NetGlycate 1.0 Output format

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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