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

NucPred

Fetching Q8IZU2 from www.uniprot.org...

The NucPred score for your sequence is 0.33 (see score help below)

   1  MAWMTYISNWFEQDDWYEGLQRANMSQVRQVGLLAAGCQPWNKDVCAASG    50
  51  DRFAYCATLAIYIYQLDHRYNEFKLHAIMSEHKKTITAISWCPHNPDLFA   100
 101  SGSTDNLVIIWNVAEQKVIAKLDSTKGIPASLSWCWNAEDVVAFVSHRGP   150
 151  LFIWTISGPDSGVIVHKDAHSFLSDICMFRWHTHQKGKVVFGHIDGSLSI   200
 201  FHPGNKNQKHVLRPESLEGTDEEDPVTALEWDPLSTDYLLVVNLHYGIRL   250
 251  VDSESLSCITTFNLPSAAASVQCLAWVPSAPGMFITGDSQVGVLRIWNVS   300
 301  RTTPIDNLKLKKTGFHCLHVLNSPPRKKFSVQSPTKNHYTSSTSEAVPPP   350
 351  TLTQNQAFSLPPGHAVCCFLDGGVGLYDMGAKKWDFLRDLGHVETIFDCK   400
 401  FKPDDPNLLATASFDGTIKVWDINTLTAVYTSPGNEGVIYSLSWAPGGLN   450
 451  CIAGGTSRNGAFIWNVQKGKIIQRFNEHGTNGIFCIAWSHKDSKRIATCS   500
 501  SDGFCIIRTIDGKVLHKYKHPAAVFGCDWSQNNKDMIATGCEDTNVRVYY   550
 551  VATSSDQPLKVFSGHTAKVFHVKWSPLREGILCSGSDDGTVRIWDYTQDA   600
 601  CINILNGHTAPVRGLMWNTEIPYLLISGSWDYTIKVWDTREGTCVDTVYD   650
 651  HGADVYGLTCHPSRPFTMASCSRDSTVRLWSLTALVTPVQINILADRSWE   700
 701  EIIGNTDYAIEPGTPPLLCGKVSRDIRQEIEKLTANSQVKKLRWFSECLS   750
 751  PPGGSDNLWNLVAVIKGQDDSLLPQNYCKGIMHLKHLIKFRTSEAQELTT   800
 801  VKMSKFGGGIGVPAKEERLKEAAEIHLRLGQIQRYCELMVELGEWDKALS   850
 851  IAPGVSVKYWKKLMQRRADQLIQEDKDDVIPYCIAIGDVKKLVHFFMSRG   900
 901  QLKEALLVAQAACEGNMQPLHVSVPKGASYSDDIYKEDFNELLHKVSKEL   950
 951  AEWYFQDGRAVLAACCHLAIDNIELAMAYLIRGNELELAVCVGTVLGESA  1000
1001  APATHYALELLARKCMMISVCFPCVGYSVPFCYVNRNLAADLLLMIPDNE  1050
1051  LHLIKLCAFYPGCTEEINDLHDKCKLPTVEECMQLAETARADDNIFETVK  1100
1101  YYLLSQEPEKALPIGISFVKEYISSSDWTLDTIYPVLDLLSYIRTEKLLL  1150
1151  HTCTEARNELLILCGYIGALLAIRRQYQSIVPALYEYTSQLLKRREVSVP  1200
1201  LKIEYLSEELDAWRACTQSTNRSLEDSPYTPPSDSQRMIYATLLKRLKEE  1250
1251  SLKGIIGPDYVTGSNLPSHSDIHISCLTGLKIQGPVFFLEDGKSAISLND  1300
1301  ALMWAKVNPFSPLGTGIRLNPF                              1322

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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