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

NucPred

Fetching Q65X71 from www.uniprot.org...

The NucPred score for your sequence is 0.29 (see score help below)

   1  MEGGRSWSIESYLNEYFDIPAKNPPGEARRRWRRAVGLIVRNRRRRFGRF    50
  51  SDVDAIDEAQRRKILVRVKQYHLPPELIEEGFCISPDELAAIANMREDYT   100
 101  MLRMHGGINGISRKIKASLEDGAKETDIATRQMLYGANRHAEKPPRSFWM   150
 151  FVWDALHDLTLIILVVCALVSIVVGLATKGWPMGIYDGFGIILSILLVVL   200
 201  VTATSDYQQARKFMELDREKQKIYIRVTRDKKTKEVLVHDLVVGDILHLS   250
 251  IGDVVPADGLFISGDCLMIDESSLSGESEPVNISEERPFLHAGNKVVDGA   300
 301  AKMLVTAVGTRTEWGKIMGTLNGDGVDETPLQVKLNGVATIIGQIGLVFA   350
 351  VLTFLVLLARFLADKGMHVGLLNWSANDALTIVNYFAIAVTIIVVAVPEG   400
 401  LPLAVTLSLAFAMKKLMHDKALVRHLAACETMGSASCICTDKTGTLTTNH   450
 451  MIVDKVWIGDVKFVGDKKNSELKSTISERVMAILIQGIFVNTASEVVKGD   500
 501  DGKNTILGLATETALLEFGLSLEEHLYDDYNKLTRIKVDPFNSVKKKMSV   550
 551  TIQLPNGGIRTFCKGASEIILEQCNTIHNTDGNIVPLSEMQKHNVLNIIN   600
 601  SFASEALRTLCIAFKDMDEFPNDQPISDDGYTLIAVFGIKDPVRPGVKDA   650
 651  VRTCMAAGIRVRMVTGDNINTAKAIAKECGILTEDGIAIEGQQLNNKSSD   700
 701  ELKELLPKIQVIARSLPMDKYKLVTSLKSMYQEVVAVTGDGTNDAPALHE   750
 751  SDIGLAMGITGTEVAKESADVIIMDDNFETIVNVARWGRAVYLNIQKFVQ   800
 801  FQLTVNIVALIVNFVSACIIGSAPLTAVQLLWVNMIMDTLGALALATEPP   850
 851  NDEMMKRPPVRRGDNFITRIMWRNILGQGLYQLLVLATLMVIGKKLLSIE   900
 901  GPQSDKTINTLIFNSFVFCQVFNEINCREMEKINVLQGIFRNWIFVGILT   950
 951  ATVIFQVIIVEFLGTFANTVPLSGELWLLSVVIGSISMIISVILKCIPVE  1000
1001  FNKTNTKPHGYELIPEGPEIL                               1021

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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