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

NucPred

Fetching Q10094 from www.uniprot.org...

The NucPred score for your sequence is 0.21 (see score help below)

   1  MSVKIHIDRGGTFTDAIATFADESRPPIVIKLLSEDPSNYKDASIEAVRR    50
  51  ILEIVQGKSIPRTEKLDTSCINHLRCGTTVATNALLERKGERCAFITTKG   100
 101  FKDGLLIGNQSRPNIFELGIRRPEVLYSKVIEVDERVTLEDYVEDPMKVK   150
 151  TTIDGSDPSLVVGRSGEVVRIMKKVDCDALRKDLQALYDEGFTSIAVCLA   200
 201  HSFTFPDHELLVGKIAEEVGFSNISLSTKLMPMIKYVPRATSATADAYLS   250
 251  PVVRRYLAGFQSGFLHGLKTKDNSKGVRCEFMQSDGGLVDVNKFSGLHAI   300
 301  LSGPAGGVVGFALTSYDEDVKIPVIGFDMGGTSTDVSRYGGSYEHVFETT   350
 351  TAGVTIQSPQLDINTVAAGGGSRLFWKNGLFVVGPESAGAHPGPVCYRKG   400
 401  GYLTVTDANLLLGRLLPESFPKIFGPNEDESLDVESTRKEFEKLTAEINS   450
 451  GLEKERQMTADEVAFGFIKIANETMARPIRALTEAKGHDISIHRLTSFGG   500
 501  AGGQHCAAIAKSLGITQVLVHKYSSILSAYGMALADVVSEVQEPSSFTLD   550
 551  DSNTESIKKRFDSLKEEAKANLEEQGFTESQISYELFLNCRYQGTDSTLM   600
 601  ISKPLESWDFKQSFFDKHKQEFGFIFENKDIIIDDIRIRASGKSFQSKEP   650
 651  SVDAQLKELKFEPVQKSLATCVKDIYFEGGRVPSEVYSLDNLPVGTIVNG   700
 701  PSLIVDKTQTIVVPPKAVARILHTHVVIDISHGNEYTANDSLAKASTIDP   750
 751  IYLSVFGSRFMAVAEQMGRALQKTSVSTNVKERLDYSCALFDAKGNLVAN   800
 801  APHMPVHLGSMSTCVRTQAKIHEGKLKPGDVLVTNHPSYGGTHLPDITTI   850
 851  TPHFEGDEIMFYVAARAHHADIGGILPGSMPSSSKELSEEGATIKSEKLV   900
 901  VDGVFQEERMIDLLYNEPAKVEGGSGSRCLRDNLNDLKAQVSANQKGINL   950
 951  ITSLIKEYGKNSVLRYMKAIQENAESAVRQLLLGVRERFLGEDLYAEDHM  1000
1001  DDGSKICLRITIDEENGDAIFDFTGTTEEIYGNINAPEAVTYSAIIYCLR  1050
1051  VLISENIPLNQGCLLPIKVIIPDNCFLKPSETAAVVGGNVLTSQRITDTI  1100
1101  LKAFQACAASQGDTNNLTFGIGGKDPETGEVKPGFGYYETICGGSGAIDG  1150
1151  LDGTSGVHTHMTNTRITDLEVLERRYPVILRKFIIRENSGGAGKYKGGDG  1200
1201  VIRDIEFRIPVTLSILSERRAYHPYGMKGGKDAECGKNIWIRKDILPSGE  1250
1251  QRVRQINVGGKNTCHMQAGDHIVIMTPGGGGYGPPSERVDTVKKANGVQH  1300
1301  FRANGTISQLQEIQHTN                                   1317

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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