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

NucPred

Fetching P21127 from www.uniprot.org...

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

   1  MGDEKDSWKVKTLDEILQEKKRRKEQEEKAEIKRLKNSDDRDSKRDSLEE    50
  51  GELRDHRMEITIRNSPYRREDSMEDRGEEDDSLAIKPPQQMSRKEKAHHR   100
 101  KDEKRKEKRRHRSHSAEGGKHARVKEKEREHERRKRHREEQDKARREWER   150
 151  QKRREMAREHSRRERDRLEQLERKRERERKMREQQKEQREQKERERRAEE   200
 201  RRKEREARREVSAHHRTMREDYSDKVKASHWSRSPPRPPRERFELGDGRK   250
 251  PGEARPAPAQKPAQLKEEKMEERDLLSDLQDISDSERKTSSAESSSAESG   300
 301  SGSEEEEEEEEEEEEEGSTSEESEEEEEEEEEEEEETGSNSEEASEQSAE   350
 351  EVSEEEMSEDEERENENHLLVVPESRFDRDSGESEEAEEEVGEGTPQSSA   400
 401  LTEGDYVPDSPALSPIELKQELPKYLPALQGCRSVEEFQCLNRIEEGTYG   450
 451  VVYRAKDKKTDEIVALKRLKMEKEKEGFPITSLREINTILKAQHPNIVTV   500
 501  REIVVGSNMDKIYIVMNYVEHDLKSLMETMKQPFLPGEVKTLMIQLLRGV   550
 551  KHLHDNWILHRDLKTSNLLLSHAGILKVGDFGLAREYGSPLKAYTPVVVT   600
 601  LWYRAPELLLGAKEYSTAVDMWSVGCIFGELLTQKPLFPGKSEIDQINKV   650
 651  FKDLGTPSEKIWPGYSELPAVKKMTFSEHPYNNLRKRFGALLSDQGFDLM   700
 701  NKFLTYFPGRRISAEDGLKHEYFRETPLPIDPSMFPTWPAKSEQQRVKRG   750
 751  TSPRPPEGGLGYSQLGDDDLKETGFHLTTTNQGASAAGPGFSLKF        795

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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