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

NucPred

Fetching O97817 from www.uniprot.org...

The NucPred score for your sequence is 0.47 (see score help below)

   1  MVSSGCRMRSLWFIIIISFLPNTEGFSRAALPFGLVRRELSCEGYSIDLR    50
  51  CPGSDVIMIESANYGRTDDKICDADPFQMENTDCYLPDAFKIMTQRCNNR   100
 101  TQCIVVTGSDVFPDPCPGTYKYLEVQYECVPYMEQKVFVCPGTLKAIVDS   150
 151  PCIYEAEQKAGAWCKDPLQAADKIYFMPWTPYRTDTLIEYASLEDFQNSR   200
 201  QTTTYKLPNRVDGTGFVVYDGAVFFNKERTRNIVKYDLRTRIKSGEAIIN   250
 251  YANYHDTSPYRWGGKTDIDLAVDENGLWVIYATEQNNGMIVISQLNPYTL   300
 301  RFEATWETVYDKRAASNAFMICGVLYVVRSVYQDNESETGKNAIDYIYNT   350
 351  RLNRGEYVDVPFPNQYQYIAAVDYNPRDNQLYVWNNNFILRYSLEFGPPD   400
 401  PAQVPTTAVTITSSAEMFKTTVSTTSTTSQKGPMSTTVAGSQEGSKGTKA   450
 451  PPAVSTTKIPPVTNIFPLPERFCEALDARGIRWPQTQRGMMVERPCPKGT   500
 501  RGTASYLCVLSTGTWNPKGPDLSNCTSHWVNQLAQKIRSGENAASLANEL   550
 551  AKHTKGPVFAGDVSSSVRLMEQLVDILDAQLQELKPSEKDSAGRSYNKLQ   600
 601  KREKTCRAYLKAIVDTVDNLLRPEALESWKHMNSSEQAHTATMLLDTLEE   650
 651  GAFVLADNLVEPTRVSMPTENIVLEVAVLSTEGQVQDFKFPLGIKGAGSS   700
 701  IQLSANTVKQNSRNGLAKLVFIIYRSLGQFLSTENATIKLGADFIGRNST   750
 751  IAVNSHVISVSINKESSRVYLTDPVLFTLPHIDPDNYFNANCSFWNYSER   800
 801  TMMGYWSTQGCKLVDTNKTRTTCACSHLTNFAILMAHREIAYKDGVHELL   850
 851  LTVITWVGIVISLVCLAICIFTFCFFRGLQSDRNTIHKNLCINLFIAEFI   900
 901  FLIGIDKTKYMIACPIFAGLLHFFFLAAFAWMCLEGVQLYLMLVEVFESE   950
 951  YSRKKYYYVAGYLFPATVVGVSAAIDYKSYGTEKACWLHVDNYFIWSFIG  1000
1001  PVTFIILLNIIFLVITLCKMVKHSNTLKPDSSRLENINNYRVCDGYYNTD  1050
1051  LPGSWVLGAFALLCLLGLTWSFGLLFINEETIVMAYLFTIFNAFQGVFIF  1100
1101  IFHCALQKKVRKEYGKCFRHSYCCGGLPTESPHSSVKASTTRTSARYSSG  1150
1151  TQSRIRRMWNDTVRKQSESSFISGDINSTSTLNQGMTGNYLLTNPLLRPH  1200
1201  GTNNPYNTLLAETVVCNAPSAPVFNSPGHSLNNARDTSAMDTLPLNGNFN  1250
1251  NSYSLRKGDYNDSVQVVDCGLSLNDTAFEKMIISELVHNNLRGSSKAHNL  1300
1301  ELTLPVKPVIGGSSSEDDAIVADASSLMHGDNPGLELHHKELEAPLIPQR  1350
1351  THSLLYQPQKKAKPEGTDSYVSQLTAEAEDHLQSPNRDSLYTSMPNLRDS  1400
1401  PYQESSPDMEEDLSPSRRSENEDIYYKSMPNLGAGHQLQMCYQISRGNSD  1450
1451  GYIIPINKEGCIPEGDVREGQMQLVTSL                        1478

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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