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

NucPred

Fetching Q9TU23 from www.uniprot.org...

The NucPred score for your sequence is 0.78 (see score help below)

   1  ERQLRKENGKQKNELMAMEAEVGEKIGRLQRFKEMAVFKIAALQKVVDNS    50
  51  VSLSELELANRQYNELTAKYRDILQKDNMLVQRTNNLEHLECENVSLKEQ   100
 101  MESINKELEITKEKLHTIEQAWEQETKLGNESNMDKAKKSVTNSEIVSIS   150
 151  KKITMLEMKELNERQRAEHSQKMYEHVKTSLQQVEERNFELETKFAELTR   200
 201  INLEAQKVEQMLRDELADSVSKTVSDADRQHILELEKSEMELKVEVSKLK   250
 251  EISDIAKRQVEILNAQQQSREKEVESLRTQLLDYQAQSDEKALIAKLHQH   300
 301  VVSLQASEAAALGKVESVASKLQKVEAHTLRLEQKLDEKEQALFYARLEG   350
 351  RNRAKHLRQTIQSLRRQFSGALPLAQQEKFSKTMIQLQNDKLKIMEEMKN   400
 401  SQQEHRSLKNKTLEMELKLKGLEDLISTLKDARGAQKVISWHTKIEELRL   450
 451  QELKLNRELVKDKEEIKYLNNIISEYENTISSLEEEIVQQNKFHEERQMA   500
 501  WDQREVELERQLDVFDRQQSEILREAQKFEEATGSMPDPSLPIPNQLEIA   550
 551  LRKIKENIRIILETQATCRSLEEKLREKESALRLAEENILSRDKVINELR   600
 601  LRLPATAEQEKLLAEFSRKEVEPKSHHTLKLAHQTIANMQARLNQKEEVL   650
 651  KKYQHLLEKAREEQREIVKKHEEELHTLHRKLELQADNSLSKFKETAWDL   700
 701  IKQSPTPVPTNKHFIRLAEMEQTVAEQDDSLSSLVIKLKQVSQDLERQKE   750
 751  ITELKIKEFENMKLRLQENHADEVKKIKAEVEDLRCLLVQSQKESQSLKS   800
 801  ELQTQKEANSRAPTTTMRNLVERLKSQLALKEKQQKALSRALLELRAEMT   850
 851  AAAEERIISMTSQKEANLNVQQIVDRHTKELKSQIEDLNENILKLKEALK   900
 901  TSKNRENTLTDNLNDLTNELQNKQKAYGKVLREKDAVDQENNELKRQIKR   950
 951  LTSGLQGKPLIDNKQSLIEELQKKIKKLESQLERKVDEAEMKPMKEKSAR  1000
1001  EEVIRWEEGKKWQTKIEGIRNKLKEKEGEVYILTKQLTTLKDLFAKADKE  1050
1051  KLTLQRKLKTTGLTVDQVMAARVLESEKELEELKKRNLDLENDISYMRSH  1100
1101  QALPRDSVIEDLHLQNKYLQEKLHALEKQLSKDAYSRPSTSGIDSDDHYQ  1150
1151  REQELQRENLKLSSENIELKFQLEQANKDLPRLKNQVRDLKEMCEFLKKE  1200
1201  KAEVERKLGRVRGSGRSGKTIPELEKTIGLMKKVVEKVQRENEQLKKASG  1250
1251  ILTSEKMANIEMENEKLKAELEKLKVHLGRQLSMHYESKAKGTEKIVAEN  1300
1301  ERLRKELKKIEILKHVPEGDETEQGLQRELRVLRLANSQLEKEKEELIHR  1350
1351  IEISKDQNGPDSTISDPDHLMEKIKDLETQLRTSDMEKQHLKEEIQKLKK  1400
1401  ELENFDPSFFEEIEDLKYNYKEEVKKNILLEEKLKKLSEQFGVELTSPVA  1450
1451  ASEQFEDEQENPVNFPIY                                  1468

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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