Output format



DESCRIPTION

For each input sequence the length and the name of the sequence are stated followed by a table with the prediction results. There is a table row for each lysine residue in the sequence; the columns are:

  • sequence name, truncated to 20 characters;

  • residue position in the sequence;

  • score, a number between -1 and 1; when the score is above 0 the residue is a predicted glycation site;

  • the word "glycate";

  • answer: either the word "YES" or a dot ("."), reflecting the score.

After the table, the whole sequence is printed alongside a summary of the predicted glycation sites and their positions.

Finally, if the 'Generate graphics' button has been checked, the server displays a figure in GIF showhing a plot of the score for each lysine residue against the sequence position of that residue.


EXAMPLE OUTPUT

The example below shows the output for the UniProt entry P19111 (PPBI_BOVIN), an intestinal alkaline phosphatase precursor whose activity is known to be inhibited by glycation ( McCarthy et al. 1998). At this point (Feb 2006) the glycation sites have not been determined experimentally and published.

>PPBI_BOVIN	533 amino acids
#
# netglycate-1.0 prediction results
#
# Sequence                      #    Score            Answer
# -----------------------------------------------------------
# PPBI_BOVIN                   43   -0.917   glycate     . 
# PPBI_BOVIN                   44   -0.883   glycate     . 
# PPBI_BOVIN                   53   -0.653   glycate     . 
# PPBI_BOVIN                   75    0.567   glycate    YES
# PPBI_BOVIN                   81   -0.808   glycate     . 
# PPBI_BOVIN                  100    0.817   glycate    YES
# PPBI_BOVIN                  123   -0.587   glycate     . 
# PPBI_BOVIN                  141    0.803   glycate    YES
# PPBI_BOVIN                  156   -0.711   glycate     . 
# PPBI_BOVIN                  157   -0.864   glycate     . 
# PPBI_BOVIN                  160   -0.885   glycate     . 
# PPBI_BOVIN                  224   -0.837   glycate     . 
# PPBI_BOVIN                  247    0.491   glycate    YES
# PPBI_BOVIN                  249   -0.704   glycate     . 
# PPBI_BOVIN                  259   -0.879   glycate     . 
# PPBI_BOVIN                  294   -0.825   glycate     . 
# PPBI_BOVIN                  303    0.972   glycate    YES
# PPBI_BOVIN                  342   -0.845   glycate     . 
# PPBI_BOVIN                  359   -0.950   glycate     . 
# PPBI_BOVIN                  400    0.721   glycate    YES
# PPBI_BOVIN                  405   -0.521   glycate     . 
#
    MQGACVLLLLGLHLQLSLGLVPVEEEDPAFWNRQAAQALDVAKKLQPIQT   #     50
    AAKNVILFLGDGMGVPTVTATRILKGQMNGKLGPETPLAMDQFPYVALSK   #    100
    TYNVDRQVPDSAGTATAYLCGVKGNYRTIGVSAAARYNQCKTTRGNEVTS   #    150
    VMNRAKKAGKSVGVVTTTRVQHASPAGAYAHTVNRNWYSDADLPADAQMN   #    200
    GCQDIAAQLVNNMDIDVILGGGRKYMFPVGTPDPEYPDDASVNGVRKRKQ   #    250
    NLVQAWQAKHQGAQYVWNRTALLQAADDSSVTHLMGLFEPADMKYNVQQD   #    300
    HTKDPTLQEMTEVALRVVSRNPRGFYLFVEGGRIDHGHHDDKAYMALTEA   #    350
    GMFDNAIAKANELTSELDTLILVTADHSHVFSFGGYTLRGTSIFGLAPSK   #    400
    ALDSKSYTSILYGNGPGYALGGGSRPDVNDSTSEDPSYQQQAAVPQASET   #    450
    HGGEDVAVFARGPQAHLVHGVEEETFVAHIMAFAGCVEPYTDCNLPAPTT   #    500
    ATSIPDAAHLAASPPPLALLAGAMLLLLAPTLY                    #    550
%1  ..................................................   #     50
%1  ........................G........................G   #    100
%1  ........................................G.........   #    150
%1  ..................................................   #    200
%1  ..............................................G...   #    250
%1  ..................................................   #    300
%1  ..G...............................................   #    350
%1  .................................................G   #    400
%1  ..................................................   #    450
%1  ..................................................   #    500
%1  .................................







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