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

NucPred

Fetching Q12888 from www.uniprot.org...

The NucPred score for your sequence is 0.94 (see score help below)

   1  MDPTGSQLDSDFSQQDTPCLIIEDSQPESQVLEDDSGSHFSMLSRHLPNL    50
  51  QTHKENPVLDVVSNPEQTAGEERGDGNSGFNEHLKENKVADPVDSSNLDT   100
 101  CGSISQVIEQLPQPNRTSSVLGMSVESAPAVEEEKGEELEQKEKEKEEDT   150
 151  SGNTTHSLGAEDTASSQLGFGVLELSQSQDVEENTVPYEVDKEQLQSVTT   200
 201  NSGYTRLSDVDANTAIKHEEQSNEDIPIAEQSSKDIPVTAQPSKDVHVVK   250
 251  EQNPPPARSEDMPFSPKASVAAMEAKEQLSAQELMESGLQIQKSPEPEVL   300
 301  STQEDLFDQSNKTVSSDGCSTPSREEGGCSLASTPATTLHLLQLSGQRSL   350
 351  VQDSLSTNSSDLVAPSPDAFRSTPFIVPSSPTEQEGRQDKPMDTSVLSEE   400
 401  GGEPFQKKLQSGEPVELENPPLLPESTVSPQASTPISQSTPVFPPGSLPI   450
 451  PSQPQFSHDIFIPSPSLEEQSNDGKKDGDMHSSSLTVECSKTSEIEPKNS   500
 501  PEDLGLSLTGDSCKLMLSTSEYSQSPKMESLSSHRIDEDGENTQIEDTEP   550
 551  MSPVLNSKFVPAENDSILMNPAQDGEVQLSQNDDKTKGDDTDTRDDISIL   600
 601  ATGCKGREETVAEDVCIDLTCDSGSQAVPSPATRSEALSSVLDQEEAMEI   650
 651  KEHHPEEGSSGSEVEEIPETPCESQGEELKEENMESVPLHLSLTETQSQG   700
 701  LCLQKEMPKKECSEAMEVETSVISIDSPQKLAILDQELEHKEQEAWEEAT   750
 751  SEDSSVVIVDVKEPSPRVDVSCEPLEGVEKCSDSQSWEDIAPEIEPCAEN   800
 801  RLDTKEEKSVEYEGDLKSGTAETEPVEQDSSQPSLPLVRADDPLRLDQEL   850
 851  QQPQTQEKTSNSLTEDSKMANAKQLSSDAEAQKLGKPSAHASQSFCESSS   900
 901  ETPFHFTLPKEGDIIPPLTGATPPLIGHLKLEPKRHSTPIGISNYPESTI   950
 951  ATSDVMSESMVETHDPILGSGKGDSGAAPDVDDKLCLRMKLVSPETEASE  1000
1001  ESLQFNLEKPATGERKNGSTAVAESVASPQKTMSVLSCICEARQENEARS  1050
1051  EDPPTTPIRGNLLHFPSSQGEEEKEKLEGDHTIRQSQQPMKPISPVKDPV  1100
1101  SPASQKMVIQGPSSPQGEAMVTDVLEDQKEGRSTNKENPSKALIERPSQN  1150
1151  NIGIQTMECSLRVPETVSAATQTIKNVCEQGTSTVDQNFGKQDATVQTER  1200
1201  GSGEKPVSAPGDDTESLHSQGEEEFDMPQPPHGHVLHRHMRTIREVRTLV  1250
1251  TRVITDVYYVDGTEVERKVTEETEEPIVECQECETEVSPSQTGGSSGDLG  1300
1301  DISSFSSKASSLHRTSSGTSLSAMHSSGSSGKGAGPLRGKTSGTEPADFA  1350
1351  LPSSRGGPGKLSPRKGVSQTGTPVCEEDGDAGLGIRQGGKAPVTPRGRGR  1400
1401  RGRPPSRTTGTRETAVPGPLGIEDISPNLSPDDKSFSRVVPRVPDSTRRT  1450
1451  DVGAGALRRSDSPEIPFQAAAGPSDGLDASSPGNSFVGLRVVAKWSSNGY  1500
1501  FYSGKITRDVGAGKYKLLFDDGYECDVLGKDILLCDPIPLDTEVTALSED  1550
1551  EYFSAGVVKGHRKESGELYYSIEKEGQRKWYKRMAVILSLEQGNRLREQY  1600
1601  GLGPYEAVTPLTKAADISLDNLVEGKRKRRSNVSSPATPTASSSSSTTPT  1650
1651  RKITESPRASMGVLSGKRKLITSEEERSPAKRGRKSATVKPGAVGAGEFV  1700
1701  SPCESGDNTGEPSALEEQRGPLPLNKTLFLGYAFLLTMATTSDKLASRSK  1750
1751  LPDGPTGSSEEEEEFLEIPPFNKQYTESQLRAGAGYILEDFNEAQCNTAY  1800
1801  QCLLIADQHCRTRKYFLCLASGIPCVSHVWVHDSCHANQLQNYRNYLLPA  1850
1851  GYSLEEQRILDWQPRENPFQNLKVLLVSDQQQNFLELWSEILMTGGAASV  1900
1901  KQHHSSAHNKDIALGVFDVVVTDPSCPASVLKCAEALQLPVVSQEWVIQC  1950
1951  LIVGERIGFKQHPKYKHDYVSH                              1972

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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