SBC logo Authors: Amine Heddad, Andrea Krings, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred

Fetching Q9Y2Q0 from www.uniprot.org...

The NucPred score for your sequence is 0.27 (see score help below)

   1  MPTMRRTVSEIRSRAEGYEKTDDVSEKTSLADQEEVRTIFINQPQLTKFC    50
  51  NNHVSTAKYNIITFLPRFLYSQFRRAANSFFLFIALLQQIPDVSPTGRYT   100
 101  TLVPLLFILAVAAIKEIIEDIKRHKADNAVNKKQTQVLRNGAWEIVHWEK   150
 151  VAVGEIVKVTNGEHLPADLISLSSSEPQAMCYIETSNLDGETNLKIRQGL   200
 201  PATSDIKDVDSLMRISGRIECESPNRHLYDFVGNIRLDGHGTVPLGADQI   250
 251  LLRGAQLRNTQWVHGIVVYTGHDTKLMQNSTSPPLKLSNVERITNVQILI   300
 301  LFCILIAMSLVCSVGSAIWNRRHSGKDWYLNLNYGGASNFGLNFLTFIIL   350
 351  FNNLIPISLLVTLEVVKFTQAYFINWDLDMHYEPTDTAAMARTSNLNEEL   400
 401  GQVKYIFSDKTGTLTCNVMQFKKCTIAGVAYGHVPEPEDYGCSPDEWQNS   450
 451  QFGDEKTFSDSSLLENLQNNHPTAPIICEFLTMMAVCHTAVPEREGDKII   500
 501  YQAASPDEGALVRAAKQLNFVFTGRTPDSVIIDSLGQEERYELLNVLEFT   550
 551  SARKRMSVIVRTPSGKLRLYCKGADTVIYDRLAETSKYKEITLKHLEQFA   600
 601  TEGLRTLCFAVAEISESDFQEWRAVYQRASTSVQNRLLKLEESYELIEKN   650
 651  LQLLGATAIEDKLQDQVPETIETLMKADIKIWILTGDKQETAINIGHSCK   700
 701  LLKKNMGMIVINEGSLDGTRETLSRHCTTLGDALRKENDFALIIDGKTLK   750
 751  YALTFGVRQYFLDLALSCKAVICCRVSPLQKSEVVEMVKKQVKVVTLAIG   800
 801  DGANDVSMIQTAHVGVGISGNEGLQAANSSDYSIAQFKYLKNLLMIHGAW   850
 851  NYNRVSKCILYCFYKNIVLYIIEIWFAFVNGFSGQILFERWCIGLYNVMF   900
 901  TAMPPLTLGIFERSCRKENMLKYPELYKTSQNALDFNTKVFWVHCLNGLF   950
 951  HSVILFWFPLKALQYGTAFGNGKTSDYLLLGNFVYTFVVITVCLKAGLET  1000
1001  SYWTWFSHIAIWGSIALWVVFFGIYSSLWPAIPMAPDMSGEAAMLFSSGV  1050
1051  FWMGLLFIPVASLLLDVVYKVIKRTAFKTLVDEVQELEAKSQDPGAVVLG  1100
1101  KSLTERAQLLKNVFKKNHVNLYRSESLQQNLLHGYAFSQDENGIVSQSEV  1150
1151  IRAYDTTKQRPDEW                                      1164

Positively and negatively influencing subsequences are coloured according to the following scale:

(non-nuclear) negative ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||| positive (nuclear)

with NucPred



If you find NucPred useful, please cite this paper:
NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022
The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold Specificity Sensitivity
see above fraction of proteins predicted to be nuclear that actually are nuclear fraction of true nuclear proteins that are predicted (coverage)
0.10 0.45 0.88
0.20 0.52 0.83
0.30 0.57 0.77
0.40 0.63 0.69
0.50 0.70 0.62
0.60 0.71 0.53
0.70 0.81 0.44
0.80 0.84 0.32
0.90 0.88 0.21
1.00 1.00 0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

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