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

NucPred

Fetching Q6WKZ4 from www.uniprot.org...

The NucPred score for your sequence is 0.88 (see score help below)

   1  MSLMVSAGRGLGAVWSPTHVQVTVLQARGLRAKGPGGTSDAYAVIQVGKE    50
  51  KYATSVSERSLGAPVWREEATFELPSLLSSGPAAAATLQLTVLHRALLGL   100
 101  DKFLGRAEVDLRDLHRDQGRRKTQWYKLKSKPGKKDKERGEIEVDIQFMR   150
 151  NNMTASMFDLSMKDKSRNPFGKLKDKIKGKNKDSGSDTASAIIPSTTPSV   200
 201  DSDDESVVKDKKKKSKIKTLLSKSNLQKTPLSQSMSVLPTSKPEKVLLRP   250
 251  GDFQSQWDEDDNEDESSSASDVMSHKRTASTDLKQLNQVNFTLPKKEGLS   300
 301  FLGGLRSKNDVLSRSNVCINGNHVYLEQPEAKGEIKDSSPSSSPSPKGFR   350
 351  KKHLFSSTENLAAGSWKEPAEGGGLSSDRQLSESSTKDSLKSMTLPSYRP   400
 401  APLVSGDLRENMAPANSEATKEAKESKKPESRRSSLLSLMTGKKDVAKGS   450
 451  EGENPLTVPGREKEGMLMGVKPGEDASGPAEDLVRRSEKDTAAVVSRQGS   500
 501  SLNLFEDVQITEPEAEPESKSEPRPPISSPRAPQTRAVKPRLEVSPEAQP   550
 551  TARLPSPTDSPSSLPPLPSSSGQASVPSELGHGADTQSSESPSVFSSLSS   600
 601  PIAAPISTSTPIESWPLVDRGQAKSEGPPLLPKAELQTESLTPVPNSGSS   650
 651  ALGSLFKQPSFPANKGTEDSLMGRTRETGTEKNTSSLELEESLPEQPETG   700
 701  RQEEELPRFPCKKQDYSPSSGEAQEVPFALSLSSDGAVSPVGELAAGGDR   750
 751  DLESQAGSLVESKARDAAEEVAPPLPMGASVPSIDSMMRKLEEMGLNLRK   800
 801  DQKKTKKRVSFSEQLFTEEAVAGAALLVEGHSSCPQELNPAWSVAGNASD   850
 851  GEPPESPHAEDSERESVTTPGPATCGAPASPADHLLLPSQEESFSEVPMS   900
 901  EASSAKDTPLFRMEGEDALVTQYQSKASDHEGLLSDPLSDLQLVSDFKSP   950
 951  IMADLNLSLPSIPEVASDDERIDQVEDDGDQVEDDGETAKSSTLDIGALS  1000
1001  LGLVVPCPERGKGPSGEADRLVLGEGLCDFRLQAPQASVTAPSEQTTEFG  1050
1051  IHKPHLGKSSSLDKQLPGPSGGEEEKPMGNGSPSPPPGTSLDNPVPSPSP  1100
1101  SEIFPVTHSFPSSAHSDTHHTSTAESQKKATAEGSAGRVENFGKRKPLLQ  1150
1151  AWVSPSETHPVSAQPGAGTGSAKHRLHPVKPMNAMATKVANCSLGTATII  1200
1201  SENLNNEVMMKKYSPSDPAFAYAQLTHDELIQLVLKQKETISKKEFQVRE  1250
1251  LEDYIDNLLVRVMEETPNILRIPTQVGKKAGKM                   1283

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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