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

NucPred

Fetching P32644 from www.uniprot.org...

The NucPred score for your sequence is 0.81 (see score help below)

   1  MDFQCRTCSQAYDAEQMMKHLSSTRHKTVFDTSNDEDICCEECQDKNIHQ    50
  51  LQIIRFGGEDMVLLCNSCFRKEYSETERPSTSYSLQNGSILKFWEKYVKV   100
 101  RECCCDECGEESNLNANRNGEVLCDKCLPKSNRAKDFVSEKSGRFLYIYL   150
 151  GLNETQNSTRKPRKKGGRRVGRGKKGRKGAKIKKEKKETFEAKISRIAYE   200
 201  VKKENSTIQSSSSSNLRNFKGFKAVESDPVVAAKVSKSETSRSNPGPSNR   250
 251  NKGKGNKANHKKNSGNGIGKEKERKTNIRNNVRNSQPIPEDRKNTNSHVT   300
 301  TNSGGKGKNESVDKHQLPQPKALNGNGSGSTNTTGLKKGKKDHAGQKTKG   350
 351  NDKTGNKNPREAKLNSAGRKNALGKKSNNQPNKGTSRWTIGSDTESSREP   400
 401  SISPNENTTSITKSRNRNKKASKPTLNEKSKTTTMPKKLETKNQEKNNGK   450
 451  TKDGKLIYEEGEPLTRYNTFKSTLSYPDLNTYLNDYSFALFLEQKLENEF   500
 501  VQNFNILWPRNEKDTAFIINVEKNNNSELEKLLPANLLALGRPAFNERQP   550
 551  FFFCTQDEQKVWYIFIKELSIQRGKYVLLVELFSWNNLSLPTKNGSSQFK   600
 601  LLPTSAQTSRILFAMTRITNPKFIDLLLGQKPIKEIYFDNRLKFSSDKLN   650
 651  RSQKTAVEHVLNNSITILQGPPGTGKTSTIEEIIIQVIERFHAFPILCVA   700
 701  ASNIAIDNIAEKIMENRPQIKILRILSKKKEQQYSDDHPLGEICLHNIVY   750
 751  KNLSPDMQVVANKTRRGEMISKSEDTKFYKEKNRVTNKVVSQSQIIFTTN   800
 801  IAAGGRELKVIKECPVVIMDEATQSSEASTLVPLSLPGIRNFVFVGDEKQ   850
 851  LSSFSNIPQLETSLFERVLSNGTYKNPLMLDTQYRMHPKISEFPIKKIYN   900
 901  GELKDGVTDEQKAWPGVQHPLFFYQCDLGPESRVRSTQRDIVGFTYENKH   950
 951  ECVEIVKIIQILMLDKKVPLEEIGVITPYSAQRDLLSDILTKNVVINPKQ  1000
1001  ISMQQEYDEIELFNAAGSQGTAGSLQNNVINIINGLHVATVDSFQGHEKS  1050
1051  FIIFSCVRNNTENKIGFLRDKRRLNVALTRAKHGLIVVGNKNVLRKGDPL  1100
1101  WKDYITYLEEQEVIFTDLTAY                               1121

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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