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

NucPred

Fetching P87253 from www.uniprot.org...

The NucPred score for your sequence is 0.92 (see score help below)

   1  MNDEDKVHDISKKIEREKALINAAQAMRQQTNNEQVRSKLDTQMREGRRN    50
  51  LEFFEEKLRELQMRRLGHGVDNMSLGASPMSGSHRQSVDDFEGYGAPSPP   100
 101  PKEDVRGHSSHQSQGSGPLMPASAPYPGGPPDSNVPRARPNYTRLDLIKF   150
 151  DTPHLGPRIQLMLSQIQFKLNVEEQYLKGIEKMVQLYQMEGDKKSKLDAA   200
 201  AKRVESKQKIVLLKQALKRYEELHIDIDVDGPDDDSINLPALRKPLSGTL   250
 251  SIRILAVKDVDHAPLGRFARSPETFIAVKAEDIVVARTKPSRNDKWEAEF   300
 301  HTFPVDKTNEIEFTVYDKPAEHPVPIAMLWVRISDIVEELRRKKIEAEMT   350
 351  SAGWVSADRVGSRAPPPQFPMGAQSPQFAAPPTSPGSQEQNTMIPPQAPP   400
 401  PSQVVSQPVDGWFNLEPYGQIHLSFNFIKGARPQGMDRLGRKGAVRQRKE   450
 451  EVHEMYGHKFVQKQFYNIMRCALCGDFLKYSAGMQCEDCKYTCHTKCYTS   500
 501  VVTKCISKSNAETDPDEEKINHRIPHRFIPFSNLTANWCCHCGYMLPIGS   550
 551  KKNSRKCSECALTAHAQCVHLVPDFCGMSMAVANQILEGMRTQKKTHKDK   600
 601  ASSMSERTLRPGSKTSISSGSIAQASTYSGSTAYTSIASPEATEAAKLMY   650
 651  SQTTPRPGGPDRTSTSSTTASAAAAAAMAPKHSSQPSQAGSIPDFGGSPG   700
 701  YGRPDSRDDEYSAQQQQGYGSPQQRKYNPADYANIDAYSSPQARPQQQQQ   750
 751  QQQQTPQQVSPMYQQNPQTPISKPQPVAPSYDNQVVPSASGVPVPTKKPL   800
 801  PSATDPGTGMRIGLDHFNFLAVLGKGNFGKVMLAETKKSRKLYAIKVLKK   850
 851  EFIIENDEVESIRSEKRVFLIANRERHPFLTNLHACFQTETRVYFVMEYI   900
 901  SGGDLMLHIQRGMFGTKRAQFYAAEVCLALKYFHENGVIYRDLKLDNILL   950
 951  TLDGHIKIADYGLCKEDMWYGSTTSTFCGTPEFMAPEILLDKKYGRAVDW  1000
1001  WAFGVLIYQMLLQQSPFRGEDEDEIYDAILADEPLYPIHMPRDSVSILQK  1050
1051  LLTREPDQRLGSGPTDAQEIMSQPFFRNINWDDIYHKRVQPPFLPQIKSA  1100
1101  TDTSNFDSEFTSVTPVLTPVQSVLSQAMQEEFRGFSYTADFE          1142

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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