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

NucPred

Fetching Q00519 from www.uniprot.org...

The NucPred score for your sequence is 0.43 (see score help below)

   1  MTRTTVDELVFFVNGKKVVEKNADPETTLLVYLRRKLGLCGTKLGCGEGG    50
  51  CGACTVMISKYDRLQNKIVHFSVNACLTPICSLHHVAVTTVEGIGNTKKL   100
 101  HPVQERIAKSHGSQCGFCTPGIVMSMYTLLRNKPEPTVEEIENAFQGNLC   150
 151  RCTGYRPILQGFRTFAKDGGCCGGSGNNPNCCMSQTKDQTIAPSSSLFNP   200
 201  EDFKPLDPTQEPIFPPELLRLKDTPRKTLRFEGERVTWIQVSTMEELLDL   250
 251  KAQHPDAKLVVGNTEIGIEMKFKNMLFPLIICPAWILELTSVAHGPEGIS   300
 301  FGAACPLSLVESVLADAIATLPEQRTEVFRGVMEQLRWFAGKQVKSVASI   350
 351  GGNIITASPISDLNPVLMASRAKLTLASRGTKRTVWMDHTFFPGYRRTLL   400
 401  SPEEILVSIVIPYSRKGEFFSAFKQASRREDDIAKVTSGMRVLFKPGTTE   450
 451  VQELSLCFGGMADRTVSALKTTPKQLSKSWNEELLQDVCAGLAEELHLAP   500
 501  DAPGGMVEFRRTLTLSFFFKFYLTVLQKLGRADLEGMCGKLDPTFASATL   550
 551  LFQKDPPANVQLFQEVPKGQSEEDMVGRPMPHLAADMQASGEAVYCDDIP   600
 601  RYENELSLRLVTSTRAHAKIMSIDTSEAKKVPGFVCFLTSEDVPGSNITG   650
 651  IFNDETVFAKDEVTCVGHIIGAVVADTPEHAHRAARGVKITYEDLPAIIT   700
 701  IQDAIKNNSFYGPEVKIEKGDLKKGFSEADNVVSGELYIGGQEHFYLETH   750
 751  CTIAVPKGEAGEMELFVSTQNTMKTQSFIAKMLGVPDNRIVVRVKRMGGG   800
 801  FGGKETRSTLISTAVALAAYKTGRPVRCMLDRDEDMLITGGRHPFLAKYK   850
 851  VGFMKTGTIVALEVAHFSNGGNSEDLSRSIMERAVFHMDNAYKIPNIRGT   900
 901  GRICKTNLPSNTAFRGFGGPQGMLIAEYWMSEVAVTCGLPAEEVRRKNMY   950
 951  KEGDLTHFNQKLEGFTLPRCWDECIASSQYQARKMEVEKFNRENCWKKRG  1000
1001  LCIIPTKFGISFTLSFLNQGGALVHVYTDGSVLLTHGGTEMGQGLHTKMV  1050
1051  QVASRALKIPTSKIHITETSTNTVPNTSPTAASASADLNGQAIYEACQTI  1100
1101  LKRLEPFKKKNPSGSWESWVMDAYTSAVSLSATGFYKTPNLGYSFETNSG  1150
1151  NPFHYFSYGVACSEVEIDCLTGDHKNLRTDIVMDVGSSLNPAIDIGQVEG  1200
1201  AFVQGLGLFTMEELHYSPEGSLHTRGPSTYKIPAFGSIPIEFRVSLLRDC  1250
1251  PNKRAIYASKAVGEPPLFLASSIFFAIKDAIRAARAQHGDSNAKQLFQLD  1300
1301  SPATPEKIRNACVDQFTTLCATGTPENCKSWSVRI                 1335

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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