Services
NetPhosYeast - 1.0
Serine and threonine phosphorylation sites in yeast proteins
The NetPhosYeast 1.0 server predicts serine and threonine phosphorylation sites in yeast proteins. This service is closely related to NetPhos and NetPhosK.
Submission
Sequence submission: paste the sequence(s) and/or upload a local file
Restrictions:
At most 2,000 sequences and 200,000 amino acids per submission;
each sequence not longer than 6,000 amino acids.
Confidentiality:
The sequences are kept confidential and will be deleted
after processing.
CITATIONS
For publication of results, please cite:
NetPhosYeast: Prediction of protein phosphorylation sites in yeast.
Christian Ravnsborg Ingrell, Martin Lee Miller, Ole Nørregaard
Jensen and Nikolaj Blom.
Accepted for publication in Bioinformatics, 2007.
Instructions
1. Specify the input sequences
All the input sequences must be in one-letter amino acid code. The allowed alphabet (not case sensitive) is as follows:
All the other symbols will be converted to X before processing. The sequences can be input in the following two ways:
-
Paste a single sequence (just the amino acids) or a number of sequences in
FASTA
format into the upper window of the main server page.
- Select a FASTA file on your local disk, either by typing the file name into the lower window or by browsing the disk.
Both ways can be employed at the same time: all the specified sequences will
be processed. However, there may be not more than 2,000 sequences and
200,000 amino acids
in total in one submission. The sequences
longer than 6,000 amino acids are not allowed.
2. Customize your run
By default the server produces graphical output illustrating the predictions (in GIF). The graphs can be very valuable for locating the "hot" spots in your proteins. The generation of graphics can be disabled by un-checking the button labelled 'Generate graphics'.3. Submit the job
Click on the "Submit" button. The status of your job (either 'queued' or 'running') will be displayed and constantly updated until it terminates and the server output appears in the browser window.At any time during the wait you may enter your e-mail address and simply leave the window. Your job will continue; you will be notified by e-mail when it has terminated. The e-mail message will contain the URL under which the results are stored; they will remain on the server for 24 hours for you to collect them.
Output format
DESCRIPTION
- sequence name, truncated to 20 characters;
- residue position in the sequence;
- residue: serine (S) or threonine (T);
- score, a number between 0 and 1; when the score is
above 0.5 the residue is a predicted phosphorylation site;
- kinase: the current version of NetPhosYeast does not make kinase
specific predictions;
- 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 showing a plot of the score for each serine or threonine residue against the sequence position of that residue.
EXAMPLE OUTPUT
The example below shows the output for the UniProt entry P17536 (TPM1_YEAST), tropomyosin 1.>TPM1_YEAST 199 amino acids # # netphosyeast-1.0a prediction results # # Sequence # x Context Score Kinase Answer # ------------------------------------------------------------------- # TPM1_YEAST 9 S REKLSNLKL 0.390 main . # TPM1_YEAST 17 S LEAESWQEK 0.692 main YES # TPM1_YEAST 45 S NQIKSLTVK 0.460 main . # TPM1_YEAST 47 T IKSLTVKNQ 0.508 main YES # TPM1_YEAST 65 S EAGLSDSKQ 0.829 main YES # TPM1_YEAST 67 S GLSDSKQTE 0.502 main YES # TPM1_YEAST 70 T DSKQTEQDN 0.383 main . # TPM1_YEAST 83 S NQIKSLTVK 0.416 main . # TPM1_YEAST 85 T IKSLTVKNH 0.338 main . # TPM1_YEAST 105 S ELAESKQLS 0.434 main . # TPM1_YEAST 109 S SKQLSEDSH 0.750 main YES # TPM1_YEAST 112 S LSEDSHHLQ 0.578 main YES # TPM1_YEAST 117 S HHLQSNNDN 0.152 main . # TPM1_YEAST 123 S NDNFSKKNQ 0.406 main . # TPM1_YEAST 136 S DLEESDTKL 0.620 main YES # TPM1_YEAST 138 T EESDTKLKE 0.308 main . # TPM1_YEAST 143 T KLKETTEKL 0.269 main . # TPM1_YEAST 144 T LKETTEKLR 0.213 main . # TPM1_YEAST 150 S KLRESDLKA 0.685 main YES # TPM1_YEAST 179 T NEELTVKYE 0.172 main . # TPM1_YEAST 195 S EIAASLENL 0.803 main YES # MDKIREKLSNLKLEAESWQEKYEELKEKNKDLEQENVEKENQIKSLTVKN # 50 QQLEDEIEKLEAGLSDSKQTEQDNVEKENQIKSLTVKNHQLEEEIEKLEA # 100 ELAESKQLSEDSHHLQSNNDNFSKKNQQLEEDLEESDTKLKETTEKLRES # 150 DLKADQLERRVAALEEQREEWERKNEELTVKYEDAKKELDEIAASLENL # 200 %1 ................S.............................T... # 50 %1 ..............S.S................................. # 100 %1 ........S..S.......................S.............S # 150 %1 ............................................S....

References
NetPhosYeast: Prediction of protein phosphorylation sites in yeast.
Christian Ravnsborg Ingrell1, Martin Lee Miller2, Ole Nørregaard Jensen1 and Nikolaj Blom2.
Accepted for publication in Bioinformatics, 2007.
1University of Southern Denmark,
Campusvej 55, DK-5230, Odense M, Denmark
2Center for Biological Sequence Analysis, BioCentrum-DTU,
The Technical University of Denmark, DK-2800 Lyngby, Denmark