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

NucPred

Fetching Q9VUM0 from www.uniprot.org...

The NucPred score for your sequence is 0.92 (see score help below)

   1  MSKKLNTSVGGTPTNTLLNYFSKSPAFDKKKLTPSVKTDPDASKSEKENL    50
  51  QNQQPKVKDGKKEASKPAAKRKLPISDDEPASGQRKRKRIVQPESDSEPE   100
 101  MEVTKSEDDFSDCASDYEPDENEASDDSVSSGAEEVSPSENDMSVDSPTP   150
 151  KKSRKKSKILNNNNNNEPSSKKVKLESTIQLAEGATFQEKLKNLQSNAKQ   200
 201  DASYDDIVTNTSNLDEPVVWPHQKLEFLQPDKIKDKEGRRPDHPDYDKST   250
 251  LHVPEKFLNGLSPGVRQWWVLKSDNYDCVLFFKVGKFYELYHMDADVGVN   300
 301  ELGFTYMRGEFAHSGFPEISFDKMSTILVDRGFKVARVEQTETPDMMTER   350
 351  CKRIKATKFDKVVAREICQITNRGTQVFGSQCKIGPNHQPNYMLAIVEKD   400
 401  EGTCSRYGVCFIDTSIGDFHLGEFEDDKNCSRLLTLVSHHMPVLFLNEKS   450
 451  ALSQRTQQIVRTVLGGILKEPVPGNGKHACSAEKTLKLLAERYYAGPGSD   500
 501  DNWPLVLRTMQSDMDHLGLTPNDNYKLALKALGQCIFFIHKCKLEPKVLP   550
 551  MARYQLYVPPDQLADAKPAVASTLRRSHMVLDATTLSNLRIIGEEHSLLS   600
 601  TLDHCCTKFGKRLLHHWLCAPSCDVSVIKERQDAIGELIRMPTELQEVRA   650
 651  LLAPMPDFERNLAQIHLFGNKQIKQMDHPDSRAILFEEKLYNKQKLQGFM   700
 701  AVLKGFNDLTKLPTMFHQCKTTLLKRITQLPESGGSFPDLSKELQYFATA   750
 751  FDHDAAAKTGVIAPQAGMDAEYDAAMDSIGEVEKRLKTYLVEQERHFGCR   800
 801  ITYFGSDKKRYQLDVPESHASKANKSYTLEGQTKGKKPSRRYTTAETRAL   850
 851  LKDMQHAEDTRNMVLKDLARRLFEKFSNHYDQWKQCIDCVANLDVLGSLA   900
 901  EYAGQQMVICVPELVSDADQPFIQLEEGYHPCANASTYIPNGLELGTASE   950
 951  APLSLLTGPNMGGKSTLMREVGLLVIMAQIGAHIPAASCRLSLVDRIFTR  1000
1001  LGAQDDILAGHSTFLVELNETSLILKHATCHSLVLLDELGRGTATYDGTA  1050
1051  IAASVVNFLANLKCRTLFSTHYHNLIDFFHNDKRITLGHMACMVENEDNA  1100
1101  DPTQETVTFLYKYTAGACPKSYGFNAAKLAGMPQGIIKRAYELSKKVEAI  1150
1151  ALQRKITAKIVAATAGNEDTKKEKINALKDLLKQLKMCQV            1190

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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