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

NucPred

Fetching Q09879 from www.uniprot.org...

The NucPred score for your sequence is 0.76 (see score help below)

   1  MVTGETLVDSQKSLINNDTLLNEKLKEDFEENVSIDVKIHEELRRALPDY    50
  51  EESGFQRFTWHIKSWHELDRRAVSPQFAVGSRQFKITYFPQGTLQSAGFT   100
 101  SIFLEYIPSEEEKLSNKYGCCCQFAFVISNPRKPSLSVANSAHCRFSPEI   150
 151  VDWGFTQFAELKKLLCRQAPDVPPIVEDGALLLTAYVRILKDPTGVLWHS   200
 201  FNDYDSKIATGYVGLKNQGATCYMNSLLQSLYIIHAFRRIVYQIPTDSPQ   250
 251  GKDSIAYALQRCFYNLQFMNEPVSTTELTKSFGWDSLDSFMQHDVQEFNR   300
 301  VLQDNLERSMRDTKVENALTNLFVGKMKSYIACVNVNFESARSEDYWDIQ   350
 351  LNVKGMKNLEDSFRSYIQVETLEGDNCYFADTYGFQEAKKGVIFESFPPI   400
 401  LHLQLKRFEYDFERDMMIKINDRYEFPLEFDAKAFLSPEADQSQNCEYVL   450
 451  YGVLVHSGDLHNGHYYALLKTEKDGPWYKYDDTRVTRATLREVLEENYGG   500
 501  DYIMHPPFRSPVKLKRFMSAYMLLYLRKDKLDELMNPVSADEIPEHLKEA   550
 551  LNPSIQLAELRRKERLESHLYTKVQLITPEFYSEHHEFDIADFGNAYKEE   600
 601  TIPQFRIKKEAKFSEFIPIVAEKLGYPQECMRFWYVVKRHNCTVRVESPV   650
 651  NELNSTMEEVKNVWNSQGEILRLYLEITPENELSSSLTHQNTGEWNAFIF   700
 701  VKYFDRKSQEISGCGTLHVNKSDEIRSICPLLCERANLPKNTPLNIYEEI   750
 751  KPGMVDFLRLEKTFTQSELSTGDIICFEPCRPSALEDDIVNSGFDSALKL   800
 801  YDFLSNKVLVLFRPRFIDQDSIIEFEMLLDRRIKYDDLCIELGQKLGIGA   850
 851  DHIRLTTCNPLTYSAGMVVPNDSNITLYEILYSSEEEMPSNVIFYETMDV   900
 901  SLSDLDRKRLVRLRWLVDGLANIELVEAYINKSGDINDLFGAVCERFPDS   950
 951  DLRKKKVRVYEVFESRYHRDLSLRTLIRTINPAATLVGEVVPLDQLQLYP  1000
1001  EEKIVQVHHFHKDIARIHGIPFSFVIKPQEKFIDTKLRLAARTQYPESIF  1050
1051  SVIKFCVVDFDNNRVVYLNDEDITYDVVEKLNGTLALDRAKKDSKKPNIL  1100
1101  DRAIQMKN                                            1108

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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