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

NucPred

Fetching P93526 from www.uniprot.org...

The NucPred score for your sequence is 0.34 (see score help below)

   1  MSSSRPAHSSSSSSRTRQSSQARILAQTTLDAELNAEYEESGDSFDYSKL    50
  51  VEAQRSTPSEQQGRSGKVIAYLQHIQRGKLIQPFGCLLALDEKSFRVIAF   100
 101  SENAPEMLTTVSHAVPNVDDPPKLGIGTNVRSLFTDPGATALQKALGFAD   150
 151  VSLLNPILVQCKTSGKPFYAIVHRATGCLVVDFEPVKPTEFPATAAGALQ   200
 201  SYKLAAKAISKIQSLPGGSMEALCNTVVKEVFELTGYDRVMAYKFHEDEH   250
 251  GEVFAEITKPGIEPYLGLHYPATDIPQAARFLFMKNKVRMICDCRAKSVK   300
 301  IIEDEALSIDISLCGSTLRAPHSCHLQYMENMNSIASLVMAVVVNENEED   350
 351  DEPGPEQPPQQQKKKRLWGLIVCHHESPRYVPFPLRYACEFLAQVFAVHV   400
 401  NKEFELEKQIREKSILRMQTMLSDMLFKEASPLSIVSGSPNIMDLVKCDG   450
 451  AALLYGDKVWRLQTAPTESQIRDIAFWLSEVHGDSTGLSTDSLQDAGYPG   500
 501  AASLGDMICGMAVAKITSKDILFWFRSHTAAEIKWGGAKHDPSDKDDNRR   550
 551  MHPRLSFKAFLEVVKMKSLPWSDYEMDAIHSLQLILRGTLNDALKPVQAS   600
 601  GLDNQIGDLKLDGLAELQAVTSEMVRLMETATVPILAVDGNGLVNGWNQK   650
 651  VAELSGLRVDEAIGRHILTLVEDSSVSIVQRMLYLALQGKEEKEVRFELK   700
 701  THGSKRDDGPVILVVNACASRDLHDHVVGVCFVAQDMTVHKLVMDKFTRV   750
 751  EGDYKAIIHNPNPLIPPIFGADQFGWCSEWNVAMTKLTGWHRDEVIDKML   800
 801  LGEVFDSSNASCLLKSKDDFVRLCIIINSALAGEEAENAPFGLFDRNGKY   850
 851  IECLLSVNRKVNADGVVTGVFCFIHVPSDDLQHALHVQQASEQTAQRRLK   900
 901  AFSYMRHAINKPLSGMLYSRETLKSTGLNEEQMRQVHVADSCHRQLNKIL   950
 951  ADLDQDNITDKSSCLDLDMAEFVLEDVVVSAVSQVLIGCQGKGIRVACNL  1000
1001  PERFMKQKVYGDGIRLQQILSDFLFVSVKFSPVGGSVDISSKLTKNSIGE  1050
1051  NLHLIDFELRIKHQGAGVPAEILSQMYEEDNKEPSEEGLSLLVSRNLLRL  1100
1101  MNGNIRHIREAGMSTFILTAELAAAPSAVGQ                     1131

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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