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

NucPred

Fetching Q99372 from www.uniprot.org...

The NucPred score for your sequence is 0.04 (see score help below)

   1  MAGLTAAVPQPGVLLILLLNLLHPAQPGGVPGAVPGGVPGGLPGGVPGGV    50
  51  YYPGAGIGGGLGGGALGPGGKPPKPGAGLLGAFGAGPGGLGGAGPGAGLS   100
 101  YASRPGGVLVPGGGAGAAAAYKAAAKAGAGLGGIGGVPGGVGVGGVPGAV   150
 151  GVGGVPGAVGGIGGIGGLGVSTGAVVPQLGAGVGAGGKPGKVPGVGLPGV   200
 201  YPGGVLPGTGARFPGVGVLPGVPTGTGVKAKVPGGGGGAFSGIPGVGPFG   250
 251  GQQPGVPLGYPIKAPKLPGGYGLPYTNGKLPYGVAGAGGKAGYPTGTGVG   300
 301  SQAAVAAAKAAKYAGAGGGGVLPGVGGGGIPGGAGAIPGIGGITGAGTPA   350
 351  AAAAAKAAAKAAKYGAAGGLVPGGPGVRVPGAGIPGVGIPGVGGIPGVGG   400
 401  IPGVGGIPGVGGPGIGGPGIVGGPGAVSPAAAAKAAAKAAKYGARGGVGI   450
 451  PTYGVGAGGFPGYGVGAGAGLGGASQAAAAAAAAKAAKYGAGGAGTLGGL   500
 501  VPGAVPGALPGAVPGALPGAVPGALPGAVPGVPGTGGVPGAGTPAAAAAA   550
 551  AAAKAAAKAGQYGLGPGVGGVPGGVGVGGLPGGVGPGGVTGIGTGPGTGL   600
 601  VPGDLGGAGTPAAAKSAAKAAAKAQYRAAAGLGAGVPGLGVGAGVPGFGA   650
 651  GAGGFGAGAGVPGFGAGAVPGSLAASKAAKYGAAGGLGGPGGLGGPGGLG   700
 701  GPGGFGGPGGLGGVPGGVAGGAPAAAAAAKAAAKAAQYGLGGAGGLGAGG   750
 751  LGAGGLGAGGLGAGGLGAGGLGAGGVIPGAVGLGGVSPAAAAKAAKYGAA   800
 801  GLGGVLGARPFPGGGVAARPGFGLSPIYPGGGAGGLGVGGKPPKPYGGAL   850
 851  GALGYQGGGCFGKSCGRKRK                                 870

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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