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

NucPred

Fetching Q753D4 from www.uniprot.org...

The NucPred score for your sequence is 0.42 (see score help below)

   1  MNEKEELHLYHVSLQKQRNYVHSCIGHFVDYRHHHIRAQGGSVEGGKKGS    50
  51  KWRKQLQICMATQTQVELYDVEEGRLRRLFTRTVFGTITGLSSVVADGRS   100
 101  VLIVVGDSGKMSVLRFKYEGGRVRLEALFNEPLSRSGVRRLSPQAHVSVD   150
 151  PQGRCVLLSAMERNKVCYLMDVKQGELQVSSPLEANRPNYVTMQTAACDV   200
 201  AFDNPIFASLEIDLADGAKYLFFYMLDLGLNHMAKVADFELGDGSANFIM   250
 251  SVPDLEQYGINTKAGGPDDGDPDAIVPFVLMGFDNYVSLKDLRGRYDINV   300
 301  QIPTRKLSQKTIITAGTVQKLKRDFFMLLQSNHGDLYKVKILPDEKTASP   350
 351  VVTISYFDTIPQAQNLHIFKHGYMFANSEYGNSYLYQFENLDDEEESMLT   400
 401  SVMPGRRLIIEPRTVLKNLLVADKLALVNPILSSQLTERVPLTIATSTLG   450
 451  DVRLFTAGVNFMDIISSPLPAAPLDIWTVATNGSRFHKLLFIALQESTMI   500
 501  LKIAAGTVEELELPHNPFVIAQDKTVLIAHMGGQSIIQVTENKMVHIIEN   550
 551  RDESYESKLEWFPPAGICILKASSNSTQLILALSNNEVVYFEIGSNESLN   600
 601  ELQDRIEVEERITALAIGNGNRSDYMIIASVDSTVKVYSLKVQDQANFLE   650
 651  VVSMQVLVSPASSLQLASSGGSLCLHIGLDSGVYVRSKLDRNTGELFDVR   700
 701  TKYLGTKPVEISLLLDMNPYINEEVDDEGEEEEEQDDEESLGGPHSRLVP   750
 751  CVVLHSGKTWISYELDSSLFIRPLLNDQSLKRVAQFTSNEIQRNGCCSIS   800
 801  SAGFLVIGRIGTFRNNDCWFQESSLALPDSEDSVNGNELENDEKDPDALL   850
 851  EEKQKVNSSIGKLIIPDPDDIKLFYYCEYNEVENSCRVSLFKQGISYKHE   900
 901  NSTEAFQLIPDCRPSTATIARFGLDMKHLVISTVNGVLKTFVIRITKAAN   950
 951  NRRFELLALHDTVAGSTIHAMCPFHDKLLVPLANAVVLYGLGKKQLLKKS  1000
1001  ISYLPTSITKIVALDQWNGTRVAVGDIHESVTLLHFDERKNQFIPVADDV  1050
1051  TKRHVTVVKFVDECTVIGGDRFGNIWLLRLPLEYDRLIKEGVDSYLLTLN  1100
1101  TGIPSNIRECVFKWQLLNHFYINDIPMSFHLIASPQMADRASILYAGLQG  1150
1151  TIGYLIPLITRREIEFFDLLEQAMRDADHLFYLDQENRLNDTSELNDGAD  1200
1201  EEGSVIDRRFPSVQKKRKIPEGAYSLVGRDAMMYRSYYNPVRHVTDGDLC  1250
1251  EQFLELYPSEKNFLAARVDNRSVQEIERRINDMRTNCM              1288

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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