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

NucPred

Fetching O60271 from www.uniprot.org...

The NucPred score for your sequence is 0.81 (see score help below)

   1  MELEDGVVYQEEPGGSGAVMSERVSGLAGSIYREFERLIGRYDEEVVKEL    50
  51  MPLVVAVLENLDSVFAQDQEHQVELELLRDDNEQLITQYEREKALRKHAE   100
 101  EKFIEFEDSQEQEKKDLQTRVESLESQTRQLELKAKNYADQISRLEEREA   150
 151  ELKKEYNALHQRHTEMIHNYMEHLERTKLHQLSGSDQLESTAHSRIRKER   200
 201  PISLGIFPLPAGDGLLTPDAQKGGETPGSEQWKFQELSQPRSHTSLKVSN   250
 251  SPEPQKAVEQEDELSDVSQGGSKATTPASTANSDVATIPTDTPLKEENEG   300
 301  FVKVTDAPNKSEISKHIEVQVAQETRNVSTGSAENEEKSEVQAIIESTPE   350
 351  LDMDKDLSGYKGSSTPTKGIENKAFDRNTESLFEELSSAGSGLIGDVDEG   400
 401  ADLLGMGREVENLILENTQLLETKNALNIVKNDLIAKVDELTCEKDVLQG   450
 451  ELEAVKQAKLKLEEKNRELEEELRKARAEAEDARQKAKDDDDSDIPTAQR   500
 501  KRFTRVEMARVLMERNQYKERLMELQEAVRWTEMIRASRENPAMQEKKRS   550
 551  SIWQFFSRLFSSSSNTTKKPEPPVNLKYNAPTSHVTPSVKKRSSTLSQLP   600
 601  GDKSKAFDFLSEETEASLASRREQKREQYRQVKAHVQKEDGRVQAFGWSL   650
 651  PQKYKQVTNGQGENKMKNLPVPVYLRPLDEKDTSMKLWCAVGVNLSGGKT   700
 701  RDGGSVVGASVFYKDVAGLDTEGSKQRSASQSSLDKLDQELKEQQKELKN   750
 751  QEELSSLVWICTSTHSATKVLIIDAVQPGNILDSFTVCNSHVLCIASVPG   800
 801  ARETDYPAGEDLSESGQVDKASLCGSMTSNSSAETDSLLGGITVVGCSAE   850
 851  GVTGAATSPSTNGASPVMDKPPEMEAENSEVDENVPTAEEATEATEGNAG   900
 901  SAEDTVDISQTGVYTEHVFTDPLGVQIPEDLSPVYQSSNDSDAYKDQISV   950
 951  LPNEQDLVREEAQKMSSLLPTMWLGAQNGCLYVHSSVAQWRKCLHSIKLK  1000
1001  DSILSIVHVKGIVLVALADGTLAIFHRGVDGQWDLSNYHLLDLGRPHHSI  1050
1051  RCMTVVHDKVWCGYRNKIYVVQPKAMKIEKSFDAHPRKESQVRQLAWVGD  1100
1101  GVWVSIRLDSTLRLYHAHTYQHLQDVDIEPYVSKMLGTGKLGFSFVRITA  1150
1151  LMVSCNRLWVGTGNGVIISIPLTETNKTSGVPGNRPGSVIRVYGDENSDK  1200
1201  VTPGTFIPYCSMAHAQLCFHGHRDAVKFFVAVPGQVISPQSSSSGTDLTG  1250
1251  DKAGPSAQEPGSQTPLKSMLVISGGEGYIDFRMGDEGGESELLGEDLPLE  1300
1301  PSVTKAERSHLIVWQVMYGNE                               1321

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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