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

NucPred

Fetching Q80YF9 from www.uniprot.org...

The NucPred score for your sequence is 0.91 (see score help below)

   1  MLQAQKQSDPILPWGASWAGRGQTLRARSTDSLDGPGEGSVQPVPTTGGP    50
  51  GTKGKPGKRLSAPRGPFPRLADCAHFHYENVDFGHIQLLLSPEREGPSLS   100
 101  GENELVFGVQVTCQGRSWPVLRSYDDFRSLDAHLHRCIFDRRFSCLPELP   150
 151  PPPEGTRAAQMLVPLLLQYLETLSGLVDSNLNCGPVLTWMELDNHGRRLL   200
 201  LSEEASLNIPAVAAAHVVKRYTAQAPDELSFEVGDIVSVIDMPPTEDRSW   250
 251  WRGKRGFQVGFFPSECVELFTERPGPGLKADADSPLCGIPAPQGISSLTS   300
 301  AVPRPRGKLAGLLRTFMRSRPSRQRLRQRGILRQRVFGCDLGEHLSNSGQ   350
 351  DVPQVLRCCSEFIEAHGVVDGIYRLSGVSSNIQRLRHEFDSERIPELSGP   400
 401  AFLQDIHSVSSLCKLYFRELPNPLLTYQLYGKFSEAMSVPGEEERLVRVH   450
 451  DVIQQLPPPHYRTLEYLLRHLARMARHSANTSMHARNLAIVWAPNLLRSM   500
 501  ELESVGLGGAAAFREVRVQSVVVEFLLTHVEVLFSDTFTSAGLDPAGRCL   550
 551  LPRPKSLAGSSPSTRLLTLEEAQARTQGRLGTPTEPTTPKTPASPVERRK   600
 601  RERAEKQRKPGGSSWKTFFALGRGPSIPRKKPLPWLGGSRAPPQPSGSRP   650
 651  DTVTLRSAKSEESLSSQASGAGLQRLHRLRRPHSSSDAFPVGPAPAGSCE   700
 701  SLSSSSSSSSSSSSSSSSESSAGGLGPLSGSPSHRTSAWLDDGDDLDFSP   750
 751  PRCLEGLRGLDFDPLTFRCSSPTPGDPAPPASPAPPASASAFPPRATPQA   800
 801  LSPHGPTKPASPTALDISEPLAVSVPPAVLELLGAGGTPASATPTPALSP   850
 851  HLIPLLLRGAEAQLSDTCQQEISSKLAPTRGAPGQQSPGGMDSPLLPPPL   900
 901  PLLRPGGAPPPPPKNPARLMALALAERAQQVAEQQSQQEQGGTPPAPHSP   950
 951  FRRSLSLEVGGEPVGTSGSGIHPPSLAHPGAWAPGPPPYLPRQQSDGSLV  1000
1001  RSQRPLGTSRRSPRGPSQVSAHLRASGAYRDAPEMAAQSPCSVPSQGSNP  1050
1051  SFFSTPRECLPPFLGVPKQGLYSLGPPSFPPSSPAPVWRNSLGAPSALDR  1100
1101  GENLYYEIGVGEGTSYSGPSRSWSPFRSMPPDRHNASYGMLGQSPPLHRS  1150
1151  PDFLLSYPPPPSCFPPEHLTHSVSQRLARRPTRPEPLYVNLALGPRGPSP  1200
1201  ASSSSSSPPAHPRSRSDPGPPVPRLPQKQRAPWGPHTPHRVPGPWGSPEP  1250
1251  FLLYRPAPPSYGRGGEVRGSLYRNGGHRGEGAGPPPPYPTPSWSLHSEGQ  1300
1301  TRSYC                                               1305

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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