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

NucPred

Fetching P97260 from www.uniprot.org...

The NucPred score for your sequence is 0.44 (see score help below)

   1  MTLTERLREKISQAFYNHGLLCASYPIPIILFTGLCILACCYPLLKLPLP    50
  51  GTGPVEFSTPVKDYSPPPVDSDHKQGEPSEQPEWYVGAPVAYIQQIFVKS   100
 101  SVSPWHKNLLAVDVFRLPLSRAFQLVEEIRNHVLRDSSGTKSLEEVCLQV   150
 151  TDLLPGLRKLRNLLPEHGCLLLSPGNFWQNDWERFHADPDIIGTIHQHEP   200
 201  KTLQTSATLKDLLFGVPGKYSGVSLYTRKRTVSYTITLVFQRYHAKFLSS   250
 251  LRARLMLLHPSPNCSLRAENLVHVHFKEEIGIAELIPLVTTYIILFAYIY   300
 301  FSTRKIDMVKSKWGLALAAVVTVLSSLLMSVGLCTLFGLTPTLNGGEIFP   350
 351  YLVVVIGLENVLVLTKSVVSTPVDLEVKLRIAQGLSSESWSIMKNVATEL   400
 401  GIILIGYFTLVPAIQEFCLFAVVGLVSDFFLQMFFFTTVLSIDIRRMELA   450
 451  DLNKRLPPESCLPSAKPVGRPARYERQLAVRPAMPHTITLQPSSFRNLRL   500
 501  PKRLRVIYFLARTRLAQRLIMAGTVVWIGILVYTDPAGLRTYLAAQVTEQ   550
 551  SPLGEGSLGPMPVPSGVLPASRPDPAFSIFPPDAPKLPENQTVPGELPEH   600
 601  AAPAEGVHDSRAPEVTWGPEDEELWRRLSFRHWPTLFNYYNITLAKRYIS   650
 651  LLPVIPVTLRLNPQEALEGRQPQDGRSAWAPPESLPAGLWEAGPKGPGGT   700
 701  QAHGDITLYKVAALGLAAGIVLVLLLLCLYRVLCPRNYGQPGGGAGRRRR   750
 751  GELPCDDYGYAPPETEIVPLVLRGHLMDIECLASDGMLLVSCCLAGQVCV   800
 801  WDAQTGDCLTRIPRPGSRRDSCGGGAFETQENWERLSDGGKTSPEEPGES   850
 851  PPLRHRPRGPPQPALFGDQPDLTCLIDTNFSVQLPPEPTQPEPRHRAGCG   900
 901  RARDSGYDFSRLVQRVYQEEGLAAVRMPALRPPSPGSPLPQASQEDGAAP   950
 951  EKGSPPLAWAPSTAGSIWSLELQGNLIVVGRSSGRLEVWDAIEGVLCCSN  1000
1001  DEVSSGITALVFLDRRIVAARLNGSLDFFSLETHTSLSPLQFRGTPGRGS  1050
1051  SPSSSVYSSSNTVACHLTHTVPCAHQKPITALRAAAGRLVTGSQDHTLRV  1100
1101  FRLEDSCCLFTLQGHSGAITTVYIDQTMVLASGGQDGAICLWDVLTGSRV  1150
1151  SHTFAHRGDVTSLTCTTSCVISSGLDDLINIWDRSTGIKLYSIQQDLGCG  1200
1201  ASLGVISDNLLVTGGQGCVSFWDLNYGDLLQTVYLGKNSEAQPARQILVL  1250
1251  DNAAIVCNFGSELSLVYVPSVLEKLD                          1276

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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