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

NucPred

Fetching Q562F6 from www.uniprot.org...

The NucPred score for your sequence is 1.00 (see score help below)

   1  MECPVMETGSLFTSGIKRHLKDKRISKTTKLNVSLASKIKTKILNNSSIF    50
  51  KISLKHNNRALAQALSREKENSRRITTEKMLLQKEVEKLNFENTFLRLKL   100
 101  NNLNKKLIDIEALMNNNLITAIEMSSLSEFHQSSFLLSASKKKRISKQCK   150
 151  LMRLPFARVPLTSNDDEDEDKEKMQCDNNIKSKTLPDIPSSGSTTQPLST   200
 201  QDNSEVLFLKENNQNVYGLDDSEHISSIVDVPPRESHSHSDQSSKTSLMS   250
 251  EMRNAQSIGRRWEKPSPSNVTERKKRGSSWESNNLSADTPCATVLDKQHI   300
 301  SSPELNCNNEINGHTNETNTEMQRNKQDLPGLSSESAREPNAECMNQIED   350
 351  NDDFQLQKTVYDADMDLTASEVSKIVTVSTGIKKKSNKKTNEHGMKTFRK   400
 401  VKDSSSEKKRERSKRQFKNSSDVDIGEKIENRTERSDVLDGKRGAEDPGF   450
 451  IFNNEQLAQMNEQLAQVNELKKMTLQTGFEQGDRENVLCNKKEKRITNEQ   500
 501  EETYSLSQSSGKFHQESKFDKGQNSLTCNKSKASRQTFVIHKLEKDNLLP   550
 551  NQKDKVTIYENLDVTNEFHTANLSTKDNGNLCDYGTHNILDLKKYVTDIQ   600
 601  PSEQNESNINKLRKKVNRKTEIISGMNHMYEDNDKDVVHGLKKGNFFFKT   650
 651  QEDKEPISENIEVSKELQIPALSTRDNENQCDYRTQNVLGLQKQITNMYP   700
 701  VQQNESKVNKKLRQKVNRKTEIISEVNHLDNDKSIEYTVKSHSLFLTQKD   750
 751  KEIIPGNLEDPSEFETPALSTKDSGNLYDSEIQNVLGVKHGHDMQPACQN   800
 801  DSKIGKKPRLNVCQKSEIIPETNQIYENDNKGVHDLEKDNFFSLTPKDKE   850
 851  TISENLQVTNEFQTVDLLIKDNGNLCDYDTQNILELKKYVTDRKSAEQNE   900
 901  SKINKLRNKVNWKTEIISEMNQIYEDNDKDAHVQESYTKDLDFKVNKSKQ   950
 951  KLECQDIINKHYMEVNSNEKESCDQILDSYKVVKKRKKESSCKAKNILTK  1000
1001  AKNKLASQLTESSQTSISLESDLKHITSEADSDPGNPVELCKTQKQSTTT  1050
1051  LNKKDLPFVEEIKEGECQVKKVNKMTSKSKKRKTSIDPSPESHEVMERIL  1100
1101  DSVQGKSTVSEQADKENNLENEKMVKNKPDFYTKAFRSLSEIHSPNIQDS  1150
1151  SFDSVREGLVPLSVSSGKNVIIKENFALECSPAFQVSDDEHEKMNKMKFK  1200
1201  VNRRTQKSGIGDRPLQDLSNTSFVSNNTAESENKSEDLSSERTSRRRRCT  1250
1251  PFYFKEPSLRDKMRR                                     1265

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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