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

NucPred

Fetching Q6FL58 from www.uniprot.org...

The NucPred score for your sequence is 0.92 (see score help below)

   1  MDRFRIQDGKYVVEKEIGKGSFATVYRGHVTTDPKSHIAVKAVARSKLKN    50
  51  KKLLENLEIEIAILKKIKHPHIVGLIDCERTTTDFYLVMDYCALGDLTFL   100
 101  IKKRKELENNHPLLQTVFNKYPPPSKEHNGLNRAFVVCYLQQLASALKFL   150
 151  RSKNLVHRDIKPQNLLLATPLTNYRDSKTFHELGYVGIYNLPILKIADFG   200
 201  FARFLPSTSLAETLCGSPLYMAPEILNYQKYNAKADLWSVGTVLFEMCCG   250
 251  VPPFTASNHLELFKKIKRAHDEINFPEVCEVEDGLKELICSLLTFDPAKR   300
 301  IGFEEFFNNKIVTEDLSHYEVDENTELESKSKDLQESNMFVSEFLIKKRN   350
 351  QKGVSSRKDTEFIPKSKQEPMLDQAYKDETEMETGVKYGVNIAPEVYQNE   400
 401  MIDPEKLAAKLIAAKQLGSDEKLTNKNISHLLSSNSSRVNKLDKSNLSGK   450
 451  SDSSLDRDYVVVEKKAVEVNSLADDLAQANVGNNDEAVKDQNIKTLEQPH   500
 501  IQVHQPHNDIQNLQRAPSTTSGGTSSRRASLVERRLSISSLNPSNALSRA   550
 551  LGLASTRIFGSSAQTNKNQTSNSTSPNYTQPLLNSQIFYDLTENLILHTE   600
 601  TLNQPALINVDHAKGINEVIRILESLSAKAFVVYSYAEVKYAQIIPLPQA   650
 651  VIRASPALQFEKRLSDDSNPVIDEDSDEELDVQKNLSNTLLSETVNTRYR   700
 701  LRNDSSRNSYNKRNSFNKERFSFSSQGSNNSKRTNSYSSTLLPAEIISIS   750
 751  KEAIVLYMKALQILAQSMKITSKWWYSCQEKICSLRLNILVQWIREKFNE   800
 801  CLDKTDFLRMKLEEYENSKPGTHNQSPKSKISNDSNEDNVAEKVYLEKLL   850
 851  YDRALEISKYAANLELQGQNLHICELAYATSLWMLTISLENSPYTDQGED   900
 901  EYDEFLKDTNDVLDSEDKIIIGKYIKSISHRLKMLRQKMAKY           942

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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