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

NucPred

Fetching P36583 from www.uniprot.org...

The NucPred score for your sequence is 0.99 (see score help below)

   1  MDMIDEAITEVVRKIERERSVIHGALSMKRLTQNQTVHQQLHSNIEESKK    50
  51  SIIYLEERLEKLKLRKNGVRKSNSEKPSVGIEKNPSFSTTKSAKSFSSTS   100
 101  SNIDSNLDLLNYDTPLTISKISFLLQQLEFKLSVEEQYRKGIEKMAKLYE   150
 151  REHDRRSIAEAEKKYVESAQKITLLKQALKRYHDLHIEIDEEDVPSTESR   200
 201  GNLNARRPQSGLLKITVGSLRNVTHSAGISKQTEMIVAIRAEDLERARTR   250
 251  PSRTDRFNETFEIDLEKTNEVEIVVYEKKNEKLLLPVGLLWIRLSDLVEK   300
 301  QRRKKVEQEVSDKGWVSADKMINQRLSIFLPSALNNISKPESTDRPNTAS   350
 351  GNQSVSAWFSLEPMGQINLTMNFTKHNTRKRPMDAGLGRQGAIRQRKESV   400
 401  HEVYGHKFLQHQFYQIMRCALCGEFLKNAAGMQCIDCHYTCHKKCYPKVV   450
 451  TKCISKSSDSASSEYEKINHRIPHHFESHTNIGANWCCHCGYILPLGRKT   500
 501  ARKCTECGITAHAQCVHLVPDFCGMSMEMANRVISEIRTTKIYKAQQHKQ   550
 551  KSSHHKHHHHKKSKSSSSKHKENDKASVSITTTTTPSITPADPVPTSPKP   600
 601  LAIEPVKRKPVHAGNLEVTSVSDNKLGATVQVVEQKVDDKADALTKPPSL   650
 651  DAVKEPIPVPSVETSVVAQDLTHKAKRIGLEDFTFLSVLGKGNFGKVMLA   700
 701  ELKSEKQLYAIKVLKKEFILENDEVESTKSEKRVFLVANRERHPFLVNLH   750
 751  SCFQTETRIYFVMDFVSGGDLMLHIQQEQFSRRRAQFYAAEVCLALKYFH   800
 801  DNGIIYRDLKLDNILLSPDGHVKVADYGLCKEDMWHDNTTATFCGTPEFM   850
 851  APEILLEQQYTRSVDWWAFGVLIYQMLLGQSPFRGEDEEEIFDAILSDEP   900
 901  LYPIHMPRDSVSILQQLLTRDPKKRLGSGPNDAEDVMTHPFFSNINWDDI   950
 951  YHKRTQPPYIPSLNSPTDTKYFDEEFTRELPVLTPVNSILTKEMQQHFEG  1000
1001  FSYSCEDDKPSTTDNA                                    1016

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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