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

NucPred

Fetching P20785 from www.uniprot.org...

The NucPred score for your sequence is 0.20 (see score help below)

   1  MGLHDSFLALLLLLGGAWAQQAEINARVLRAQDCPVDLFFVLDTSESVAL    50
  51  RVKPFGDLVAQVKDFTNRFIDKLTERYFRCDRFLAWNAGALHYSDSVVII   100
 101  KDLTAMPSGRAELKNSVSAINYIGKGTHTDCAIKQGIERLLLGGSHLKEN   150
 151  KYLIVVTDGHPLEGYKEPCGGLDDAANEAKHLGIKVFSVAISPHHLDQRL   200
 201  NIIATDHAYRRNFTATSLKPTRDLDVEETINNIIEMIKDNMEQSCCSFEC   250
 251  HPPRGPPGPPGDPGHEGERGKPGLPGQKGDAGDPGRPGDMGPVGYQGMKG   300
 301  DKGSRGEKGSRGAKGAKGEKGKRGIDGIDGMKGEAGYPGLPGCKGSPGFD   350
 351  GTQGPPGPKGDPGAYGPKGGKGEPGEDGKPGRQGIPGSPGEKGAPGNRGE   400
 401  PGPLGETGDEGSPGADGPPGERGSNGERGPPGSPGDRGPRGDLGEPGPPG   450
 451  DQGREGPLGPPGDQGEPGPPGPKGYRGDDGPRGNEGPKGSPGAPGLPGDP   500
 501  GLMGERGEDGPPGNGTIGFPGAPGQQGDRGDPGINGTKGYVGPKGDEGEA   550
 551  GDPGNDNPTAGPSGIKGAKGHRGPEGRPGPPGPVGPPGPDECEILDIIMK   600
 601  MCSCCECTCGPVDLLFVLDSSESIGLQNFQIAKDFIIKVIDRLSKDERVK   650
 651  FEPGESRVGVVQYSHNNTQELVAMGDANIDNIGALKQAVKNLKWIAGGTH   700
 701  TGEALQFSKENLLRRFTSNNNVAIVITDGRSDTLRDRTPLTSLCEVTPVV   750
 751  SLGIGDIFRNNPNPDQLNDIACLGMPRRQGLSIQRDNYAELLDDSFLQNI   800
 801  TSYVCREKKCPDYTCPITFANPADIMLLVDSSTSVGSKNFDTTKNFVKRL   850
 851  AERFLEASKPAEDSVRVSVVQYSGRNQQKVEVPFQRNYTVIAKAVDNMEF   900
 901  MNEATDVNAALQYIMGLYQRSSRSGAKKKVLVFSDGNSQGITARAIERTV   950
 951  QEVQQAGIEVYVLAVGSQVNEPNVRVLVTGKSTNYDVAYGERHLFRVPDY  1000
1001  TSLLRGVFYQTVSRKIAVD                                 1019

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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