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

NucPred

Fetching Q9QYM2 from www.uniprot.org...

The NucPred score for your sequence is 0.87 (see score help below)

   1  MSAGPGCEPCTKRPRWGAAGTSAPTASDSRSFPGRQKRVLDPKDAPVQFR    50
  51  VPPSSSACVSGRAGPHRGSVTSFVFKQKPITTWMDTKGPKTAESESKENN   100
 101  NTRTDPMMSSVQKDNFYPHKVEKLGNVPQLNLDKSPTEKSTPYLNQQQTA   150
 151  GVCKWHSAGERAEQLSASEPSAVTQAPKQLSNANIDQSPPTDGHSDTDHE   200
 201  EDRDNQQFLTPVKLANAKQTVGDGQARSNCKCSASCQCGQDCAGCQREEA   250
 251  DVIPESPLSDVGAEDIGTGSKNDNKLTGQESGLGDSPPFEKESEPESPMD   300
 301  VDNSKTSCQDSEADEEASPVFDEQDDQDDRSSQTANKLSSRQAREVDGDL   350
 351  RKRYLTKGSEIRLHFQFEGGSNAGTSDLNAKPSGNSSSLNVDGRSSKQHG   400
 401  KRDSKITDHFVRIPKSEDKRKEQCEVRHQRAERKIPKYVPPNLPPDKKWL   450
 451  GTPIEEMRKMPRCGVRLPLLRPSASHTVTVRVDLLRAGEVPKPFPTHYKD   500
 501  LWDNKHVKMPCSEQNLYPVEDENGERTAGSRWELIQTALLNKFTRPQNLK   550
 551  DAILKYNVAYSKKWDFTALVDFWDKVLEEAEAQHLYQSILPDMVKIALCL   600
 601  PNICTQPIPLLKQKMNHSVTMSQEQIASLLANAFFCTFPRRNAKMKSEYS   650
 651  SYPDINFNRLFEGRSSRKPEKLKTLFCYFRRVTEKKPTGLVTFTRQSLED   700
 701  FPEWERCDKPLTRLHVTYEGTIEGNGRGMLQVDFANRFVGGGVTGAGLVQ   750
 751  EEIRFLINPELIVSRLFTEVLDHNECLIITGTEQYSEYTGYAETYRWARS   800
 801  HEDGSEKDDWQRCCTEIVAIDALHFRRYLDQFVPEKVRRELNKAYCGFLR   850
 851  PGVPPENLSAVATGNWGCGAFGGDARLKALIQLLAAAAAERDVVYFTFGD   900
 901  SELMRDIYSMHTFLTERKLNVGKVYRLLLRYYREECRDCSSPGPDTKLYP   950
 951  FIYHAAESSAETSDQPGQRTGT                               972

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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