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

NucPred

Fetching Q10185 from www.uniprot.org...

The NucPred score for your sequence is 0.49 (see score help below)

   1  MVLEQDLDPFVGGNWMNSAYKGFTFLSATWLAPNIYLLISGCLQYFYEVR    50
  51  KRSHYFHFRRFWTIWLKSLVIMVLLFTHIYDCYKTNESVWNVLSIITYFL   100
 101  ALFLHVVEQPTLRIPMASLLMFWLFKFLASALVLLLRPNYTMFPMLNVVP   150
 151  SITFFCSLVCLLAEIYVPPANRVWYPDDAAELEETGLRPSRFTYANIFSR   200
 201  ISFGWLSPLMKFGYRNYLTESDAWSLPPAERSSNLTIVFEKNWISHAKKK   250
 251  KSSLYMWGVLFLNHWKLTVVIIVLKLVQDVVAFIQPNLIRKIVIFVSSYS   300
 301  SEHPQPPQVGFSLAIAMFLTNVVQTALLQQYFQLGMVLGMRWRSELITAI   350
 351  YRKSLRLSSAARQSRSVGDIVNYMSVDTQKVCDLTMFLFVIVSGPFQIVL   400
 401  ALTNLYHLVGYGALSGAFVTFLLFPCNVVIASIFKRFQNRQMKNKDARSQ   450
 451  FMTEIINNIRSIKLYAWENIFLQKLLQLRNTRELRMLKKIGIVNTIGNFT   500
 501  WLFAPILVSAATFGTFIVLYGKTRVLSVDIVFACLSLFNLLQFPLTMLPI   550
 551  VVSSVLEASVAISRIYGFLTAGELDSNAVQRYPANKEPSGVCLEIKKGTF   600
 601  SWSGPGQNAAEPTLRDIDFVARRGELCCIVGKVGMGKSSLLEACLGNMQK   650
 651  HSGSVFRCGSIAYAAQQPWILNATIQENILFGLELDPEFYEKTIRACCLL   700
 701  RDFEILADGDQTEVGEKGISLSGGQKARISLARAVYSRSDIYLLDDILSA   750
 751  VDQHVNRDLVRNLLGSKGLLRSRCVILSTNSLTVLKEASMIYMLRNGKII   800
 801  ESGSFTQLSSSPDSQLFQLLSEFSKKDTASSTGADTPLSRSQSVITSSTD   850
 851  VTSSASRSSDTVSNYPKATIKGTGRIRKRLTDEDNVKATGQAAEKMERGK   900
 901  VKWKVYWTYFKACSLFLIFLYFLFIIGGIGMNVGTNVWLKHWSEVNTQLG   950
 951  YNPKPYFYLGIYTLFGLLSCALISLSSLTITVFCAIKSCRYLHDSMVKAV  1000
1001  LRAPMSFFETTPTGRILNRFSSDVYRVDEVISRVFMFFFRNLFQIVFVLA  1050
1051  VICYSSPMFMILIVPLFFLYRYNQVYYTQTSRELKRLDSVTRSPLYAHFQ  1100
1101  ESLGGLSTIRAYDMEDTFISENDIRVDTNHRIWFLYFSSNRWQAIRVEAI  1150
1151  GALVVFSSAFFGVLSAVRGNPNSGLVGLSLSYAVQITQSLTFVVRQSVDV  1200
1201  ETNIVSVERMLEYIGLPSEAPSIIPDHRPPEGWPSHGAIKFDHYSVRYRE  1250
1251  NLPLVLNDISVNIKPQEKIGIVGRTGAGKSTLTLALFRLIEPTSGDIQLD  1300
1301  DINITSIGLHDLRSRLAIIPQENQAFEGTIRENLDPNANATDEEIWHALE  1350
1351  AASLKQFIQTLDGGLYSRVTEGGANLSSGQRQLMCLTRALLTPTRVLLLD  1400
1401  EATAAVDVETDAIVQRTIRERFNDRTILTIAHRINTVMDSNRILVLDHGK  1450
1451  VVEFDSTKKLLENKASLFYSLAKESGLI                        1478

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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