Experiment set2IT005 for Agrobacterium fabrum C58

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L-ascorbate carbon source

Group: carbon source
Media: MOPS minimal media_noCarbon + L-ascorbate (10 mM)
Culturing: Agro_ML11, 24-well transparent microplate; Multitron, Aerobic, at 28 (C), shaken=200 rpm
By: Mitchell Thompson on 10/20/20
Media components: 40 mM 3-(N-morpholino)propanesulfonic acid, 4 mM Tricine, 1.32 mM Potassium phosphate dibasic, 0.01 mM Iron (II) sulfate heptahydrate, 9.5 mM Ammonium chloride, 0.276 mM Aluminum potassium sulfate dodecahydrate, 0.0005 mM Calcium chloride, 0.525 mM Magnesium chloride hexahydrate, 50 mM Sodium Chloride, 3e-09 M Ammonium heptamolybdate tetrahydrate, 4e-07 M Boric Acid, 3e-08 M Cobalt chloride hexahydrate, 1e-08 M Copper (II) sulfate pentahydrate, 8e-08 M Manganese (II) chloride tetrahydrate, 1e-08 M Zinc sulfate heptahydrate

Specific Phenotypes

For 77 genes in this experiment

For carbon source L-ascorbate in Agrobacterium fabrum C58

For carbon source L-ascorbate across organisms

SEED Subsystems

Subsystem #Specific
Molybdenum cofactor biosynthesis 5
Photorespiration (oxidative C2 cycle) 4
D-gluconate and ketogluconates metabolism 3
Glycolate, glyoxylate interconversions 3
Isobutyryl-CoA to Propionyl-CoA Module 2
Peptidoglycan Biosynthesis 2
Valine degradation 2
4-Hydroxyphenylacetic acid catabolic pathway 1
Allantoin Utilization 1
Aromatic amino acid degradation 1
Bacterial RNA-metabolizing Zn-dependent hydrolases 1
Conenzyme B12 related Hypothetical: Clusters with cobST 1
D-galactarate, D-glucarate and D-glycerate catabolism 1
Deoxyribose and Deoxynucleoside Catabolism 1
Entner-Doudoroff Pathway 1
Flagellar motility 1
Flagellum 1
Formate hydrogenase 1
Glutathione-dependent pathway of formaldehyde detoxification 1
Glycine and Serine Utilization 1
Glycogen metabolism 1
Heat shock dnaK gene cluster extended 1
Homogentisate pathway of aromatic compound degradation 1
Lipid A modifications 1
Nudix proteins (nucleoside triphosphate hydrolases) 1
Orphan regulatory proteins 1
Pentose phosphate pathway 1
Pyridoxin (Vitamin B6) Biosynthesis 1
Ribitol, Xylitol, Arabitol, Mannitol and Sorbitol utilization 1
Serine Biosynthesis 1
Sex pheromones in Enterococcus faecalis and other Firmicutes 1
Sialic Acid Metabolism 1
Synechocystis experimental 1
Transcription initiation, bacterial sigma factors 1
Trehalose Biosynthesis 1
Triacylglycerol metabolism 1
Type IV pilus 1
ZZ gjo need homes 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-idonate degradation 3 3 3
bis(guanylyl molybdenum cofactor) biosynthesis 2 2 2
D-gluconate degradation 1 1 1
guanylyl molybdenum cofactor biosynthesis 1 1 1
acetaldehyde biosynthesis I 1 1 1
bis(guanylyl tungstenpterin) cofactor biosynthesis 1 1 1
formate oxidation to CO2 1 1 1
glycolate and glyoxylate degradation II 2 2 1
glycolate and glyoxylate degradation I 4 2 2
ethanol degradation I 2 1 1
pyruvate fermentation to ethanol II 2 1 1
ketogluconate metabolism 8 4 3
benzoyl-CoA biosynthesis 3 3 1
pentose phosphate pathway (oxidative branch) I 3 3 1
sorbitol biosynthesis II 3 3 1
L-serine biosynthesis I 3 3 1
formaldehyde oxidation II (glutathione-dependent) 3 3 1
ethanol degradation II 3 3 1
2-deoxy-D-ribose degradation I 3 2 1
L-cysteine biosynthesis IX (Trichomonas vaginalis) 3 2 1
L-valine degradation II 3 2 1
L-leucine degradation III 3 2 1
2-deoxy-α-D-ribose 1-phosphate degradation 3 2 1
NAD salvage pathway III (to nicotinamide riboside) 3 2 1
L-isoleucine degradation II 3 2 1
glycolate and glyoxylate degradation III 3 1 1
pyruvate fermentation to ethanol III 3 1 1
pyruvate fermentation to ethanol I 3 1 1
L-methionine degradation III 3 1 1
superpathway of glycol metabolism and degradation 7 4 2
superpathway of L-serine and glycine biosynthesis I 4 4 1
glycogen biosynthesis I (from ADP-D-Glucose) 4 4 1
phytol degradation 4 3 1
L-valine degradation I 8 5 2
D-glucarate degradation I 4 2 1
L-phenylalanine degradation III 4 2 1
phospholipid remodeling (phosphatidylethanolamine, yeast) 4 2 1
D-galactarate degradation I 4 2 1
L-tyrosine degradation III 4 2 1
salidroside biosynthesis 4 1 1
L-serine biosynthesis II 4 1 1
oxalate degradation VI 4 1 1
glycogen biosynthesis II (from UDP-D-Glucose) 4 1 1
2-methyl-branched fatty acid β-oxidation 14 9 3
adipate degradation 5 5 1
pyruvate fermentation to isobutanol (engineered) 5 4 1
adipate biosynthesis 5 4 1
NAD salvage pathway II (PNC IV cycle) 5 4 1
starch biosynthesis 10 6 2
D-xylose degradation VI 5 3 1
acrylate degradation I 5 3 1
fatty acid β-oxidation II (plant peroxisome) 5 3 1
protein S-nitrosylation and denitrosylation 5 3 1
propanoyl-CoA degradation II 5 3 1
superpathway of D-glucarate and D-galactarate degradation 5 3 1
tRNA-uridine 2-thiolation (thermophilic bacteria) 5 2 1
fatty acid β-oxidation IV (unsaturated, even number) 5 2 1
L-ascorbate degradation IV 5 1 1
phenylethanol biosynthesis 5 1 1
(S)-propane-1,2-diol degradation 5 1 1
ethanolamine utilization 5 1 1
acetylene degradation (anaerobic) 5 1 1
benzoate biosynthesis III (CoA-dependent, non-β-oxidative) 5 1 1
oxalate degradation III 5 1 1
(8E,10E)-dodeca-8,10-dienol biosynthesis 11 6 2
superpathway of pyrimidine deoxyribonucleosides degradation 6 5 1
D-arabinose degradation IV 6 4 1
methyl ketone biosynthesis (engineered) 6 3 1
β-alanine biosynthesis II 6 3 1
superpathway of C1 compounds oxidation to CO2 12 5 2
L-arabinose degradation V 6 2 1
noradrenaline and adrenaline degradation 13 4 2
NAD salvage pathway I (PNC VI cycle) 7 6 1
superpathway of purine deoxyribonucleosides degradation 7 6 1
3-methylbutanol biosynthesis (engineered) 7 6 1
fatty acid β-oxidation I (generic) 7 4 1
L-rhamnose degradation III 7 4 1
serotonin degradation 7 3 1
benzoyl-CoA degradation I (aerobic) 7 3 1
fatty acid β-oxidation VI (mammalian peroxisome) 7 3 1
pentose phosphate pathway 8 8 1
L-fucose degradation III 8 5 1
4-hydroxyphenylacetate degradation 8 4 1
butanol and isobutanol biosynthesis (engineered) 8 3 1
glycogen biosynthesis III (from α-maltose 1-phosphate) 8 2 1
peptidoglycan biosynthesis IV (Enterococcus faecium) 17 12 2
peptidoglycan biosynthesis II (staphylococci) 17 12 2
peptidoglycan biosynthesis V (β-lactam resistance) 17 11 2
superpathway of sulfate assimilation and cysteine biosynthesis 9 9 1
photorespiration III 9 6 1
photorespiration I 9 6 1
valproate β-oxidation 9 5 1
phenylacetate degradation I (aerobic) 9 3 1
benzoate biosynthesis I (CoA-dependent, β-oxidative) 9 3 1
superpathway of fermentation (Chlamydomonas reinhardtii) 9 3 1
superpathway of coenzyme A biosynthesis II (plants) 10 7 1
photorespiration II 10 6 1
3-phenylpropanoate degradation 10 4 1
NAD salvage (plants) 11 6 1
superpathway of phenylethylamine degradation 11 3 1
Spodoptera littoralis pheromone biosynthesis 22 4 2
oleate β-oxidation 35 27 3
peptidoglycan biosynthesis I (meso-diaminopimelate containing) 12 11 1
peptidoglycan maturation (meso-diaminopimelate containing) 12 3 1
superpathway of Clostridium acetobutylicum solventogenic fermentation 13 5 1
formaldehyde assimilation I (serine pathway) 13 5 1
(4Z,7Z,10Z,13Z,16Z)-docosapentaenoate biosynthesis (6-desaturase) 13 2 1
L-tryptophan degradation V (side chain pathway) 13 1 1
superpathway of glyoxylate cycle and fatty acid degradation 14 12 1
docosahexaenoate biosynthesis III (6-desaturase, mammals) 14 2 1
peptidoglycan biosynthesis III (mycobacteria) 15 11 1
purine nucleobases degradation I (anaerobic) 15 5 1
mixed acid fermentation 16 9 1
superpathway of glucose and xylose degradation 17 16 1
superpathway of Clostridium acetobutylicum acidogenic and solventogenic fermentation 17 5 1
heterolactic fermentation 18 12 1
superpathway of anaerobic sucrose degradation 19 13 1
hexitol fermentation to lactate, formate, ethanol and acetate 19 10 1
superpathway of N-acetylneuraminate degradation 22 12 1
purine nucleobases degradation II (anaerobic) 24 14 1
platensimycin biosynthesis 26 6 1
superpathway of microbial D-galacturonate and D-glucuronate degradation 31 22 1