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

NucPred

Fetching P40318 from www.uniprot.org...

The NucPred score for your sequence is 0.20 (see score help below)

   1  MDVDSDVNVSRLRDELHKVANEETDTATFNDDAPSGATCRICRGEATEDN    50
  51  PLFHPCKCRGSIKYMHESCLLEWVASKNIDISKPGADVKCDICHYPIQFK   100
 101  TIYAENMPEKIPFSLLLSKSILTFFEKARLALTIGLAAVLYIIGVPLVWN   150
 151  MFGKLYTMMLDGSSPYPGDFLKSLIYGYDQSATPELTTRAIFYQLLQNHS   200
 201  FTSLQFIMIVILHIALYFQYDMIVREDVFSKMVFHKIGPRLSPKDLKSRL   250
 251  KERFPMMDDRMVEYLAREMRAHDENRQEQGHDRLNMPAAAADNNNNVINP   300
 301  RNDNVPPQDPNDHRNFENLRHVDELDHDEATEEHENNDSDNSLPSGDDSS   350
 351  RILPGSSSDNEEDEEAEGQQQQQQPEEEADYRDHIEPNPIDMWANRRAQN   400
 401  EFDDLIAAQQNAINRPNAPVFIPPPAQNRAGNVDQDEQDFGAAVGVPPAQ   450
 451  ANPDDQGQGPLVINLKLKLLNVIAYFIIAVVFTAIYLAISYLFPTFIGFG   500
 501  LLKIYFGIFKVILRGLCHLYYLSGAHIAYNGLTKLVPKVDVAMSWISDHL   550
 551  IHDIIYLYNGYTENTMKHSIFIRALPALTTYLTSVSIVCASSNLVSRGYG   600
 601  RENGMSNPTRRLIFQILFALKCTFKVFTLFFIELAGFPILAGVMLDFSLF   650
 651  CPILASNSRMLWVPSICAIWPPFSLFVYWTIGTLYMYWFAKYIGMIRKNI   700
 701  IRPGVLFFIRSPEDPNIKILHDSLIHPMSIQLSRLCLSMFIYAIFIVLGF   750
 751  GFHTRIFFPFMLKSNLLSVPEAYKPTSIISWKFNTILLTLYFTKRILESS   800
 801  SYVKPLLERYWKTIFKLCSRKLRLSSFILGKDTPTERGHIVYRNLFYKYI   850
 851  AAKNAEWSNQELFTKPKTLEQAEELFGQVRDVHAYFVPDGVLMRVPSSDI   900
 901  VSRNYVQTMFVPVTKDDKLLKPLDLERIKERNKRAAGEFGYLDEQNTEYD   950
 951  QYYIVYVPPDFRLRYMTLLGLVWLFASILMLGVTFISQALINFVCSFGFL  1000
1001  PVVKLLLGERNKVYVAWKELSDISYSYLNIYYVCVGSVCLSKIAKDILHF  1050
1051  TEGQNTLDEHAVDENEVEEVEHDIPERDINNAPVNNINNVEEGQGIFMAI  1100
1101  FNSIFDSMLVKYNLMVFIAIMIAVIRTMVSWVVLTDGILACYNYLTIRVF  1150
1151  GNSSYTIGNSKWFKYDESLLFVVWIISSMVNFGTGYKSLKLFFRNRNTSK  1200
1201  LNFLKTMALELFKQGFLHMVIYVLPIIILSLVFLRDVSTKQIIDISHGSR  1250
1251  SFTLSLNESFPTWTRMQDIYFGLLIALESFTFFFQATVLFIQWFKSTVQN  1300
1301  VKDEVYTKGRALENLPDES                                 1319

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.)

Go back to the NucPred Home Page.