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

NucPred

Fetching Q8CJ27 from www.uniprot.org...

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

   1  MATMQAASCPEERGRRARPDPEAGDPSPPVLLLSHFCGVPFLCFGDVRVG    50
  51  TSRTRSLVLHNPHEEPLQVELSLLRAAGQGFSVAPNRCELKPKEKLTISV   100
 101  TWTPLREGGVREIVTFLVNDFLKHQAILLGNAEEPKKKKRSLWNTSKKIP   150
 151  ASSKHTKRTSKNQHFNESFTISQKDRIRSPLQPCENLAMSECSSPTENKV   200
 201  PTPSISPIRECQSETCLPLFLRESTAYSSLHESENTQNLKVQDASISQTF   250
 251  DFNEEVANETFINPISVCHQSEGDRKLTLAPNCSSPLNSTQTQIHFLSPD   300
 301  SFVNNRYTSDNDLKSMKNVLSDTFRKDPAESVCLESQTVHEVCQTILSPD   350
 351  SFLNDNYGLKKGLNFKSVNPVLSPTQFVKDSMGHVGQQTGKSNEASQDWR   400
 401  INEGLAYTPECQHAQTPSSRSEKQNPVEVKPHTYDFTKQKPKISEFQDAF   450
 451  CHQSKQPHKRRPILSATVTKRKPTNAREKLPEINKPDAKRCLEGLVGERG   500
 501  KEVGSLREKGFHSSLPVVEPGVSKALSYRDEVTPATVVVARKRKSHGTVG   550
 551  DANGKVAAEEWMDMCEVKRIHFSPLESTPSTVARTTKKEGHTSKRISSLE   600
 601  RSGLKKKMDSSILKTPLSKTKKKRRSIVAVAQSHLTFIKPLKAAIPRHPM   650
 651  PFAAKNMFYDERWKEKQEQGFTWWLNYILTPDDFTVKTNVSKVNAASLVL   700
 701  GAESQHKISVPKAPTKEEVSLRAYTASCRLNRLRRTACSLFTSEKMVKAI   750
 751  KKVEIEIEVGRLLVRKDRHLWKDIGQRQKVLNWLLSYNPLWLRIGLETVF   800
 801  GELIPLADNSDVTGLAMFILNRLLWNPDIAAEYRHPTVPLLFRDGHEAAL   850
 851  SKFTLKKLLLLICFLDHAKISRLIDHDPCLFCKDAEFKASKELLLAFSRD   900
 901  FLSGEGDLSRHLSFLGLPVSHVQTPLDEFDFAVTNLAVDLQCGVRLVRTV   950
 951  ELLTQNWNLSDKLRIPAISRVQKMHNVDLVLQVLKSRGVPLTDEHGSAIS  1000
1001  SKDVVDRHREKTLGLLWKIALAFQVDISLNLDQLKEEIDFLKHTHSIKRA  1050
1051  MSALTCPSQAITNKQRDKRISGNFERYGDSVQLLMDWVNAVCAFYNKKVE  1100
1101  NFTVSFSDGRILCYLIHHYHPCYVPFDAICQRTSQSVACAQTGSVVLNSS  1150
1151  SESEGGCLDLSLEALDHESTPEMYKELLENEKKNFHLVRSAARDLGGIPA  1200
1201  MIHHSDMSNTIPDEKVVITYLSFLCARLLDLRKEIRAARLIQTTWRKYKL  1250
1251  KRDLKHHQERDKAARVIQSVVLNFLSRRRLQKNVSAALVIQKCWRRVSAQ  1300
1301  RKLRMLKNEKLAKLQNKSAVLIQAYWRRYSTRKRFLRLKHYSVILQSRIR  1350
1351  MKIALTSYKRYLWATVTIQRHWRAYLSRKRDQQIFRKLKSSSLVIQFMFR  1400
1401  RWKRRKLQLQTKAAVTLQRAFREWHLRKQIRERSAVVIQSWYRMHRELQK  1450
1451  YIYIRSCVIVIQRRVRCFQAQKLYKRRKDAILTLQKHYRARQKGKLAHAD  1500
1501  YLQKRAATIRLQAAFRGMKARHSYRLQIGAACVLQSYWRMRQERVRFLNL  1550
1551  KKMVIKLQAHIRKYQQLQKYKKIKKAAITIQTHFRASISARRVLASYQKT  1600
1601  RSSVIVLQSACRGMQARKAFRHALASVIKIQSYYRAYICRKTFQNFKNAT  1650
1651  IKLQSIVKMKQSRKQYLQIRAAALFIQRWYRSQKLASQKRKEYIQVRESC  1700
1701  IKLQSHFRGCLVRKQLRLQCKAAISLQSYFRMRTARQRYLKMCKAALVIQ  1750
1751  SFYCAYRAQISQRKNFLQVKRAAICLQAAYRGCKVRRQIKQQSTAAVTIQ  1800
1801  RVFRGHSQRMKYQTMLQSAVKIQRWYRAQKVAYDMRIQFLKTREAVVCLQ  1850
1851  SAYRGWQVRQQLRRQHEAAVKIQSTFRMAVAQQQYKLLRAAAAVIQQHVR  1900
1901  ARAAGKRQHLAYIQLRHAALVFQAAWKGKMLRRQIARQHQCAALIQSYYR  1950
1951  MHIQRRKWSIMKTAALQIQLCYRAYKVGKEQRHLYLKTKAAVVTLQSAYR  2000
2001  GMKVRKRVAECHKAAVTIQSKFRAYRTQKKYTTYRTSAIVIQRWYRNIKI  2050
2051  TTQQHQEYLNLRRAAVQVQAAYRGIRVRRRIQHMHMAATLIEAMFKMRQS  2100
2101  RVRYLKMRTAALIIQVRYRAYYLGKIQHEKYLRTLKAIKTLQAGVRGARV  2150
2151  RRTVRKMHFAATLIQSHFRGHRQQTYFHRLRKAATMVQQRYRAVKEGSAE  2200
2201  FQRYSRLRRSVLLIQAAFRGLRTRRHLKAMHLAATLIQRRFRTFAMRRKF  2250
2251  LSLRKTAIWIQRQYRARLYAKYSRQQLLLEKAVIKIQSSYRGWVVRKRVQ  2300
2301  KMHRAATVIQATFRMHGAYMRYQHLKRASVVIQVHTAAELQRQKHAAVIL  2350
2351  QAAVRGMKTRSHLKTMHSSATLIQSQFRAFIVRRRFIALRKAAIFVQRKF  2400
2401  RATLYAKHKLHQFLQLRKAAITIQSSYRRLMVQKKLQEMHRAAALIQATF  2450
2451  RMHRTYVAFHIWKCASIRIQQCYRTYRTIKLQKEKLIREEQHSAAVLIQS  2500
2501  TYRMYRQRCFYQQRRWAAKVIQKTYRANKRRQDLLYVCKEETPLLQMHFQ  2550
2551  GLNTAKQGRQQHGAAMITQKHFRAFKARRLMEAERGFQAGCRKYKAKKYL  2600
2601  SKVEAACRIQAWYRRWRAHKKYLTLLKAVNIIEGYLSAQLARRRFLKMRA  2650
2651  AAIIIQRKWRATLSVRGARENLKRHRAACVIQAHFRGYQARQSFLQQRSA  2700
2701  VLIIQRHVRAMVAAKQERIKYIKLKKSTVVVQALVRGWLVRKRVSEQKAK  2750
2751  TRLFHFTAAAYCHMCALKIQRAYRLHVTLRNAKKHMDSVIFIQRWFRKRL  2800
2801  QRKRFIEQYHKILSTRREAHACWLQQDRAASVIQKAVRRFLLCRRQEKIT  2850
2851  SCATRIQALWRGYSWRKKNDHTEIKAIRRSLRAVSTTVEEENKLYRRTER  2900
2901  ALHHLLTYKHLSAILDALKHLEVVTRLSPLCCENMAESGAVSTIFVVIRS  2950
2951  CNRSVPCMEVVGYAVQVLLNVAKYDKTIAAVYEAENCVDTLLELLQVYRE  3000
3001  KPGDRVAEKSASIFTRTCCLLAVLLKTEQCAFDAQSRSKVTDRIYRLYKF  3050
3051  TVPKHKVNTQGLFDKQKQNSCVGFPCIPERTMKTRLVSRLKPQWVLRRDN  3100
3101  VEEITNSLQAIQLVMDTLGISY                              3122

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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