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

NucPred

Fetching P38873 from www.uniprot.org...

The NucPred score for your sequence is 0.82 (see score help below)

   1  MPEIYGPQPLKPLNTVMRHGFEEQYQSDQLLQSLANDFIFYFDDKRHKTN    50
  51  GNPIPEEDKQRDVNRYYQPITDWKIMKDRQKTVSAALLLCLNLGVDPPDV   100
 101  MKTHPCARVEAWVDPLNFQDSKKAIEQIGKNLQAQYETLSLRTRYKQSLD   150
 151  PCVEDVKRFCNSLRRTSKEDRILFHYNGHGVPKPTKSGEIWVFNRGYTQY   200
 201  IPVSLYDLQTWLGAPCIFVYDCNSAENILINFQKFVQKRIKDDEEGNHDV   250
 251  AAPSPTSAYQDCFQLASCTSDELLLMSPELPADLFSCCLTCPIEISIRIF   300
 301  LMQSPLKDSKYKIFFENSTSNQPFGDSKNSFKSKIPNVNIPGMLSDRRTP   350
 351  LGELNWIFTAITDTIAWTSLPRPLFKKLFRHDLMIAALFRNFLLAKRIMP   400
 401  WYNCHPVSDPELPDSITTHPMWKSWDLAMDEVLTKIVIDLKNAPPATALE   450
 451  SQMILQQQETLQNGGSSKSNAQDTKAGSIQTQSRFAVANLSTMSLVNNPA   500
 501  LQSRKSISLQSSQQQLQQQQQQQQQFTGFFEQNLTAFELWLKYASNVRHP   550
 551  PEQLPIVLQVLLSQVHRIRALVLLSRFLDLGPWAVYLSLSIGIFPYVLKL   600
 601  LQSPAPELKPILVFIWARIMSIDYKNTQSELIKEKGYMYFVTVLVPDWGV   650
 651  NGMSATNGSAMINSGNPLTMTASQNINGPSSRYYERQQGNRTSNLGHNNL   700
 701  PFYHSNDTTDEQKAMAVFVLASFVRNFPLGQKNCFSLELVNKLCFYIDNS   750
 751  EIPLLRQWCVILLGLLFADNPLNRFVCMNTGAVEILLKSLKDPVPEVRTA   800
 801  SIFALKHFISGFQDAEVILRLQQEFEEQYQQLHSQLQHLQNQSHLQQQQS   850
 851  QQQQQHLEQQQMKIEKQIRHCQVMQNQLEVIDLRKLKRQEIGNLISILPL   900
 901  INDGSSLVRKELVVYFSHIVSRYSNFFIVVVFNDLLEEIKLLEKSDINTR   950
 951  NTSDKYSVSQGSIFYTVWKSLLILAEDPFLENKELSKQVIDYILLELSAH  1000
1001  KELGGPFAVMEKFLLKRSSKAHQTGKFGFNSSQVQFVKSSLRSFSPNERV  1050
1051  DNNAFKKEQQQHDPKISHPMRTSLAKLFQSLGFSESNSDSDTQSSNTSMK  1100
1101  SHTSKKGPSGLYLLNGNNNIYPTAETPRFRKHTEPLQLPLNSSFLDYSRE  1150
1151  YFQEPQMKKQEADEPGSVEYNARLWRRNRNETIIQETQGEKKLSIYGNWS  1200
1201  KKLISLNNKSQPKLMKFAQFEDQLITADDRSTITVFDWEKGKTLSKFSNG  1250
1251  TPFGTKVTDLKLINEDDSALLLTGSSDGVIKIYRDYQDVDTFKIVSAWRG  1300
1301  LTDMLLTPRSTGLLTEWLQIRGSLLTTGDVKVIRVWDAHTETVEVDIPAK  1350
1351  TSSLITSLTADQLAGNIFVAGFADGSLRVYDRRLDPRDSMIRRWRAGNDK  1400
1401  QGVWINNVHLQRGGYRELVSGATNGVVELWDIRSEDPVESFVDQNVTSQY  1450
1451  GSQQKPTTMTCMQVHEHAPIIATGTKQIKIWTTSGDLLNSFKNSHNNGVT  1500
1501  STLAATGIPKSLSYSSTSDAFLSSMAFHPHRMMIAATNSHDSIVNIYKCE  1550
1551  DERIDYF                                             1557

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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