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

NucPred

Fetching Q8LKW0 from www.uniprot.org...

The NucPred score for your sequence is 0.98 (see score help below)

   1  MPRRRRRRRAAPGGQVPPELRLAYGARALTLGRAVFSLLPSPRHCESPCP    50
  51  ACRGRVASGCLACRRWEHLLRDGDPVAYRRLITRAVCAIAADDLSAPPPP   100
 101  RYTPGNSGHSQARLVREMMKSIVADQSHGTKNVLCNGLHEGGQSICISDL   150
 151  VSSSSWSILLHRIGDLLMCYLLRCTSIFLPVKKNDYFQVSGVPLNVVLRN   200
 201  PIFASTVARKHQPQTTKAKCHTCYLWKSANMAENLSICHDSSNSGVNSSF   250
 251  SSTCKIVTQQSCETCGSIRRAESKDPSEGCNCPKFPSDGRSGECCNCYTH   300
 301  NTRKRKRLYSWQRRSKKKQVCSVDESSAEWSKLNGSNFNMSNGPSENLAG   350
 351  KMNDQAQSVELTVDNTSLARSNDDSSSEIKVINATILSSEKSPCSVFDIR   400
 401  GSQGLSCHYSLSEVQYQSTCPQVGPSSYLHLNSCSICFNCIISNASKHLS   450
 451  LDSLISRNGIFYNRRTTYSVFHCKHILSKRKRPDALSLVKHIFGINSCCA   500
 501  SLLKYNCHESTIRKSNCLCCWLPKSIKNLIRNSKRCQYKKLFLKHCSVKC   550
 551  KVAPDVTKNDGKAHYPPGGKAAYYDRSFSRLEAYSTHQQVASFVWAVLKR   600
 601  IVPKPLLGNSFGKRSLRTNIWKFIKLRRFETFQLSDCIGDLKVSHYSWLS   650
 651  NIEFSNCFCSAIIGKQTGSSTSAEEQKQKNILHCWISWLFSDIVIPVVRT   700
 701  YFYVTERESKRYDVFYYPKSVWRDLTSNAIASLNKKNFRILRGEPRKAVR   750
 751  HLNCSSRVRFLPKAKDMRPLVDLRAKSKDANLNKCHLIMKKLRDEKPEMF   800
 801  GSSVFDYNNVHQNLSQFISSKRSQLMKKLKVYIVVADVSKAFDCVSHDMV   850
 851  LKMIDDAFKCDEYTVRKCSKVICNRSKNSLYRFDSNASIGNGNSIYDLSI   900
 901  QLSSGGGIFVDQGTICRILKEQFHHLLYEQIKCNILKIGQKYYLQQVGIA   950
 951  QGSKLSPNLCSLYYGHLENSVLSKFLHDSKLNAGEAFSEPEYLLMRFIDD  1000
1001  FIFISFSLEHAQKFLNRMRRGFVFYNCYMNDSKYGFNFCAGNSEPSSNRL  1050
1051  YRGDDGVSFMPWSGLLINCETLEIQADYTRYLDITIISTITVKMHSSTKY  1100
1101  IHSKLCHYMRPKCHPIFYDSNINSPGTIRVNIYQAFLLCAMKFHCYIRSV  1150
1151  SDANVSKLELLQVIKRTFRYMHSLIVRRMQDVELHYNVRPVLKLRRKETI  1200
1201  WLGLTAYIRVLQQKQSRYKDMLTLLTAELGRYCHLGHECDTLRYAVDDSH  1250
1251  SSMFWKFKF                                           1259

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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