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

NucPred

Fetching Q24574 from www.uniprot.org...

The NucPred score for your sequence is 0.88 (see score help below)

   1  MTDKESEQCTVSVFDQTPGSEQKKINVVVRSHFTVKRVIDLIGTQFSYEK    50
  51  FELLLQPHDNKDLVNLNALESQLMYEVAGFEPQLKNHLILLPSGSWDGDV   100
 101  TKRFELPIKRVVVKKVMKSDGEKAKSPATGEKKKRVVGEKTKKKPASGSS   150
 151  SPSKAKTTSEDSLAKTSISSESSPEKTSKIKTTAAKISKPGSEKAPRASP   200
 201  EECPELSTEINSKNTSSESPVAKKTAKVTSKPTLELLSPIKPSSPIKELD   250
 251  CEPVDTLSKQQLSEQLQLYPQGRNLISPVDDAPSDLFISDAEQLSDDDLA   300
 301  LGASASPTMLGPGYDYGAPTGDSDVEGVTGVTDPSTIGTDDGTYPALSNF   350
 351  YRRKYGGDELRAWQRVNTTGADFVSSATTETEAEARQASLGPRGYVGLVN   400
 401  QAMTCYLNSLLQALFMTPEFRNALYRWEFDNDNEAKNIPYQLQKLFLNLQ   450
 451  TSPKAAVETTDLTRSFGWDSTEAWQQHDIQELCRVMFDALEHKFKNTKQA   500
 501  NLISNLYEGKMNDYVKCLECNTEKTREDTFLDIPLPVRPFGSSSAYGSIE   550
 551  EALRAFVQPETLDGNNQYLCEKCKKKCDAHKGLHFKSFPYILTLHLKRFD   600
 601  FDYQTMHRIKLNDRVTFPQTLNLNTFINRSGNSGEQNSQLNGTVDDCSTA   650
 651  DSGSAMEDDNLSSGVVTTASSSQHENDLNDEDEGIDMSSSTSKSAKQGSG   700
 701  PYLYELFAIMIHSGSASGGHYYAYIKDFDNNEWFCFNDQNVTSITQEDIQ   750
 751  RSFGGPNGSYYSSAYTSSTNAYMLMYRQVDAKRNELVAKVADFPEHIKTL   800
 801  LPKLHSEEETRVSRLGRHITVTDLALPDLYKPRVYFYNPSLKKMKITRVY   850
 851  VSQSFNINLVLMSAYEMLNVEQFAPLSRCRLVAYNSSMDTIIQSLESCTD   900
 901  PALTELRAAQNYSLDFLLEYRAEDQEFEVYPPNGITWYVFKVDLSTMAMD   950
 951  GPFLVYSAAREREASDVLRRSIALRLHISEQQFLLATVRATVPKAFVSYD  1000
1001  PHPTPEALQHLQNMANTQFKSITYFYLNVPNTDAATLEMLGVPTVESVEC  1050
1051  ASGGDVVDAAMMNGVAPGHMSSSNDYDWRRYKRDLVEPMSQPSPSHGHES  1100
1101  NSEDSSLSDGDRTLVETDNMAHRGGGDSQVSSTSHSPQLSSPEDEAASHD  1150
1151  AMMRVHAYCNGNGSYAAADVVDPLLLPTSTNHFFYATKVECVDVVGTGSS  1200
1201  SGHQSDEEAQLRKPTRAYKLLVGTHMRMGAFKKHIEQLIQVPAAHFKLQR  1250
1251  KHDNNLSNNQNNSLVHLIEGETLTVELGKTLEPDEFKAKIHFLRLADIDN  1300
1301  ETSKLPCVCEWVYNANTTAEQAKKELVAKLHRIDAKYATLSVQNCRIWLK  1350
1351  GGRIPIKILSDDETLYCDMRSSIAAEFIVQECEEEVDPQPKDDSLTLFVR  1400
1401  RWCPAKLEFGKFQEITLDQDSEIRLSLSQISDIPIDKLSYMKLNSNFPCT  1450
1451  SISALSVNESSSWYSVPTTLDKYPLNSTQTGNIYLYKDRTVPARELTLEE  1500
1501  RRLMNAREKARLDRVGCVSTTRYAQRRERALKIYLDSPEKSSNVTASAPM  1550
1551  DVHVNN                                              1556

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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