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

NucPred

Fetching P07248 from www.uniprot.org...

The NucPred score for your sequence is 0.94 (see score help below)

   1  MANVEKPNDCSGFPVVDLNSCFSNGFNNEKQEIEMETDDSPILLMSSSAS    50
  51  RENSNTFSVIQRTPDGKIITTNNNMNSKINKQLDKLPENLRLNGRTPSGK   100
 101  LRSFVCEVCTRAFARQEHLKRHYRSHTNEKPYPCGLCNRCFTRRDLLIRH   150
 151  AQKIHSGNLGETISHTKKVSRTITKARKNSASSVKFQTPTYGTPDNGNFL   200
 201  NRTTANTRRKASPEANVKRKYLKKLTRRASFSAQSASSYALPDQSSLEQH   250
 251  PKDRVKFSTPELVPLDLKNPELDSSFDLNMNLDLNLNLDSNFNIALNRSD   300
 301  SSGSTMNLDYKLPESANNYTYSSGSPTRAYVGANTNSKNASFNDADLLSS   350
 351  SYWIKAYNDHLFSVSESDETSPMNSELNDTKLIVPDFKSTIHHLKDSRSS   400
 401  SWTVAIDNNSNNNKVSDNQPDFVDFQELLDNDTLGNDLLETTAVLKEFEL   450
 451  LHDDSVSATATSNEIDLSHLNLSNSPISPHKLIYKNKEGTNDDMLISFGL   500
 501  DHPSNREDDLDKLCNMTRDVQAIFSQYLKGEESKRSLEDFLSTSNRKEKP   550
 551  DSGNYTFYGLDCLTLSKISRALPASTVNNNQPSHSIESKLFNEPMRNMCI   600
 601  KVLRYYEKFSHDSSESVMDSNPNLLSKELLMPAVSELNEYLDLFKNNFLP   650
 651  HFPIIHPSLLDLDLDSLQRYTNEDGYDDAENAQLFDRLSQGTDKEYDYEH   700
 701  YQILSISKIVCLPLFMATFGSLHKFGYKSQTIELYEMSRRILHSFLETKR   750
 751  RCRSTTVNDSYQNIWLMQSLILSFMFALVADYLEKIDSSLMKRQLSALCS   800
 801  TIRSNCLPTISANSEKSINNNNEPLTFGSPLQYIIFESKIRCTLMAYDFC   850
 851  QFLKCFFHIKFDLSIKEKDVETIYIPDNESKWASESIICNGHVVQKQNFY   900
 901  DFRNFYYSFTYGHLHSIPEFLGSSMIYYEYDLRKGTKSHVFLDRIDTKRL   950
 951  ERSLDTSSYGNDNMAATNKNIAILIDDTIILKNNLMSMRFIKQIDRSFTE  1000
1001  KVRKGQIAKIYDSFLNSVRLNFLKNYSVEVLCEFLVALNFSIRNISSLYV  1050
1051  EEESDCSQRMNSPELPRIHLNNQALSVFNLQGYYYCFILIIKFLLDFEAT  1100
1101  PNFKLLRIFIELRSLANSILLPTLSRLYPQEFSGFPDVVFTQQFINKDNG  1150
1151  MLVPGLSANEHHNGASAAVKTKLAKKINVEGLAMFINEILVNSFNDTSFL  1200
1201  NMEDPIRNEFSFDNGDRAVTDLPRSAHFLSDTGLEGINFSGLNDSHQTVS  1250
1251  TLNLLRYGENHSSKHKNGGKGQGFAEKYQLSLKYVTIAKLFFTNVKENYI  1300
1301  HCHMLDKMASDFHTLENHLKGNS                             1323

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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