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

NucPred

Fetching Q9USI6 from www.uniprot.org...

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

   1  MTEVISNKITAKDGATSLKDIDDKRWVWISDPETAFTKAWIKEDLPDKKY    50
  51  VVRYNNSRDEKIVGEDEIDPVNPAKFDRVNDMAELTYLNEPAVTYNLEQR   100
 101  YLSDQIYTYSGLFLVAVNPYCGLPIYTKDIIQLYKDKTQERKLPHVFAIA   150
 151  DLAYNNLLENKENQSILVTGESGAGKTENTKRIIQYLAAIASSTTVGSSQ   200
 201  VEEQIIKTNPVLESFGNARTVRNNNSSRFGKFIKVEFSLSGEISNAAIEW   250
 251  YLLEKSRVVHQNEFERNYHVFYQLLSGADTALKNKLLLTDNCNDYRYLKD   300
 301  SVHIIDGVDDKEEFKTLLAAFKTLGFDDKENFDLFNILSIILHMGNIDVG   350
 351  ADRSGIARLLNPDEIDKLCHLLGVSPELFSQNLVRPRIKAGHEWVISARS   400
 401  QTQVISSIEALAKAIYERNFGWLVKRLNTSLNHSNAQSYFIGILDIAGFE   450
 451  IFEKNSFEQLCINYTNEKLQQFFNHHMFVLEQEEYMKEEIVWDFIDFGHD   500
 501  LQPTIDLIEKANPIGILSCLDEECVMPKATDATFTSKLDALWRNKSLKYK   550
 551  PFKFADQGFILTHYAADVPYSTEGWLEKNTDPLNENVAKLLAQSTNKHVA   600
 601  TLFSDYQETETKTVRGRTKKGLFRTVAQRHKEQLNQLMNQFNSTQPHFIR   650
 651  CIVPNEEKKMHTFNRPLVLGQLRCNGVLEGIRITRAGFPNRLPFNDFRVR   700
 701  YEIMAHLPTGTYVESRRASVMILEELKIDEASYRIGVSKIFFKAGVLAEL   750
 751  EERRVATLQRLMTMLQTRIRGFLQRKIFQKRLKDIQAIKLLQANLQVYNE   800
 801  FRTFPWAKLFFNLRPLLSSTQNDKQLKKRDAEIIELKYELKKQQNSKSEV   850
 851  ERDLVETNNSLTAVENLLTTERAIALDKEEILRRTQERLANIEDSFSETK   900
 901  QQNENLQRESASLKQINNELESELLEKTSKVETLLSEQNELKEKLSLEEK   950
 951  DLLDTKGELESLRENNATVLSEKAEFNEQCKSLQETIVTKDAELDKLTKY  1000
1001  ISDYKTEIQEMRLTNQKMNEKSIQQEGSLSESLKRVKKLERENSTLISDV  1050
1051  SILKQQKEELSVLKGVQELTINNLEEKVNYLEADVKQLPKLKKELESLND  1100
1101  KDQLYQLQATKNKELEAKVKECLNNIKSLTKELENKEEKCQNLSDASLKY  1150
1151  IELQEIHENLLLKVSDLENYKKKYEGLQLDLEGLKDVDTNFQELSKKHRD  1200
1201  LTFNHESLLRQSASYKEKLSLASSENKDLSNKVSSLTKQVNELSPKASKV  1250
1251  PELERKITNLMHEYSQLGKTFEDEKRKALIASRDNEELRSLKSELESKRK  1300
1301  LEVEYQKVLEEVKTTRSLRSEVTLLRNKVADHESIRSKLSEVEMKLVDTR  1350
1351  KELNSALDSCKKREAEIHRLKEHRPSGKENNIPAVKTTEPVLKNIPQRKT  1400
1401  IFDLQQRNANQALYENLKRDYDRLNLEKHNLEKQVNELKGAEVSPQPTGQ  1450
1451  SLQHVNLAHAIELKALKDQINSEKAKMFSVQVQYEKREQELQKRIASLEK  1500
1501  VNKDSLIDVRALRDRIASLEDELRAA                          1526

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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