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

NucPred

Fetching Q7TMY7 from www.uniprot.org...

The NucPred score for your sequence is 0.71 (see score help below)

   1  MDLNRIIQALKGTIDPKLRIAAETELNQSYKIINFAPSLLRIIVSDHVEF    50
  51  PVRQAAAIYLKNMVTQYWPDREPPPGEVIFPFNIHENDRQQIRDNIVEGI   100
 101  IRSPDLVRVQLTMCLRVIIRHDFPGHWPAVVDKIDYYLQSPNSGSWLGSL   150
 151  LCLYQLVKTYEYKKAEEREPLLAAMQIFLPRIQQQILQLLPDASHYSVLL   200
 201  QKQILKIFYALVQYALPLQLVNHQTMTTWMEIFRTIIDRTVPPETLQIDE   250
 251  DDRPELVWWKCKKWALHIVARLFERYGSPGNVTKEYFEFSEFFLKTYAVG   300
 301  IQQVLLKILDQYRQKEYIAPRVLQQAFNYLNQGVVHAVTWKQMKPHIQNI   350
 351  SEDVIFSVMCYKDEDEELWQEDPYEYIRMKFDIFEDYASPTTAAQTLLYT   400
 401  AAKKRKEVLPKMMAFCYQILTDPNFDPRKKDGALHVIGSLAEILLKKSLF   450
 451  KDQIELFLQNHVFPLLMSNLGYLRARSCWVLHAFSSLKFHNELNLRNAVE   500
 501  LAKKSLIEDEEMPVKVEAALALQSLISNQAQAKEHMKPYVRFIMQELLHI   550
 551  VRETENDDVTNVIQKLICEYSQDVASIAVDTTQHLAEIFGKVLQSDEYEE   600
 601  IEDKTVMAMGILHTIDTILTVVEDHPEIIQQLENICLRIIDLVLQKHVIE   650
 651  FYEEILSLAYNLTCHTISPQMWQLLGILYEVFQQDCFEYFTDMMPLLHNY   700
 701  VTVDTNALLSNPKHLEVLFTMCRKVLCGEAGEDAECYAAKLLEVIILQCK   750
 751  GRGIDQCIPLFIQLVLERLTRGVKTSELRTMCLQVAIAALYYSPELLFHT   800
 801  LEQVQLPHNPGPVTSQFINQWMNDTDYFLGHHDRKMCIIGLSVLLELQNR   850
 851  PPAVDAVAAQILPSILFLFLGLKQVCATRQTVNRENHSKAEKVDIEENEE   900
 901  ISSEEEEETSVSAQAMQSQIGRSEEEDDDDWDEEVLEETALEGFSTPLDL   950
 951  DNSVDEYQFFTQALLTVQNRDAAWYQLLVAPLSEDQKRKLQEVYTLAEHR  1000
1001  RTLAAGQFHI                                          1010

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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