HCV Database
HCV sequence database
 



To our users Please note that the HCV database site is no longer funded. We try to keep the database updated and the tools running, but unfortunately, we cannot guarantee we can provide help for using this site. Data won't be manually curated either.


N-GlycoSite

Purpose: This tool highlights and tallies predicted N-linked glycosylation sites (Nx[ST] patterns, where x can be any amino acid).

Input
Paste your input here
or upload your file

Option
Exclude NP[ST] pattern
Group sequences Do not group
Summarize results by grouped sequences according to:
first character(s) in sequence names
the column in field of sequence names delimited by
paste or upload grouped sequence names (see example below)

Details:
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:
Input can be one amino acid sequence, or an alignment of amino acid sequences. 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.

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.

Below is an example of a list of grouped sequence names to show how the sequences in the Sample Input could be grouped. 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, the names Group-1, Group-2, etc., will be generated for reporting. 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 with the Sample Input for testing the Grouped Sequence Names option:

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

References:

  1. Zhang M et al., Glycobiology. 14(12):1229-46 (2004) -- please cite this reference if you use our tool in a publication.
  2. Marshall RD, Biochem Soc Symp. 40:17-26 (1974)
  3. Kasturi et al., Biochem J. 323 (Pt 2):415-9 (1997)
  4. Mellquist JL et al., Biochemistry. 37(19):6833-7 (1998)



Questions or comments? Contact us at hcv-info@lanl.gov