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

NucPred

Fetching Q09449 from www.uniprot.org...

The NucPred score for your sequence is 0.77 (see score help below)

   1  MLPTSSNNEENRKPENSFPPTHFDTWERLSDYQKPSSSTTDDAYGKPVAK    50
  51  ISPTASIDERETGIIGSTLRQDSTDSDSTGSSNMNPYDRLDKEVISKKNA   100
 101  HTNSYRNDVDELEGSLRTLGLQKVNAPTISSFSAWKSQSSALPAPSSSET   150
 151  SKIVKAEIKAPQQPMSLNPNYFDVMREMEKSMNIFTKLFRGSQIRNKNDL   200
 201  PSGRHLVNYRQNHAFDFAAMSHIWKENKMENLPKLPHRANLVMTLPSSRV   250
 251  RNSKICAFYRVLEKKEDKYILVACHVNIHGFHRGDLRFVEVNNRTVLKGF   300
 301  ERSSVIGHLFLGDILTVTELTRCNETVSNVASSVEDASPDAPCQWMASKV   350
 351  VLFPRHEPVNVQFKFTCNGMASVVSTNEPMSVILNNLTEAKTNVEYTGIA   400
 401  FKSASYTVHTEDYTKKWYERIQEEISNIMIYPKALSTIYQYEEYTPNFVV   450
 451  EKQEQEEHPYQQDLEDLDLYRQHEMQTNVFTKFFDIGKSEKRKFGPGKSI   500
 501  SNCRHSDAIDFAAMSYIWKNIRQQHLPKLPKLPNMVLPLPTSMPLDSEIC   550
 551  AFYRVLVENKSKYILIACHMNVHGYHRGDLRFLEINESTKLYGFEGRSVI   600
 601  GQLFLGDIVAVTELARCNGHGSDAFKIPFDVSMSSQNTCTWMASKITLPS   650
 651  RPPPASVLFSFMKNRMAVVKGCDEPMNVEVKSIQNVEPDLIYKGTAFKPE   700
 701  KPELNFTEGFIKKKRHQIGSITLRIASYPNSFGTIYNFQESDIDNEHYKI   750
 751  GINAFSEEKFTEISLDEREKIVETCSLMGFSAANTIFNGRFDCRAFKMEE   800
 801  IKKNGMTVMFCIENPTSQPTLGLWCAGNRIVIGGPNGDVNGAIETVIDDP   850
 851  DIGYLRIAARLSRDIPKKFSFKGDGEFFVSQREVFENEILDDGYFKTLDP   900
 901  GCNGRRIIETLYGGKPLERVVVDKRDSSIERMMSQLFGVGSGISEHKTSG   950
 951  KKSEDTPTQFYFPSTPEPLALNKYQCEYVQMLLDGNPLIIGSSPFGCGKS  1000
1001  MTIITAALELYKLKKNRKQLLITQSNYASVNLIDIAQRVCLSGDDDLKDL  1050
1051  KFVRFVSEKNWNELPSNCRTDSDMPYLMNKLFKDWAMGRIDLTNLTCLKT  1100
1101  HHYVQMVSHIIKNDLVNPMLFGDHIAQIYDKLSADFSRAPHAQTLVEAFF  1150
1151  MIYKPDLVMVTADSAKGLLNILRDVCAVQIDEASQLAECTLLGLLKSFNN  1200
1201  ASFGLIGDIHQLPPYCEEGLEGKLKDFGIGNTMERAIKEKMFPVCTLRNV  1250
1251  YRCHPKTTELLSELFYDGALVSGVSELARSDFMTKRDDFWPNPKFPMMFV  1300
1301  NNTGASTKMGTSTSNSSEKSIVGEIVQNLINDPRNPVNPSDIGVISFYSA  1350
1351  QTSILTEHLRGSGVKCGTVDAFQGSEKEIIIMCSTNERISDFMQLSNRLN  1400
1401  VAMSRAKQVTIIIGHLDGLRRANYWSTIVNKIEQNGNLVNANDWYQNQRR  1450
1451  NKVSLSSYPLISTSRQSKQQRANEYNSQHKHVKRQSNNDYGSQRSVTNSL  1500
1501  NPEFVGKWDDETYGDWPTIQKST                             1523

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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