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

NucPred

Fetching Q9ES67 from www.uniprot.org...

The NucPred score for your sequence is 0.85 (see score help below)

   1  MSIRLPHSIDRSASKKQSHLSSPIASWLSSLSSLGDSTPERTSPSHHRQP    50
  51  SDTSETTAGLVQRCVIIQKDQHGFGFTVSGDRIVLVQSVRPGGAAMKAGV   100
 101  KEGDRIIKVNGTMVTNSSHLEVVKLIKSGAYAALTLLGSSPPSVGVSGLQ   150
 151  QNPSVAGVLRVNPIIPPPPPPPPLPPPQHITGPKPLQDPEVQKHATQILW   200
 201  NMLRQEEEELQDILPPCGETSQRTCEGRLSVDSQEADSGLDSGTERFPSI   250
 251  SESLMNRNSVLSDPGLDSPQTSPVILARVAQHHRRQGSDAALLPLNHQGI   300
 301  DQSPKPLIIGPEEDYDPGYFNNESDIIFQDLEKLKSHPAYLVVFLRYILS   350
 351  QADPGPLLFYLCSEVYQQTNPKDSRSLGKDIWNIFLEKNAPLRVKIPEML   400
 401  QAEIDLRLRNNEDPRNVLCEAQEAVMLEIQEQINDYRSKRTLGLGSLYGE   450
 451  NDLLGLDGDPLRERQMAEKQLAALGDILSKYEEDRSAPMDFAVNTFMSHA   500
 501  GIRLRESRSSCTAEKTQSAPDKDKWLPFFPKTKKQSSNSKKEKDALEDKK   550
 551  RNPILRYIGKPKSSSQSIKPGNVRNIIQHFENSHQYDVPEPGTQRLSTGS   600
 601  FPEDLLESDSSRSEIRLGRSGSLKGREEMKRSRKAENVPRPRSDVDMDAA   650
 651  AEAARLHQSASSSASSLSTRSLENPTPPFTPKMGRRSIESPNLGFCTDVI   700
 701  LPHLLEDDLGQLSDLEPEPEVQNWQHTVGKDVVANLTQREIDRQEVINEL   750
 751  FVTEASHLRTLRVLDLIFYQRMRKENLMPREELARLFPNLPELIEIHNSW   800
 801  CEAMKKLREEGPIIRDISDPMLARFDGPAREELQQVAAQFCSYQSVALEL   850
 851  IRTKQRKESRFQLFMQEAESHPQCRRLQLRDLIVSEMQRLTKYPLLLENI   900
 901  IKHTEGGTSEHEKLCRARDQCREILKFVNEAVKQTENRHRLEGYQKRLDA   950
 951  TALERASNPLAAEFKSLDLTTRKMIHEGPLTWRISKDKTLDLQVLLLEDL  1000
1001  VVLLQRQEERLLLKCHSKTAVGSSDSKQTFSPVLKLNAVLIRSVATDKRA  1050
1051  FFIICTSELGPPQIYELVALTSSDKNIWMELLEEAVQNATKHPGAAPIPI  1100
1101  HPSPPGSQEPAYQGSTSSRVEINDSEVYHTEKEPKKLPEGPGPEQRVQDK  1150
1151  QLIAQGEPVQEEDEEELRTLPRAPPSLDGENRGIRTRDPVLLALTGPLLM  1200
1201  EGLADAALEDVENLRHLILWSLLPGHTVKTQAAGEPEDDLTPTPSVVSIT  1250
1251  SHPWDPGSPGQAPTISDSTRLARPEGSQPEGEDVAVSSLAHLPPRTRSSG  1300
1301  VWDSPELDRNPAAEAASTEPAASYKVVRKVSLLPGGGVGAAKVAGSNAIP  1350
1351  DSGQSESELSEVEGGAQATGNCFYVSMPAGPLDSSTEPTGTPPSPSQCHS  1400
1401  LPAWPTEPQPYRGVRGGQCSSLVRRDVDVIFHTIEQLTIKLHRLKDMELA  1450
1451  HRELLKSLGGESSGGTTPVGSFHTEAARWTDYSLSPPAKEALASDSQNGQ  1500
1501  EQGSCPEEGSDIALEDSATDTAVSPGP                         1527

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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