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

NucPred

Fetching Q8X1T3 from www.uniprot.org...

The NucPred score for your sequence is 0.30 (see score help below)

   1  MAQVEDYSSLHRLRKNSEILSNANKILVANRGEIPIRIFRSAHELSMQTV    50
  51  AIYSHEDRLSMHRLKADEAYVIGARGQYSPVQAYLQIDEIINIALEHNVS   100
 101  MIHPGYGFLSENSEFARKVEDSGMIWIGPPHNVIDAVGDKVSARNLAGKC   150
 151  NVPVVPGTDGPIDSVEQAQEFVDKYGYPVIIKAAFGGGGRGMRVVREGES   200
 201  IADAFQRATSEAKTAFGNGTCFIERFLDKPKHIEVQLLADNYGNVIHLFE   250
 251  RDCSVQRRHQKVVEIAPAKTLPVEVRDAILTDAVKLAKAANYRNAGTAEF   300
 301  LVDNQNRHYFIEINPRIQVEHTITEEVTGVDIVAAQIQIAAGASLQQLGL   350
 351  LQDKITTRGFAIQCRITTEDPAKNFQPDTGKIEVYRSSGGNGVRLDGGNG   400
 401  FAGAIISPHYDSMLVKCSTSGSNYEIARRKMIRALVEFRIRGVKTNIPFL   450
 451  LALLTHPTFVSGDCWTTFIDDTPSLFEMVQSKNRAQKLLSYLADLCVNGS   500
 501  SIKGQIGLPKLTRDADIPVIHDINGWDIDIKNTPPPESFRQYLLDYGPEQ   550
 551  FANQIRAFDGCLIMDTTWRDAHQSLLATRVRTIDLLNIAPATAHAFRYAF   600
 601  ALECWGGATFDVAMRFLHEDPWDRLRKLRKAVPNIPFQMLLRGANGVAYS   650
 651  SLPDNAIDHFVKQAKDAGVDIFRVFDALNDLEQLKVGVDAVKKAGGVVEA   700
 701  TVCYSGDMLKPGKKYNLKYYLETVDKIMEMGTHLLGIKDMAGTLKPAAAK   750
 751  LLISSIRKKYPSVPIHVHTHDSAGTGVITYVACALAGADVVDCAVNSMSG   800
 801  LTSQPSMSAFIAALDNEINTGITEQNAREIDAYWSEMRLLYSCFEADLKG   850
 851  PDPEVYNHEIPGGQLTNLLFQAQQVGLGEKWLETKKAYEEANMLLGDIVK   900
 901  VTPTSKVVGDLAQFMVSNKLSPKDVERLASELDFPDSVLDFFEGLMGTPY   950
 951  GGFPEPLRTNILAGKRRKLTRRPGLELEPFDLKKIKEELQSRFGNSITEC  1000
1001  DVASYNMYPKVFESFKKIQEKYGDLSVLPTRFFLAPPKLNEEISVEIEQG  1050
1051  KTFVIKVMAIGDLSPQTGTREVYFEFNGEMRKVTVEDKLAAVETVTRPKA  1100
1101  DAHNPNEVGAPMAGVVIEVRVHPGVEVKKGDPLCVLSAMKMEMVISSPVS  1150
1151  GRVGEVIVHENDSVDAGDLICKITK                           1175

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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