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

NucPred

Fetching Q9WTK5 from www.uniprot.org...

The NucPred score for your sequence is 0.71 (see score help below)

   1  MDNCYDPGLDGIPEYDDFEFSPSIVEPKDPAPETADGPYLVIVEQPKQRG    50
  51  FRFRYGCEGPSHGGLPGASSEKGRKTYPTVKICNYEGPAKIEVDLVTHSD   100
 101  PPRAHAHSLVGKQCSELGVCAVSVGPKDMTAQFNNLGVLHVTKKNMMEIM   150
 151  IQKLQRQRLRSKPQGLTEAERRELEQEAKELKKVMDLSIVRLRFSAFLRA   200
 201  SDGSFSLPLKPVISQPIHDSKSPGASNLKISRMDKTAGSVRGGDEVYLLC   250
 251  DKVQKDDIEVRFYEDDENGWQAFGDFSPTDVHKQYAIVFRTPPYHKMKIE   300
 301  RPVTVFLQLKRKRGGDVSDSKQFTYYPLVEDKEEVQRKRRKALPTFSQPF   350
 351  GGGSHMGGGSGGSAGGYGGAGGGGSLGFFSSSLAYNPYQSGAAPMGCYPG   400
 401  GGGGAQMAGSRRDTDAGEGAEEPRTPPEAPQGEPQALDTLQRAREYNARL   450
 451  FGLAQRSARALLDYGVTADARALLAGQRHLLMAQDENGDTPLHLAIIHGQ   500
 501  TGVIEQIAHVIYHAQYLGVINLTNHLHQTPLHLAVITGQTRVVSFLLQVG   550
 551  ADPTLLDRHGDSALHLALRAGAAAPELLQALLRSGAHAVPQILHMPDFEG   600
 601  LYPVHLAVHARSPECLDLLVDCGAEVEAPERQGGRTALHLATEMEELGLV   650
 651  THLVTKLHANVNARTFAGNTPLHLAAGLGSPTLTRLLLKAGADIHAENEE   700
 701  PLCPLPSPSTSGSDSDSEGPERDTQRNFRGHTPLDLTCSTKVKTLLLNAA   750
 751  QNTTEPPLAPPSPAGPGLSLGDAALQNLEQLLDGPEAQGSWAELAERLGL   800
 801  RSLVDTYRKTPSPSGSLLRSYKLAGGDLVGLLEALSDMGLHEGVRLLKGP   850
 851  ETRDKLPSTEVKEDSAYGSQSVEQEAEKLCPPPEPPGGLCHGHPQPQVH    899

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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