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

NucPred

Fetching Q9Y117 from www.uniprot.org...

The NucPred score for your sequence is 0.84 (see score help below)

   1  MGLRFQQLKKLWLLYLFLLFFAFFMFAISINLYVASIQGGDAEMRHPKPP    50
  51  PKRRSLWPHKNIVAHYIGKGDIFGNMTADDYNINLFQPINGEGADGRPVV   100
 101  VPPRDRFRMQRFFRLNSFNLLASDRIPLNRTLKDYRTPECRDKKYASGLP   150
 151  STSVIIVFHNEAWSVLLRTITSVINRSPRHLLKEIILVDDASDRSYLKRQ   200
 201  LESYVKVLAVPTRIFRMKKRSGLVPARLLGAENARGDVLTFLDAHCECSR   250
 251  GWLEPLLSRIKESRKVVICPVIDIISDDNFSYTKTFENHWGAFNWQLSFR   300
 301  WFSSDRKRQTAGNSSKDSTDPIATPGMAGGLFAIDRKYFYEMGSYDSNMR   350
 351  VWGGENVEMSFRIWQCGGRVEISPCSHVGHVFRSSTPYTFPGGMSEVLTD   400
 401  NLARAATVWMDDWQYFIMLYTSGLTLGAKDKVNVTERVALRERLQCKPFS   450
 451  WYLENIWPEHFFPAPDRFFGKIIWLDGETECAQAYSKHMKNLPGRALSRE   500
 501  WKRAFEEIDSKAEELMALIDLERDKCLRPLKEDVPRSSLSAVTVGDCTSH   550
 551  AQSMDMFVITPKGQIMTNDNVCLTYRQQKLGVIKMLKNRNATTSNVMLAQ   600
 601  CASDSSQLWTYDMDTQQISHRDTKLCLTLKAATNSRLQKVEKVVLSMECD   650
 651  FKDITQKWGFIPLPWRM                                    667

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.)

Go back to the NucPred Home Page.