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

NucPred

Fetching P35992 from www.uniprot.org...

The NucPred score for your sequence is 0.90 (see score help below)

   1  MLYQLSKATTRIRLKRQKAVPQHRWLWSLAFLAAFTLKDVRCADLAISIP    50
  51  NNPGLDDGASYRLDYSPPFGYPEPNTTIASREIGDEIQFSRALPGTKYNF   100
 101  WLYYTNFTHHDWLTWTVTITTAPDPPSNLSVQVRSGKNAIILWSPPTQGS   150
 151  YTAFKIKVLGLSEASSSYNRTFQVNDNTFQHSVKELTPGATYQVQAYTIY   200
 201  DGKESVAYTSRNFTTKPNTPGKFIVWFRNETTLLVLWQPPYPAGIYTHYK   250
 251  VSIEPPDANDSVLYVEKEGEPPGPAQAAFKGLVPGRAYNISVQTMSEDEI   300
 301  SLPTTAQYRTVPLRPLNVTFDRDFITSNSFRVLWEAPKGISEFDKYQVSV   350
 351  ATTRRQSTVPRSNEPVAFFDFRDIAEPGKTFNVIVKTVSGKVTSWPATGD   400
 401  VTLRPLPVRNLRSINDDKTNTMIITWEADPASTQDEYRIVYHELETFNGD   450
 451  TSTLTTDRTRFTLESLLPGRNYSLSVQAVSKKMESNETSIFVVTRPSSPI   500
 501  IEDLKSIRMGLNISWKSDVNSKQEQYEVLYSRNGTSDLRTQKTKESRLVI   550
 551  KNLQPGAGYELKVFAVSHDLRSEPHAYFQAVYPNPPRNMTIETVRSNSVL   600
 601  VHWSPPESGEFTEYSIRYRTDSEQQWVRLPSVRSTEADITDMTKGEKYTI   650
 651  QVNTVSFGVESPVPQEVNTTVPPNPVSNIIQLVDSRNITLEWPKPEGRVE   700
 701  SYILKWWPSDNPGRVQTKNVSENKSADDLSTVRVLIGELMPGVQYKFDIQ   750
 751  TTSYGILSGITSLYPRTMPLIQSDVVVANGEKEDERDTITLSYTPTPQSS   800
 801  SKFDIYRFSLGDAEIRDKEKLANDTDRKVTFTGLVPGRLYNITVWTVSGG   850
 851  VASLPIQRQDRLYPEPITQLHATNITDTEISLRWDLPKGEYNDFDIAYLT   900
 901  ADNLLAQNMTTRNEITISDLRPHRNYTFTVVVRSGTESSVLRSSSPLSAS   950
 951  FTTNEAVPGRVERFHPTDVQPSEINFEWSLPSSEANGVIRQFSIAYTNIN  1000
1001  NLTDAGMQDFESEEAFGVIKNLKPGETYVFKIQAKTAIGFGPEREYRQTM  1050
1051  PILAPPRPATQVVPTEVYRSSSTIQIRFRKNYFSDQNGQVRMYTIIVAED  1100
1101  DAKNASGLEMPSWLDVQSYSVWLPYQAIDPYYPFENRSVEDFTIGTENCD  1150
1151  NHKIGYCNGPLKSGTTYRVKVRAFTGADKFTDTAYSFPIQTDQDNTSLIV  1200
1201  AITVPLTIILVLLVTLLFYKRRRNNCRKTTKDSRANDNMSLPDSVIEQNR  1250
1251  PILIKNFAEHYRLMSADSDFRFSEEFEELKHVGRDQPCTFADLPCNRPKN  1300
1301  RFTNILPYDHSRFKLQPVDDDEGSDYINANYVPGHNSPREFIVTQGPLHS  1350
1351  TRDDFWRMCWESNSRAIVMLTRCFEKGREKCDQYWPNDTVPVFYGDIKVQ  1400
1401  ILNDSHYADWVMTEFMLCRGSEQRILRHFHFTTWPDFGVPNPPQTLVRFV  1450
1451  RAFRDRIGAEQRPIVVHCSAGVGRSGTFITLDRILQQINTSDYVDIFGIV  1500
1501  YAMRKERVWMVQTEQQYICIHQCLLAVLEGKENIVGPAREMHDNEGYEGQ  1550
1551  QVQLDENGDVVATIEGHLSHHDLQQAEAEAIDDENAAILHDDQQPLTSSF  1600
1601  TGHHTHMPPTTSMSSFGGGGGGHTNVDAPDRXHSVVNQSDNNNSVVIVLV  1650
1651  DNKPSSMICKDSKGGNIDVLESQQQQQQQQQQQPNQGGHNITTISAINGY  1700
1701  NTLQHRRKSQLITFSSSSCDIKNSLSHEYINGSNGSAANGPPSSGSGSGS  1750
1751  GPGSNRASRANVRLSFAEEDVMILPQNHSQQSNHQDDEVFTRRRSLLEVE  1800
1801  IGVEVGEDGELAPHEMEEDLEEEDEDEELYMHDEFETHIDTKSNNANDDS  1850
1851  GGGSYEDSHALHSSLGGSNRNSLEKDDDDIEVDVISTDVSCYDQLLGSSC  1900
1901  NTRNGDDDDIATLVGDGDYSTTKLSKASRLSGAGVGGLVVSGGGGGTAIG  1950
1951  GGIAVNGGGVLGNGVGSEAGGGIIYANPFMDDEGIAESGM            1990

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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