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

NucPred

Fetching Q9NUA8 from www.uniprot.org...

The NucPred score for your sequence is 0.90 (see score help below)

   1  MELPNYSRQLLQQLYTLCKEQQFCDCTISIGTIYFRAHKLVLAAASLLFK    50
  51  TLLDNTDTISIDASVVSPEEFALLLEMMYTGKLPVGKHNFSKIISLADSL   100
 101  QMFDVAVSCKNLLTSLVNCSVQGQVVRDVSAPSSETFRKEPEKPQVEILS   150
 151  SEGAGEPHSSPELAATPGGPVKAETEEAAHSVSQEMSVNSPTAQESQRNA   200
 201  ETPAETPTTAEACSPSPAVQTFSEAKKTSTEPGCERKHYQLNFLLENEGV   250
 251  FSDALMVTQDVLKKLEMCSEIKGPQKEMIVKCFEGEGGHSAFQRILGKVR   300
 301  EESLDVQTVVSLLRLYQYSNPAVKTALLDRKPEDVDTVQPKGSTEEGKTL   350
 351  SVLLLEHKEDLIQCVTQLRPIMESLETAKEEFLTGTEKRVILNCCEGRTP   400
 401  KETIENLLHRMTEEKTLTAEGLVKLLQAVKTTFPNLGLLLEKLQKSATLP   450
 451  STTVQPSPDDYGTELLRRYHENLSEIFTDNQILLKMISHMTSLAPGEREV   500
 501  MEKLVKRDSGSGGFNSLISAVLEKQTLSATAIWQLLLVVQETKTCPLDLL   550
 551  MEEIRREPGADAFFRAVTTPEHATLETILRHNQLILEAIQQKIEYKLFTS   600
 601  EEEHLAETVKEILSIPSETASPEASLRAVLSRAMEKSVPAIEICHLLCSV   650
 651  HKSFPGLQPVMQELAYIGVLTKEDGEKETWKVSNKFHLEANNKEDEKAAK   700
 701  EDSQPGEQNDQGETGSLPGQQEKEASASPDPAKKSFICKACDKSFHFYCR   750
 751  LKVHMKRCRVAKSKQVQCKECSETKDSKKELDKHQLEAHGAGGEPDAPKK   800
 801  KKKRLPVTCDLCGREFAHASGMQYHKLTEHFDEKPFSCEECGAKFAANST   850
 851  LKNHLRLHTGDRPFMCKHCLMTFTQASALAYHTKKKHSEGKMYACQYCDA   900
 901  VFAQSIELSRHVRTHTGDKPYVCRDCGKGFRQANGLSIHLHTFHNIEDPY   950
 951  DCKKCRMSFPTLQDHRKHIHEVHSKEYHPCPTCGKIFSAPSMLERHVVTH  1000
1001  VGGKPFSCGICNKAYQQLSGLWYHNRTHHPDVFAAQNHRSSKFSSLQCSS  1050
1051  CDKTFPNTIEHKKHIKAEHADMKFHECDQCKELFPTPALLQVHVKCQHSG  1100
1101  SQPFRCLYCAATFRFPGALQHHVTTEHFKQSETTFPCELCGELFTSQAQL  1150
1151  DSHLESEHPKVMSTETQAAASQMAQVIQTPEPVAPTEQVITLEETQLAGS  1200
1201  QVFVTLPDSQASQASSELVAVTVEDLLDGTVTLICGEAK             1239

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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