Enzyme simulator: glycan entry

Control panel
Iterations: 1 +  Columns: 1 +  Style: CFG | UOXF  
GlcNAc limit: 5 +  Cell height: 1 +

GlycoForm
Enter initial O-glycan
VT α
Properties
 
Monoisotopic mass:221.09 g/mol
Average mass:221.208 g/mol
 
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Pathway
Structure identifier: VT
IUPAC condensed name: GalNAc
Linear Code: ANa;
GlycoCT condensed: show/hide


Instructions
Enter a glycan into the text box as either an IUPAC name, or a structure identifier based on single-letter codes for monosaccharides, according to the table below. Click the Draw button to draw the structure; (optionally) click Select to choose a knockout set of enzymes to act on this structure; click React to submit the currect structure to O-Glycologue as a substrate of the enzymes of O-linked glycosylation. Click Predict to run the enzyme simulator in reverse, to discover a minimal set of enzymes required to produce the current glycan. The Pathway button generates a random walk through the predicted network in the biosynthetic direction.

(Example) Enter Galb1-4GlcNAcb1-6[Galb1-4GlcNAcb1-3Galb1-3]GalNAc

or

[L4Y6][L4Y3L3]VT

The anomericity of monosaccharides is implicit, based on the enzymes of O-glycosylation: L and Y are β-linked while f, S and V are assumed to be α-linked. This can be overridden by placing ‘a’ or ‘b’ after the sugar symbol, thus ‘La3’ would draw an α1,3-linked galactose.

The size of networks produced in simulations can be limited by decreasing the maximum number of GlcNAc residues per glycan using the Control panel. The default value is set to 4.

LetterSymbolIUPAC SymbolDefinition
fFucL-Fucose
KKdn2-Keto-3-deoxy-D-glycero-D-galacto-nononic acid
LGalD-Galactose
NNeu5GcN-Glycolylneuraminic acid
SNeu5AcN-Acetylneuraminic acid (sialic acid)
VGalNAcN-Acetyl-D-galactosamine
YGlcNAcN-Acetyl-D-glucosamine
s-HSO3Sulfate
a,bα, βAnomeric linkage type


Site last updated 2019-01-18