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

NucPred

Fetching P22793 from www.uniprot.org...

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

   1  MSPLLRSIFNITKIFNQYASHDCDGTTLSKKDLKNLLEREFGEILRKPHD    50
  51  PETVDLVLELQDRDRDGLIDFHEFLAIVFKVAAACYYALGQASGLNEKEA   100
 101  KCERKGNPLQDRRREDQRRFEPQDRQLEERRLKRQELEELAEEEELREKQ   150
 151  VRREQRLQRREQEEYGGEEELQQRPKGRELEELLNREQRFERQEQRERQR   200
 201  LQVEQQQRQRGELRERQEEVQLQKRETQELQRERLEEEQQLQKQKRGLEE   250
 251  RLLEQERREQELRRKEQERREQQLRQEQEEATQEEISERGESRTSRCQWQ   300
 301  LESEADARQRKVYSRPHRQEQQSRRQEQELLERQQEQQISEEVQSLQEDQ   350
 351  GRQRLKQEQRYDQNWRWQLEEESQRRRYTLYAKPAQREQVREEEQLRLKE   400
 401  EKLQREKRRQERERQYREVELQREEERLQREEEQLQREEREKRRRQEREK   450
 451  QYLEKVELWEEEQLQREEREKRRQEREKQYLEKVELREEEQLQRQEREKR   500
 501  RQERERQYLEKVELQEEEQLQREEREKRRQERERQYLEKVELQEEEQLQR   550
 551  QEREKRRQEREKQYLEKVELQEEEQLQRQERQKRRQEREKQYLEKVELQE   600
 601  EEQLQRQEREKRRQERERQYLEKVELQEEEQVQRQEREKRRQERERQYLE   650
 651  KELQRQEERLQEEEQLLREEREKRRQERERQYLEKVELQEEEQLQREERE   700
 701  KRRQERERQYLEKEELQRQEERLQREKEQLQREDREKRRQVRERKYLEEE   750
 751  LQQEEDRLQREKQLLREDREKRQYLEKVELQREEEQLQREKRRQERERQY   800
 801  REEELLREEERLHRKEQQLQREECEKRRRQELERQLEEEELQRLDRKRQF   850
 851  RDDDQHQNEVRNSRVYSKHRENKEKSRQLDDSWVRESQFQQDLRPLQDEQ   900
 901  EEKREREQEWRSRQKRDSQFPAEQLLEREQQKETERRDRKFREEEQLLKG   950
 951  QREEKIRYLEEDRKFREEEQQLRRLEREQQLRQERDRKFREELSRQERDR  1000
1001  KFREEEQLLQEREEQLRRQERDRKFREEEQLLQEREEQLRRQERDRKFRE  1050
1051  EEQLLQEREEQLRRQERDRKFREEEQQLRLLEREQQLRQERNRKFREEQL  1100
1101  LREREEQLRLQEGEPQLRQKRDRKFHEEEQLLQEREEQLRRQERDRKFRE  1150
1151  EAQILKEREEQLRRQERDRKFREEEQLLQEREELRRQEREPQLRQERDRK  1200
1201  FREEEQLLQEREKLRRQEREPQLRQERDRKFHEEEQLLQEREEQLRRQER  1250
1251  DRKFREEAQLLQEREEQLRRQERDRKFREEEQLLQEREEQLRRQERDRKF  1300
1301  REEEQLLQEREEQLRRQERDRKFREEEQLLKESEEQLRRQERDRKFHEKE  1350
1351  HLLREREEQQLRRQELEGVFSQEEQLRRAEQEEEQRRQRQRDRKFLEEEQ  1400
1401  SLQREREEEKRRVQEQDRKFLEQEEQLHREEQEELRRRQQLDQQYRAEEQ  1450
1451  FAREEKRRRQEQELRQEEQRRRQERERKFREEEQLRRQQQEEQKRRQERD  1500
1501  VQQSRRQVWEEDKGRRQVLEAGKRQFASAPVRSSPLYEYIQEQRSQYRP   1549

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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