Purpose: Highlight and tally predicted N-linked glycosylation sites (Nx[ST] patterns, where x can be any amino acid).
During glycosylation, an oligosaccharide chain is attached to asparagine (N) occurring in the tripeptide sequence N-X-S or N-X-T, where X can be any amino acid except Pro. This sequence is called a glycosylation sequon. The N-GlycoSite tool marks and tallies the locations where this pattern occurs.
The likelihood of N-linked glycosylation of a particular site can be influenced by the context in which it is embedded, and could be expanded to a 4-amino acid NX[ST]Z pattern, where the amino acid in the X or Z position can be important determinants of glycosylation efficiency. For example, a proline in position X or Z strongly disfavors N-linked glycosylation.
O-linked glycosylation signals are more difficult predict, but one can estimate their positions using the NetPhos program at Center for Biological Sequence Analysis.
Input can be one amino acid sequence, or an alignment of amino acid sequences, from any organism. If you just want to tally the number of N-glycosylation sites, the protein sequences do not need to be aligned. Standard sequence alignment formats are recognized.
Exclude NP[ST] pattern:
A second position proline (site pattern NP[ST]) is strongly disfavored for glycosylation. Thus the default option excludes these patterns. You may uncheck the box to include them.
Exclude NN[ST][ST] pattern:
Sites in close proximity to each other may be hindered from being glycosylated at the same time. If you check the box, the tool will exclude a first position asparagine but include a second one.
Grouped Sequence Names:
If you are analyzing multiple sequences, you can choose how to group them in the analysis. If you are analyzing a single sequence, or you do not want to group your sequences, just ignore these options. Your sequences can be grouped by the first character in the sequence names, or by a set of characters delimiting the sequence names, or by providing a list of groups.
Each sequence must be on a separate line, and groups are separated by an empty line. The first item ending in ':' in a group will be taken as the group name, but this line is optional. If group names are omitted, names will be assigned as Group-1, Group-2, etc. Sequences that are not present in any group will be named 'Others' and colored gray. This is useful for highlighting some groups of sequences out of a target set.
The following can be pasted in as the "grouped sequence names" for testing with the Sample Input:
Non-recombinants: A1.KE.93.Q23-17 B.FR.HXB2 C.BR.92.92BR025 D.UG.94.94UG1141 O.CM.-.ANT70 CPZ.CM.-.CAM3 Recombinants: 01_AE.CF.90.90CF11697 02_AG.CM.97.97CM-MP807
If your sequences are HIV-1, HIV-2, or SIV, your results can show the position of the glycosylation sites relative to the relevant reference sequence coordinates. For best accuracy of coordinates, we recommend having the reference sequence included in the alignment (as the first sequence).