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

NucPred

Fetching Q6Y9H0 from www.uniprot.org...

The NucPred score for your sequence is 0.16 (see score help below)

   1  GHGAVTSPQTQRGYTAFVHTKLSRVIGASGIHTGTMSFGKMEGDASDKNI    50
  51  GFMLQDDVADGPYYRQEWEGMKQTTPIISGGMNALRLPAFFENLGHSNVI   100
 101  LTAGGGAFGHKDGPKQGAISCAQGEESWKLWKAGTYGDVSLSDGVVEYAK   150
 151  THEELKGAFLTFQKDADQIYPGWKEKLGYTGESSVQAASFNWQKKDLAAA   200
 201  FVGASTTRKASSVARRALDQSSRYADLSLTEEDLIKNGQHVLVAYIMKPK   250
 251  AGYDYLATAAHFAAESSTGTNVNVCTTDDFTKTVDALVYYIDPENEEMKI   300
 301  AYPTALFDRNITDGRAMMCSVLTLSIGNNQGMGDVDYGKIYDIYFPPQYL   350
 351  RLFDGPSCCVIDMWRILGRGTVGGGLVVGTIIKPKLGLQPKPFGQACYGF   400
 401  WQGGDFIKNDEPQGNQTFCQMNECIPEVVKAMRAAQEETGQGKLFSANIT   450
 451  ADDPNEMIARAKYILNQMGPMAENCAFLVDGYVAGGTAVTVARRNFPKQF   500
 501  LHYHRAGHGAVTSPQTQRGYTAFVHTKLSRVIGASGIHTGTMSFGKMEGD   550
 551  ASDKNIGFMLQDDVADGPYYRQEWEGMKQTTPIISGGMNALRLPAFFENL   600
 601  GHSNVILTAGGGAFGHKDGPKQGAISCAQGEESWKLWKAGTYGDVSLSDG   650
 651  VVEYAKTHEELKGAFLTFQKDADQIYPGWKEKLGYTGESSVQAASFNWQK   700
 701  KDLAAAFVGASTTRKASSVARRALDQSSRYADLSLTEEDLIKNGQHVLVA   750
 751  YIMKPKAGYDYLATAAHFAAESSTGTNVNVCTTDDFTKTVDALVYYIDPE   800
 801  NEEMKIAYPTALFDRNITDGRAMMCSVLTLSIGNNQGMGDVDYGKIYDIY   850
 851  FPPQYLRLFDGPSCCVIDMWRILGRGTVGGGLVVGTIIKPKLGLQPKPFG   900
 901  QACYGFWQGGDFIKNDEPQGNQTFCQMNECIPEVVKAMRAAQEETGQGKL   950
 951  FSANITADDPNEMIARAKYILNQMGPMAENCAFLVDGYVAGGTAVTVARR  1000
1001  NFPKQFLHYHRAGHGAVTSPQTQRGYTAFVHTKLSRVIGASGIHTGTMSF  1050
1051  GKMEGDASDKNIGFMLQDDVADGPYYRQEWEGMKQTTPIISGGMNALRLP  1100
1101  AFFENLGHSNVILTAGGGAFGHKDGPKQGAISCAQGEESWKLWKAGTYGD  1150
1151  VSLSDGVVEYAKTHEELKGAFLTFQKDADQIYPGWKEKLGYTGESSVQAA  1200
1201  SFNWQKKDLAAAFVGASTTRKASSVARRALDQSSRYADLSLTEEDLIKNG  1250
1251  QHVLVAYIMKPKAGYDYLATAAHFAAESSTGTNVNVCTTDDFTKTVDALV  1300
1301  YYIDPENEEMKIAYPTALFDRNITDGRAMMCSVLTLSIGNNQGMGDVDYG  1350
1351  KIYDIYFPPQYLRLFDGPSCCVIDMWRILGRGTVGGGLVVGTIIKPKLGL  1400
1401  QPKPFGQACYGFWQGGDFIKNDEPQGNQTFCQMNECIPEVVKAMRAAQEE  1450
1451  TGQGKLFSANITADDPNEMIARAKYILNQMGPMAENCAFLVDGYVAGGTA  1500
1501  VTVARRNFPKQFLHYHRAGHGAVTSPQTQRGYTAFVHTKLSRVIGASGIH  1550
1551  TGTMSFGKMEGDA                                       1563

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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