosynthesis I (from ADP-D-Glucose) 4 4 1
heme b biosynthesis II (oxygen-independent) 4 3 1
superpathway of L-aspartate and L-asparagine biosynthesis 4 3 1
phytol degradation 4 3 1
aerobic respiration I (cytochrome c) 4 3 1
aerobic respiration II (cytochrome c) (yeast) 4 2 1
trans-4-hydroxy-L-proline degradation II 4 2 1
arsenic detoxification (bacteria) 4 2 1
starch degradation V 4 2 1
starch degradation III 4 2 1
glycogen biosynthesis II (from UDP-D-Glucose) 4 1 1
wax esters biosynthesis II 4 1 1
long chain fatty acid ester synthesis (engineered) 4 1 1
ethene biosynthesis II (microbes) 4 1 1
phosphatidylcholine acyl editing 4 1 1
sporopollenin precursors biosynthesis 18 4 4
D-glucuronate degradation II 5 5 1
D-galacturonate degradation II 5 5 1
NAD salvage pathway V (PNC V cycle) 5 4 1
starch biosynthesis 10 6 2
D-galactose degradation I (Leloir pathway) 5 3 1
sphingosine and sphingosine-1-phosphate metabolism 10 4 2
cyclohexanol degradation 5 2 1
N-(1-deoxy-D-fructos-1-yl)-L-asparagine degradation 5 2 1
D-xylose degradation III 5 2 1
D-xylose degradation V 5 2 1
octane oxidation 5 2 1
stearate biosynthesis II (bacteria and plants) 6 5 1
fatty acid salvage 6 5 1
stearate biosynthesis IV 6 4 1
superpathway of heme b biosynthesis from uroporphyrinogen-III 6 4 1
D-arabinose degradation III 6 3 1
arsenate detoxification I 6 3 1
6-gingerol analog biosynthesis (engineered) 6 2 1
Fe(II) oxidation 6 2 1
arsenic detoxification (plants) 6 2 1
L-arabinose degradation III 6 2 1
(5R)-carbapenem carboxylate biosynthesis 6 1 1
stearate biosynthesis I (animals) 6 1 1
NAD salvage pathway I (PNC VI cycle) 7 6 1
L-Nδ-acetylornithine biosynthesis 7 5 1
nylon-6 oligomer degradation 7 4 1
4-aminobutanoate degradation V 7 2 1
ceramide degradation by α-oxidation 7 2 1
icosapentaenoate biosynthesis III (8-desaturase, mammals) 7 1 1
icosapentaenoate biosynthesis II (6-desaturase, mammals) 7 1 1
arachidonate biosynthesis III (6-desaturase, mammals) 7 1 1
L-glutamate degradation XI (reductive Stickland reaction) 7 1 1
capsaicin biosynthesis 7 1 1
pentose phosphate pathway 8 8 1
UDP-N-acetylmuramoyl-pentapeptide biosynthesis I (meso-diaminopimelate containing) 8 8 1
L-citrulline biosynthesis 8 7 1
UDP-N-acetylmuramoyl-pentapeptide biosynthesis II (lysine-containing) 8 7 1
sucrose biosynthesis II 8 5 1
ceramide and sphingolipid recycling and degradation (yeast) 16 4 2
glycogen biosynthesis III (from α-maltose 1-phosphate) 8 2 1
2-deoxy-D-ribose degradation II 8 2 1
3,8-divinyl-chlorophyllide a biosynthesis II (anaerobic) 9 2 1
L-glutamate degradation V (via hydroxyglutarate) 10 4 1
suberin monomers biosynthesis 20 3 2
superpathway of fatty acid biosynthesis II (plant) 43 38 4
NAD salvage (plants) 11 6 1
peptidoglycan biosynthesis I (meso-diaminopimelate containing) 12 11 1
superpathway of L-citrulline metabolism 12 9 1
arsenic detoxification (yeast) 12 3 1
folate transformations I 13 8 1
superpathway of NAD biosynthesis in eukaryotes 14 6 1
peptidoglycan biosynthesis III (mycobacteria) 15 11 1
palmitate biosynthesis II (type II fatty acid synthase) 31 29 2
cutin biosynthesis 16 1 1
superpathway of glucose and xylose degradation 17 16 1
peptidoglycan biosynthesis II (staphylococci) 17 12 1
peptidoglycan biosynthesis IV (Enterococcus faecium) 17 12 1
peptidoglycan biosynthesis V (β-lactam resistance) 17 11 1
methylaspartate cycle 19 12 1
superpathway of pentose and pentitol degradation 42 16 2
superpathway of bacteriochlorophyll a biosynthesis 26 6 1
superpathway of fatty acids biosynthesis (E. coli) 53 49 2
palmitate biosynthesis III 29 28 1
superpathway of microbial D-galacturonate and D-glucuronate degradation 31 22 1
oleate β-oxidation 35 27 1
mycolate biosynthesis 205 21 3
superpathway of mycolate biosynthesis 239 22 3