Experiment set2IT004 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 68 genes in this experiment

For carbon source L-ascorbate in Agrobacterium fabrum C58

For carbon source L-ascorbate across organisms

SEED Subsystems

Subsystem #Specific
Photorespiration (oxidative C2 cycle) 5
Glycolate, glyoxylate interconversions 4
D-gluconate and ketogluconates metabolism 3
Molybdenum cofactor biosynthesis 3
Peptidoglycan Biosynthesis 3
Folate Biosynthesis 2
4-Hydroxyphenylacetic acid catabolic pathway 1
Allantoin Utilization 1
Aromatic amino acid degradation 1
Bacterial RNA-metabolizing Zn-dependent hydrolases 1
Chorismate: Intermediate for synthesis of PAPA antibiotics, PABA, anthranilate, 3-hydroxyanthranilate and more. 1
Conenzyme B12 related Hypothetical: Clusters with cobST 1
D-Sorbitol(D-Glucitol) and L-Sorbose Utilization 1
D-galactarate, D-glucarate and D-glycerate catabolism 1
D-ribose utilization 1
DNA-binding regulatory proteins, strays 1
Deoxyribose and Deoxynucleoside Catabolism 1
Entner-Doudoroff Pathway 1
Glycine and Serine Utilization 1
Glycogen metabolism 1
Heat shock dnaK gene cluster extended 1
Isobutyryl-CoA to Propionyl-CoA Module 1
Nudix proteins (nucleoside triphosphate hydrolases) 1
Oxidative stress 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
Thioredoxin-disulfide reductase 1
Trehalose Biosynthesis 1
Tryptophan synthesis 1
Type IV pilus 1
Valine degradation 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
D-gluconate degradation 1 1 1
L-glutamine degradation I 1 1 1
glycolate and glyoxylate degradation II 2 2 1
4-aminobenzoate biosynthesis I 2 2 1
L-glutamate biosynthesis I 2 2 1
glycolate and glyoxylate degradation I 4 2 2
ketogluconate metabolism 8 4 3
ammonia assimilation cycle III 3 3 1
sorbitol biosynthesis II 3 3 1
dTMP de novo biosynthesis (mitochondrial) 3 3 1
pentose phosphate pathway (oxidative branch) I 3 3 1
L-serine biosynthesis I 3 3 1
tetrahydrofolate biosynthesis I 3 3 1
NAD salvage pathway III (to nicotinamide riboside) 3 2 1
L-cysteine biosynthesis IX (Trichomonas vaginalis) 3 2 1
glycolate and glyoxylate degradation III 3 1 1
superpathway of glycol metabolism and degradation 7 4 2
L-asparagine biosynthesis III (tRNA-dependent) 4 4 1
superpathway of L-serine and glycine biosynthesis I 4 4 1
glutaminyl-tRNAgln biosynthesis via transamidation 4 4 1
glycogen biosynthesis I (from ADP-D-Glucose) 4 4 1
tetrahydromonapterin biosynthesis 4 2 1
D-galactarate degradation I 4 2 1
D-glucarate degradation I 4 2 1
glycogen biosynthesis II (from UDP-D-Glucose) 4 1 1
L-serine biosynthesis II 4 1 1
photorespiration III 9 6 2
photorespiration I 9 6 2
superpathway of tetrahydrofolate biosynthesis 10 8 2
NAD salvage pathway II (PNC IV cycle) 5 4 1
photorespiration II 10 6 2
starch biosynthesis 10 6 2
D-xylose degradation VI 5 3 1
superpathway of D-glucarate and D-galactarate degradation 5 3 1
tRNA-uridine 2-thiolation (thermophilic bacteria) 5 2 1
L-ascorbate degradation IV 5 1 1
superpathway of tetrahydrofolate biosynthesis and salvage 12 10 2
D-arabinose degradation IV 6 4 1
L-arabinose degradation V 6 2 1
NAD salvage pathway I (PNC VI cycle) 7 6 1
L-glutamate and L-glutamine biosynthesis 7 4 1
L-rhamnose degradation III 7 4 1
D-xylose degradation IV 7 3 1
pentose phosphate pathway 8 8 1
L-citrulline biosynthesis 8 7 1
L-valine degradation I 8 5 1
L-fucose degradation III 8 5 1
4-hydroxyphenylacetate degradation 8 4 1
L-arabinose degradation IV 8 3 1
glycogen biosynthesis III (from α-maltose 1-phosphate) 8 2 1
peptidoglycan biosynthesis II (staphylococci) 17 12 2
peptidoglycan biosynthesis IV (Enterococcus faecium) 17 12 2
peptidoglycan biosynthesis V (β-lactam resistance) 17 11 2
superpathway of sulfate assimilation and cysteine biosynthesis 9 9 1
folate transformations III (E. coli) 9 8 1
chloramphenicol biosynthesis 9 1 1
folate transformations II (plants) 11 8 1
NAD salvage (plants) 11 6 1
superpathway of candicidin biosynthesis 11 4 1
peptidoglycan biosynthesis I (meso-diaminopimelate containing) 12 11 1
superpathway of L-citrulline metabolism 12 9 1
peptidoglycan maturation (meso-diaminopimelate containing) 12 3 1
formaldehyde assimilation I (serine pathway) 13 5 1
peptidoglycan biosynthesis III (mycobacteria) 15 11 1
superpathway of glucose and xylose degradation 17 16 1
superpathway of chorismate metabolism 59 38 2
superpathway of microbial D-galacturonate and D-glucuronate degradation 31 22 1
superpathway of pentose and pentitol degradation 42 16 1