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

NucPred

Fetching Q12680 from www.uniprot.org...

The NucPred score for your sequence is 0.35 (see score help below)

   1  MPVLKSDNFDPLEEAYEGGTIQNYNDEHHLHKSWANVIPDKRGLYDPDYE    50
  51  HDACGVGFVANKHGEQSHKIVTDARYLLVNMTHRGAVSSDGNGDGAGILL   100
 101  GIPHEFMKREFKLDLDLDIPEMGKYAVGNVFFKKNEKNNKKNLIKCQKIF   150
 151  EDLAASFNLSVLGWRNVPVDSTILGDVALSREPTILQPLLVPLYDEKQPE   200
 201  FNETKFRTQLYLLRKEASLQIGLENWFYVCSLNNTTIVYKGQLTPAQVYN   250
 251  YYPDLTNAHFKSHMALVHSRFSTNTFPSWDRAQPLRWLAHNGEINTLRGN   300
 301  KNWMRSREGVMNSATFKDELDKLYPIIEEGGSDSAALDNVLELLTINGTL   350
 351  SLPEAVMMMVPEAYHKDMDSDLKAWYDWAACLMEPWDGPALLTFTDGRYC   400
 401  GAILDRNGLRPCRYYITSDDRVICASEVGVIPIENSLVVQKGKLKPGDLF   450
 451  LVDTQLGEMVDTKKLKSQISKRQDFKSWLSKVIKLDDLLSKTANLVPKEF   500
 501  ISQDSLSLKVQSDPRLLANGYTFEQVTFLLTPMALTGKEALGSMGNDAPL   550
 551  ACLNENPVLLYDYFRQLFAQVTNPPIDPIREANVMSLECYVGPQGNLLEM   600
 601  HSSQCDRLLLKSPILHWNEFQALKNIEAAYPSWSVAEIDITFDKSEGLLG   650
 651  YTDTIDKITKLASEAIDDGKKILIITDRKMGANRVSISSLIAISCIHHHL   700
 701  IRNKQRSQVALILETGEAREIHHFCVLLGYGCDGVYPYLAMETLVRMNRE   750
 751  GLLRNVNNDNDTLEEGQILENYKHAIDAGILKVMSKMGISTLASYKGAQI   800
 801  FEALGLDNSIVDLCFTGTSSRIRGVTFEYLAQDAFSLHERGYPSRQTISK   850
 851  SVNLPESGEYHFRDGGYKHVNEPTAIASLQDTVRNKNDVSWQLYVKKEME   900
 901  AIRDCTLRGLLELDFENSVSIPLEQVEPWTEIARRFASGAMSYGSISMEA   950
 951  HSTLAIAMNRLGAKSNCGEGGEDAERSAVQENGDTMRSAIKQVASARFGV  1000
1001  TSYYLSDADEIQIKIAQGAKPGEGGELPAHKVSKDIAKTRHSTPNVGLIS  1050
1051  PPPHHDIYSIEDLKQLIYDLKCANPRAGISVKLVSEVGVGIVASGVAKAK  1100
1101  ADHILVSGHDGGTGAARWTSVKYAGLPWELGLAETHQTLVLNDLRRNVVV  1150
1151  QTDGQLRTGFDIAVAVLLGAESFTLATVPLIAMGCVMLRRCHLNSCAVGI  1200
1201  ATQDPYLRSKFKGQPEHVINFFYYLIQDLRQIMAKLGFRTIDEMVGHSEK  1250
1251  LKKRDDVNAKAINIDLSPILTPAHVIRPGVPTKFTKKQDHKLHTRLDNKL  1300
1301  IDEAEVTLDRGLPVNIDASIINTDRALGSTLSYRVSKKFGEDGLPKDTVV  1350
1351  VNIEGSAGQSFGAFLASGITFILNGDANDYVGKGLSGGIIVIKPPKDSKF  1400
1401  KSDENVIVGNTCFYGATSGTAFISGSAGERFGVRNSGATIVVERIKGNNA  1450
1451  FEYMTGGRAIVLSQMESLNAFSGATGGIAYCLTSDYDDFVGKINKDTVEL  1500
1501  ESLCDPVEIAFVKNLIQEHWNYTQSDLAARILGNFNHYLKDFVKVIPTDY  1550
1551  KKVLLKEKAEAAKAKAKATSEYLKKFRSNQEVDDEVNTLLIANQKAKEQE  1600
1601  KKKSITISNKATLKEPKVVDLEDAVPDSKQLEKNSERIEKTRGFMIHKRR  1650
1651  HETHRDPRTRVNDWKEFTNPITKKDAKYQTARCMDCGTPFCLSDTGCPLS  1700
1701  NIIPKFNELLFKNQWKLALDKLLETNNFPEFTGRVCPAPCEGACTLGIIE  1750
1751  DPVGIKSVERIIIDNAFKEGWIKPCPPSTRTGFTVGVIGSGPAGLACADM  1800
1801  LNRAGHTVTVYERSDRCGGLLMYGIPNMKLDKAIVQRRIDLLSAEGIDFV  1850
1851  TNTEIGKTISMDELKNKHNAVVYAIGSTIPRDLPIKGRELKNIDFAMQLL  1900
1901  ESNTKALLNKDLEIIREKIQGKKVIVVGGGDTGNDCLGTSVRHGAASVLN  1950
1951  FELLPEPPVERAKDNPWPQWPRVMRVDYGHAEVKEHYGRDPREYCILSKE  2000
2001  FIGNDEGEVTAIRTVRVEWKKSQSGVWQMVEIPNSEEIFEADIILLSMGF  2050
2051  VGPELINGNDNEVKKTRRGTIATLDDSSYSIDGGKTFACGDCRRGQSLIV  2100
2101  WAIQEGRKCAASVDKFLMDGTTYLPSNGGIVQRDYKLLKELASQV       2145

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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