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

NucPred

Fetching Q7S1I0 from www.uniprot.org...

The NucPred score for your sequence is 0.73 (see score help below)

   1  MASSQPTSSGPILDSPPSPNPQSQLNTETSSSQHRANPSEAPAQPGPGPA    50
  51  RPSALTKRPSHREVAAYRMSRKLQRLRADSNQPHSPTMELPDRLKDNGKE   100
 101  EDNEEDVLQPQGGMFMNMNQSIFGLIAAAGSTVDFHDRFEGQSSEDEDDV   150
 151  PNHMAMTFAGPGIKGTARNRETAGTVKSLSQTVVFNKPPASATVDAGPSN   200
 201  IHRRRLPGHKLLQSVPSLSRLSSSHKSKKTKQHNATAMADNKIEEEEDPD   250
 251  PSSPLPPLSKDETESLGLAPPIEIVRAEGNGAPLMSRMLEARAEMEARPS   300
 301  FDLDRLSGEHRRDDAGVTGQLAKKLKDIFEFDTAEEVIEEYPCWLLQHVL   350
 351  LQGYMYITANHIAFYAHLPKKAHEIAKSGYLSKSGKRNPKYNRYWFRLKG   400
 401  DVLSYYQDPKDHYFPAGQIDLRYGISASVNDKEKEGNYFSVSTHHRTYHF   450
 451  KADSARSAKEWVKSLQRVIFRSHNDGDSVKISIPIRNILDIEEAQMVEFA   500
 501  DTCKIRVIDNDETYAIDEYFFSFFSFGKKAIQVLKVLVEDSSPEDSGAND   550
 551  APKGTGGDRAIGDNLGSPRTRTFSEGVKATLSPVSPIQIASPSSRASGDY   600
 601  FKSSFDGTRPFSRRSFDASPGTAGYAGSPPRRLHGDGRRSFSKPRHEPHA   650
 651  STDSYAQSFDDPSQASLSALVASGSEDQSASQILRGSDVFHSPIFRRSAS   700
 701  ATRATTEGEGVAAPPIVRQHTAGLVRLHGPHHAATTGQIGDHMAEAEGGP   750
 751  STPMLQSIAMMGNYPLQRANAFMGYLDQQSRRMSNLLATESMGYVEKVSG   800
 801  MWKGGKKHYDHPAGRRTEREDVEDDPEERALSEARFQAHFALPETERLQA   850
 851  AYFGFIVRVLPLYGKIYISNRHFCFRSLLPGTRTKLILPLKDIETVDKEK   900
 901  GFRFGYSGLVVVIRGHEEIFFEFAKAENRDDCAITIIQSLDAARYLAESQ   950
 951  EVEEAQAAEAERDALNQARNEEFPDHEIELPRQASGVSDAPTILFDDPKA  1000
1001  SFLNFKPSEPMRITCLTIGSRGDVQPYIALCKRLLEEGHRPKIVTHREFK  1050
1051  DWIESHGIEFGPVEGDPSELMRICIENGTFTYAFLREANSKFRGWLDELL  1100
1101  TSAWEACQGSDLLIESPSAMAGIHIAEALGIPYFRAFTMPWTRTRAYPHA  1150
1151  FIMPGQKMGGAYNYITYVMFDNVFWKATAHQVNRWRNKYLGLPNTSLEKL  1200
1201  QPNKVPFLYNFSPSVVPPPIDYSDWIRVTGYWFLDEGGDKWQPPKELTDF  1250
1251  IAKARADEKKLVYIGFGSIIVSDPAKMTQEIIDAVLKADVRCILSKGWSD  1300
1301  RSATVDGVEKPKVADPSFPPEILQIQSAPHDWLFQQVDAAAHHGGSGTTG  1350
1351  ASLRAGIPTIIRPFFGDQFFFAGRVEDLGVGIYLKKWGVQSFARALWEAT  1400
1401  HSSRMQMRAEVLGGQIRAENGVDTAIQAIYRDLDYARNLITLKRQKHQSR  1450
1451  RNSVATPTPGAKPNAPEDDQGQAAEEDDIDADDEEEESWTFVGGNEDDLT  1500
1501  GSMSMSRSDMLSQTVADLRGVKVGKAPALGSRVLSSPPTSPGAMRGAGGV  1550
1551  KYV                                                 1553

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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