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

NucPred

Fetching P01025 from www.uniprot.org...

The NucPred score for your sequence is 0.46 (see score help below)

   1  MGSTSGPRLLLLLLTSLPLALGDPIYTIITPNVLRLESEEMVVLEAHEGQ    50
  51  GDIRVSVTVHDFPAKRQVLSSETTTLNNANNYLSTVNIKIPASKEFKSEK   100
 101  GHKFVTVQALFGNVQVEKVVLVSLQSGYLFIQTDKTIYTPGSTVLYRIFT   150
 151  VDHKLLPVGQTIVVTIETPEGIDIKRDSLSSHNQFGILALSWNIPELVNM   200
 201  GQWKIRAHYEDAPQQVFSAEFEVKEYVLPSFEVQVEPSEKFYYIDDPNGL   250
 251  TVNIIARFLYGESVDGTAFVIFGVQDGDQRISLSQSLTRVPIIDGTGEAT   300
 301  LSQGVLLNGVHYSSVNDLVGKSIYVSVTVILNSGSDMVEAERTGIPIVTS   350
 351  PYQIHFTKTPKFFKPAMPFDLMVYVTNPDGSPARHIPVVTEDFKVRSLTQ   400
 401  EDGVAKLSINTPDNRNSLPITVRTEKDGIPAARQASKTMHVLPYNTQGNS   450
 451  KNYLHLSLPRVELKPGENLNVNFHLRTDPGYQDKIRYFTYLIMNKGKLLK   500
 501  VGRQPRESGQVVVVLPLTITTDFIPSFRLVAYYTLIAANGQREVVADSVW   550
 551  VDVKDSCVGTLVVKGGGKQDKQHRPGQQMTLEIQGERGARVGLVAVDKGV   600
 601  FVLNKKNKLTQRRIWDVVEKADIGCTPGSGKDFAGVFTDAGLAFKSSKGL   650
 651  QTPQRADLECPKPAARKRRSVQLMEKRMDKLGQYSKDVRRCCEHGMRDNP   700
 701  MKFSCQRRAQFIQHGDACVKAFLDCCEYIAKLRQQHSRNKPLGLARSDLD   750
 751  EEIIPEEDIISRSQFPESWLWTIEEFKEPDKNGISTKTMNVFLKDSITTW   800
 801  EILAVSLSDKKGICVADPYEVVVKQDFFIDLRLPYSVVRNEQVEIRAILY   850
 851  NYREAEDLKVRVELLYNPAFCSLATAKKRHQQTLTVPAKSSVPVPYIIVP   900
 901  LKTGLQEVEVKAAVYNHFISDGVKKTLKVVPEGMRVNKTVVTRTLDPEHK   950
 951  GQQGVQREEIPPADLSDQVPDTESETKILLQGTPVAQMVEDAIDGDRLKH  1000
1001  LIQTPSGCGEQNMIGMTPTVIAVHYLDSTEQWEKFGLEKRQEALELIKKG  1050
1051  YTQQLAFRQKNSAFAAFQDRLSSTLLTAYVVKVFAMAANLIAIDSQVLCG  1100
1101  AVKWLILEKQKPDGVFEENGPVIHQEMIGGFKNTEEKDVSLTAFVLIALQ  1150
1151  EAKDICEPQVNSLLRSINKARDFLADYYLELKRPYTVAIAGYALALSDKL  1200
1201  DEPFLNKLLSTAKERNRWEEPGQKLHNVEATSYALLALLVVKDFDSVPPI  1250
1251  VRWLNEQRYYGGGYGSTQATFMVFQALAQYQKDVPDHKDLNLDVSIHLPS  1300
1301  RSAPVRHRILWESASLLRSEETKENEGFTLIAEGKGQGTLSVVTMYHGKA  1350
1351  KGKTTCKKFDLKVSIHPAPEPVKKPQEAKSSMVLDICTRYLGNQDATMSI  1400
1401  LDISMMTGFSPDTEDLKLLSTGVDRYISKYELNKALSNKNTLIIYLDKIS  1450
1451  HTLEDCISFKVHQYFNVGLIQPGSVKVYSYYNLDESCTRFYHPEKEDGML  1500
1501  NKLCHKEMCRCAEENCFMHHDEEEVTLDDRLERACEPGVDYVYKTRLLKK  1550
1551  ELSDDFDDYIMVIEQIIKSGSDEVQVGQERRFISHIKCREALKLKEGGHY  1600
1601  LVWGVSSDLWGEKPNISYIIGKDTWVELWPDGDVCQDEENQKQCQDLANF  1650
1651  SENMVVFGCPN                                         1661

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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