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

NucPred

Fetching P28742 from www.uniprot.org...

The NucPred score for your sequence is 0.90 (see score help below)

   1  MARSSLPNRRTAQFEANKRRTIAHAPSPSLSNGMHTLTPPTCNNGAATSD    50
  51  SNIHVYVRCRSRNKREIEEKSSVVISTLGPQGKEIILSNGSHQSYSSSKK   100
 101  TYQFDQVFGAESDQETVFNATAKNYIKEMLHGYNCTIFAYGQTGTGKTYT   150
 151  MSGDINILGDVQSTDNLLLGEHAGIIPRVLVDLFKELSSLNKEYSVKISF   200
 201  LELYNENLKDLLSDSEDDDPAVNDPKRQIRIFDNNNNNSSIMVKGMQEIF   250
 251  INSAHEGLNLLMQGSLKRKVAATKCNDLSSRSHTVFTITTNIVEQDSKDH   300
 301  GQNKNFVKIGKLNLVDLAGSENINRSGAENKRAQEAGLINKSLLTLGRVI   350
 351  NALVDHSNHIPYRESKLTRLLQDSLGGMTKTCIIATISPAKISMEETAST   400
 401  LEYATRAKSIKNTPQVNQSLSKDTCLKDYIQEIEKLRNDLKNSRNKQGIF   450
 451  ITQDQLDLYESNSILIDEQNLKIHNLREQIKKFKENYLNQLDINNLLQSE   500
 501  KEKLIAIIQNFNVDFSNFYSEIQKIHHTNLELMNEVIQQRDFSLENSQKQ   550
 551  YNTNQNMQLKISQQVLQTLNTLQGSLNNYNSKCSEVIKGVTEELTRNVNT   600
 601  HKAKHDSTLKSLLNITTNLLMNQMNELVRSISTSLEIFQSDSTSHYRKDL   650
 651  NEIYQSHQQFLKNLQNDIKSCLDSIGSSILTSINEISQNCTTNLNSMNVL   700
 701  IENQQSGSSKLIKEQDLEIKKLKNDLINERRISNQFNQQLAEMKRYFQDH   750
 751  VSRTRSEFHDELNKCIDNLKDKQSKLDQDIWQKTASIFNETDIVVNKIHS   800
 801  DSIASLAHNAENTLKTVSQNNESFTNDLISLSRGMNMDISSKLRSLPINE   850
 851  FLNKISQTICETCGDDNTIASNPVLTSIKKFQNIICSDIALTNEKIMSLI   900
 901  DEIQSQIETISNENNINLIAINENFNSLCNFILTDYDENIMQISKTQDEV   950
 951  LSEHCEKLQSLKILGMDIFTAHSIEKPLHEHTRPEASVIKALPLLDYPKQ  1000
1001  FQIYRDAENKSKDDTSNSRTCIPNLSTNENFPLSQFSPKTPVPVPDQPLP  1050
1051  KVLIPKSINSAKSNRSKTLPNTEGTGRESQNNLKRRFTTEPILKGEETEN  1100
1101  NDILQNKKLHQ                                         1111

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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