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

NucPred

Fetching P29551 from www.uniprot.org...

The NucPred score for your sequence is 0.83 (see score help below)

   1  MPGNVVSPKVLMDLIPKLKISMQETDKNEVIKNSEQHSSVSWDPDTCENL    50
  51  YITLEEQIESKDTLAREQALKALLLTLDATNKRVEPYLVRLLPRVLKQVG   100
 101  LEKVAAVRTQASTVAEDIIKTMNPYAVKTILSHVTNSIKTSGKWMEKMCA   150
 151  FRLLDMLVEKAPCQMSYRLPELIPILSESMWDTRTDIKNQARKTMTSVCT   200
 201  LISNPDIDKFIPVLIDCIAQPEKVPETIHTLGATTFVQEVHASTLSIMVP   250
 251  LLYRGLNERETTIKRKSAVIIDNMCKLVEDPYIIAPFLPKLIPTLEHIKE   300
 301  TIGDPECRSVVNRSLATLIRVGNVKEGKIPEVLNIAKPENCMETLLSILK   350
 351  GQELVPVSDVYLNYISCIASQLIDEKNNEVVDWDVNISPYLQPIILKADI   400
 401  NCIIDQFRKRSISGFHSSSAESEEEEGEDLCNCEFSLAYGAKILLNRTSL   450
 451  NLKRGYRYGLCGPNGSGKSTLLRSIFNGQLEGFPTELKTAYVEHDIDDTE   500
 501  SKTSVFDFIANDPSVVVKNKQEVISSLLEHSFTEDMLSIPISNLSGGWKM   550
 551  KLALVRAMLRQVDILLLDEPTNHLDVKNVAWLENFLTSQTHITSIIVSHD   600
 601  SKFLDNVVQAIIHYEHFKLKKYMGNMSKFITLVPSARSYQDISMSEIEFS   650
 651  FPEPGYLEGVKTKQRAICRMRDIEFQYEGTSEPQIKNVSLQVSLSSRIAV   700
 701  IGPNGAGKSTLIKVLCGELIPQKGEVWCHPNLRIAYVAQAAFVHLGSHEN   750
 751  KTPSEYIQWRYRTAEDSETIDRASRQLTENDEHLMNKIFKINGTSRKIQG   800
 801  IHSRRKLKNSYEYECSFLVGENVGEKNERWVPLPSMNNEWLPRGELIESH   850
 851  SKMVAEVDMKEALKSGSFRPLVRKEIEKHCESFGLDAEIVTHSRIKGLSG   900
 901  GQKVKLVLAAGSWLKPHVIVLDEPTNYLDRDSLGALSKALKSFEGGVVII   950
 951  THSVEFTKNLTEEVWSVQNGQMTPSGHNWVQGQGTGPRLQEQEEEDTFDA  1000
1001  LGNKIEAKKKAKKLTSSELRKKKKERMARRKKGEEVFSDEDD          1042

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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