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

NucPred

Fetching Q19954 from www.uniprot.org...

The NucPred score for your sequence is 0.39 (see score help below)

   1  MDETHENEASDSFDPVFENSYHDDVTFNTEDDDEPPLEPRFKYERLKGEE    50
  51  TLPFMKTATFTSIDLHDKFIAIGTATGLIYILDHHGYGNFDSVPPLKPHR   100
 101  CAVSKVKFDETGSYVLSCANDSKIVVSGVGNDKLCCTINIQVMPKSIYFS   150
 151  PDFIRQQSGHCFIMGERNLVLYEKRMFQYKASSLYSGSERDGFIHCCSWN   200
 201  ENLIAFTNDTGTRVYERGAERIITSVQPSHDVDRVRSSRSPPKHTWMPEN   250
 251  NLVIGWADTVTILKIRDDDGVKKGEVHHIFHVSMFICGISYIPESGIDNM   300
 301  ELFLVGLQLEGEDFDDCASVISTVTTLTALESSACTILKTSVIRPLGLKE   350
 351  FELQSEDMIESVKLSNHTLPYMIHGLGIPYLATYFILTTKHIIMAVPYGP   400
 401  EDGIRWRLKYKLYDEALDMAKHNADLLSKTDLSPKKVGRMIIEGYLTGKR   450
 451  ARAAASRLPLICGECKEEWEWAVNQFEEVKLCTLLAEVLPDGTPTLDPEC   500
 501  YQKVLIACLFNNVKQFRKLVQTWSPDLYMTSFIIDRTQWRIQQISKSGNL   550
 551  ADVDETERVLMDALAHLYLYERKYESALKILMSCQDFQIFNVIDKHQLFD   600
 601  LVKDQITELMNINSERALRLLLDNADSVEPSFVMEKIGRQPKLQLAYLTK   650
 651  LMSRNEGTEFADKAVQLYAEYDQKKLLPFLRKNANYNVNKARKLCSDKGY   700
 701  IEETIYLLAKSGNHYDAVKMMVREYRNMEKVIDYCKDQNDPDLWIHLLGV   750
 751  VAEFPAHFSQLIIEASNCLDPLLIMDKLPDDSDIPNLSEALDKLLVDYTN   800
 801  HAELQQCCYDSTLNDLNVLTQGLISAADESVSVNIVSRCSLCAQIIINSN   850
 851  QETTKKFSDIKVFKCGHIFHLACSTSEMERRQSIEEGLCIACSDQIELIN   900
 901  V                                                    901

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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