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

NucPred

Fetching Q5BLK4 from www.uniprot.org...

The NucPred score for your sequence is 0.96 (see score help below)

   1  MGDTAKPYFVKRTKDRGIIDDDDFRRGHPQQDYLIMDDYAKGHSSKMEKG    50
  51  LPKKKISPGNYGNTPRKGLYGVSSNPYAFKNPIYSQPAWMNDNHKDQNKK   100
 101  WLSDELAGNADSWREFKPGPRIPVISRSRKESFQESDDAYRWQEGRGCRA   150
 151  VRRLFQKDLSSLEAMSEMEAGSPENKKQRSRPRKPRRTRTEDSEQDGDLD   200
 201  GPVIDESVLSTKELLGLQQAEERLKRDCIDRLKRRPRNCPTAKYTCKLCD   250
 251  ALIDSIPFAHKHIKEKRHKKNLKEKQEEELLTTLPPPAPSQIHAVGSAID   300
 301  RVVQEFGLHSENLDQRLEIKRVMESVFRHKLPDCSLRLYGSSCSRLGFRD   350
 351  SDVNIDVQFPAVMSQPDVLLLVQECLKNSDSFIDVDADFHARVPVVVCRD   400
 401  KQSGLLCKVSAGNENAWLTTKHLTALGKLEPRLVPLVIAFRYWAKLCSID   450
 451  RPEEGGLPPYVFALMAVFFLQQRKEPLLPVYLGSWIEEFSLNKLGNFSLK   500
 501  DVEKDSVVWEYTDNSTGDTSSAKEEAPKETAAKKGQVPLTFNIKHQPSVP   550
 551  VGQLWVELLRFYALEFNLADLVISIRVKELISRESKDWPKKRIAIEDPYS   600
 601  VKRNVARTLNNQPVFEYILHCLRTTYKYFALPHKVTKPNLTKPPSPVTCV   650
 651  SDPYREAKNGGPEPQATNIDKLGNAAVAQDPGVQTSGDCRAQLVTLKNTT   700
 701  EEVGSPAKEKTGGVHIPAHQESSGCVQAEVSCEGLEDATAELPETGSDNE   750
 751  EVRRKTKHPLSTDDQGLSSSKHPELQNCGSLCGLQADNTLELVAEECNSC   800
 801  ASLDNKAEVNEERIEGAEELEEAAALSCFSPSVQSRTSAAMHFDDEEEEE   850
 851  EEEEEEEPRLSINLTEDEEGVANEHQVDSRYAGSGEEDALSEEDDLAEPA   900
 901  KGEDTGECGENVGGTLLIDLNRITLKEESFPEEDLPGDQSEFFYEFRKLT   950
 951  FTKGKSPTVVCSLCKREGHLKKDCPEDFKRVQLEPLPPLTPKFSNILDQV  1000
1001  CVQCYKDFSPTIVEDQAREHIRQNLESFIKQDFPGTKLSLFGSSKNGFGF  1050
1051  KQSDLDVCMTINGHETAEGLDCVRTIEELARVLRKHSGLRNILPITTAKV  1100
1101  PIVKFFHLRSGLEVDISLYNTLALHNTRLLSAYSAIDPRVKYLCYTMKVF  1150
1151  TKMCDIGDASRGSLSSYAYTLMVLYFLQQRSPPVIPVLQEIYKGEKKPEI  1200
1201  LVDGWNIYFFDQINELPTCWPEYGKNTEPVGQLWLGLLRFYTEEFDFKEH  1250
1251  VISIRRKSLLTTFKKQWTSKYIVIEDPFDLNHNLGAGLSRKMTNFIMKAF  1300
1301  INGRRVFGIPVKGFPKDNPSKLAYFFDPDVLTEGELAPNDRCCRICGKIG  1350
1351  HFMKDCPMRRKVRRRRDQEDTPNQRYSESKEKRSKEDKEIQNKYTEKEVS  1400
1401  TKEDKLTPCAAAKAKPVRAAVDLGREKLLRTPTEKWKRQDDRDSREKRCF  1450
1451  ICGREGHIKKECPQFKGSPGSLSSKYMTQGRASVKRTQQES           1491

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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