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

NucPred

Fetching P39769 from www.uniprot.org...

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

   1  MDRRALKFMQKRADTESDTTTPVSTTASQGISASAILAGGTLPLKDNSNI    50
  51  REKPLHHNYNHNNNNSSQHSHSHQQQQQQQVGGKQLERPLKCLETLAQKA   100
 101  GITFDEKYDVASPPHPGIAQQQATSGTGPATGSGSVTPTSHRHGTPPTGR   150
 151  RQTHTPSTPNRPSAPSTPNTNCNSIARHTSLTLEKAQNPGQQVAATTTVP   200
 201  LQISPEQLQQFYASNPYAIQVKQEFPTHTTSGSGTELKHATNIMEVQQQL   250
 251  QLQQQLSEANGGGAASAGAGGAASPANSQQSQQQQHSTAISTMSPMQLAA   300
 301  ATGGVGGDWTQGRTVQLMQPSTSFLYPQMIVSGNLLHPGGLGQQPIQVIT   350
 351  AGKPFQGNGPQMLTTTTQNAKQMIGGQAGFAGGNYATCIPTNHNQSPQTV   400
 401  LFSPMNVISPQQQQNLLQSMAAAAQQQQLTQQQQQFNQQQQQQLTQQQQQ   450
 451  LTAALAKVGVDAQGKLAQKVVQKVTTTSSAVQAATGPGSTGSTQTQQVQQ   500
 501  VQQQQQQTTQTTQQCVQVSQSTLPVGVGGQSVQTAQLLNAGQAQQMQIPW   550
 551  FLQNAAGLQPFGPNQIILRNQPDGTQGMFIQQQPATQTLQTQQNQIIQCN   600
 601  VTQTPTKARTQLDALAPKQQQQQQQVGTTNQTQQQQLAVATAQLQQQQQQ   650
 651  LTAAALQRPGAPVMPHNGTQVRPASSVSTQTAQNQSLLKAKMRNKQQPVR   700
 701  PALATLKTEIGQVAGQNKVVGHLTTVQQQQQATNLQQVVNAAGNKMVVMS   750
 751  TTGTPITLQNGQTLHAATAAGVDKQQQQLQLFQKQQILQQQQMLQQQIAA   800
 801  IQMQQQQAAVQAQQQQQQQVSQQQQVNAQQQQAVAQQQQAVAQAQQQQRE   850
 851  QQQQVAQAQAQHQQALANATQQILQVAPNQFITSHQQQQQQQLHNQLIQQ   900
 901  QLQQQAQAQVQAQVQAQAQQQQQQREQQQNIIQQIVVQQSGATSQQTSQQ   950
 951  QQHHQSGQLQLSSVPFSVSSSTTPAGIATSSALQAALSASGAIFQTAKPG  1000
1001  TCSSSSPTSSVVTITNQSSTPLVTSSTVASIQQAQTQSAQVHQHQQLISA  1050
1051  TIAGGTQQQPQGPPSLTPTTNPILAMTSMMNATVGHLSTAPPVTVSVTST  1100
1101  AVTSSPGQLVLLSTASSGGGGSIPATPTKETPSKGPTATLVPIGSPKTPV  1150
1151  SGKDTCTTPKSSTPATVSASVEASSSTGEALSNGDASDRSSTPSKGATTP  1200
1201  TSKQSNAAVQPPSSTTPNSVSGKEEPKLATCGSLTSATSTSTTTTITNGI  1250
1251  GVARTTASTAVSTASTTTTSSGTFITSCTSTTTTTTSSISNGSKDLPKAM  1300
1301  IKPNVLTHVIDGFIIQEANEPFPVTRQRYADKDVSDEPPKKKATMQEDIK  1350
1351  LSGIASAPGSDMVACEQCGKMEHKAKLKRKRYCSPGCSRQAKNGIGGVGS  1400
1401  GETNGLGTGGIVGVDAMALVDRLDEAMAEEKMQTEATPKLSESFPILGAS  1450
1451  TEVPPMSLPVQAAISAPSPLAMPLGSPLSVALPTLAPLSVVTSGAAPKSS  1500
1501  EVNGTDRPPISSWSVDDVSNFIRELPGCQDYVDDFIQQEIDGQALLLLKE  1550
1551  KHLVNAMGMKLGPALKIVAKVESIKEVPPPGEAKDPGAQ             1589

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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