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

NucPred

Fetching Q28298 from www.uniprot.org...

The NucPred score for your sequence is 0.80 (see score help below)

   1  MDIYDTQTLGVMVFGGFMVVSAIGIFLVSTFSMKETSYEEALANQRKEMA    50
  51  KTHHQKVEKKKKEKTVEKKGKTKKKEEKPNGKIPDHEPAPNVTILLKDPV   100
 101  RAPAVPVAPTPVQPPVVIAPVATVPAMPQEKLAPSPKDKKKKEKKVAKVE   150
 151  PAVSSVVNSVQVLASKAAILETAPKEVPMVVVPPVGAKAGTPATSTAQGK   200
 201  KAEGAQNQSRKAEGAPNQGKKAEGALNQGKKAEGAQNQGKKVEVAPNQGK   250
 251  KAEGGQNQGKKVEGAQNQGKKAEGTPNQGKKAEGAPNQGKKTDGAPNQGK   300
 301  KSEGAPNQGKKAEGAQNQGKKVEVAPNQGKKAEGGQNQGKKVEGAQNQGK   350
 351  KAEGTPNQGKKAEGAPNQGKKTDGAPNQGKKSEGAPNQGKKVEGAQNQGK   400
 401  KVEGVQNQGKKAEGAQNQGKKAEGTSSQGRKEEGTPNLGKKAEGSPNQGK   450
 451  KVEVVQNQSKKVEGAPNQGKKAEGSQNQGKKTEGASNQGKKVDGAQNQGK   500
 501  KAEGAPNQGKKVEGAQNQGKKAEGTPNQGKKAEGAQNQGKKAEGAPNQGK   550
 551  KAEGAPNQGKKAEGAPNQGKKAEGAPNQGKKAEAAPNQGKKAEGAPNQGK   600
 601  KAEGAPNQGKKAEAAPNQGKKAEGAPNQGKKAEGAPNQGKKAEGAPNQGK   650
 651  KAEGAQNQGKKAEGAPNQGKKADLVANQGTKAEGVAGQGKKAEGAPNQGK   700
 701  KGEGTPNQGKKSEGSPNQGKKVDASANQSKRAESAPIQGKNADMVQSQEA   750
 751  PKQEAPAKKKSGSKKKGEPGPPDSDSPLYLPYKTLVSTVGSMVFNEGEAQ   800
 801  RLIEILSEKAGVIQDTWHKATQKGDPVAILKRQLEEKEKLLATEQEDAAV   850
 851  AKSKLREVNKELAAEKAKAAAGEAKVKKQLVAREQEITAVQARIEASYRE   900
 901  HVKEVQQLQGKIRTLQEQLENGPNTQLARLQQENSILRDALNQATSQVES   950
 951  KQNTELAKLRQELSKVSKELVEKSEAARQEEQQRKALETKTAALEKQVLQ  1000
1001  LQASHKESEEALQKRLDEVSRELCRSQTSHASLRADAEKAQEQQQQMAEL  1050
1051  HSKLQSSEAEVKSKSEELSGLHGQLKEARAENSQLMERIRSIEALLEAGQ  1100
1101  ARDTQDAQASRAEHQARLKELESQVWCLEKEATELKEAVEQQKVKNNDLR  1150
1151  EKNWKAMEALASAERACEEKLRSLTQAKEESEKQLSLTEAQTKEALLALL  1200
1201  PALSSSAPQSYTEWLQELREKGPELLKQRPADTDPSSDLASKLREAEETQ  1250
1251  NNLQAECDQYRTILAETEGMLKDLQKSVEEEEQVWKAKVSATEEELQKSR  1300
1301  VTVKHLEDIVEKLKGELESSEQVREHTSHLEAELEKHMAAASAECQSYAK  1350
1351  EVAGLRQLLLESQSQLDAAKSEAQKQSNELALVRQQLSEMKSHVEDGDVA  1400
1401  GSPAAPPAEQDPVELKAQLERTEATLEDEQALRRKLTAEFQEAQSSACRL  1450
1451  QAELEKLRSTGPLESSAAEEATQLKERLEKEKKLTSDLGHAATKLQELLK  1500
1501  TTQEQLAKERDTVKKLQEQLDKTDDSSSKEGTSV                  1534

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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