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

NucPred

Fetching P25054 from www.uniprot.org...

The NucPred score for your sequence is 0.99 (see score help below)

   1  MAAASYDQLLKQVEALKMENSNLRQELEDNSNHLTKLETEASNMKEVLKQ    50
  51  LQGSIEDEAMASSGQIDLLERLKELNLDSSNFPGVKLRSKMSLRSYGSRE   100
 101  GSVSSRSGECSPVPMGSFPRRGFVNGSRESTGYLEELEKERSLLLADLDK   150
 151  EEKEKDWYYAQLQNLTKRIDSLPLTENFSLQTDMTRRQLEYEARQIRVAM   200
 201  EEQLGTCQDMEKRAQRRIARIQQIEKDILRIRQLLQSQATEAERSSQNKH   250
 251  ETGSHDAERQNEGQGVGEINMATSGNGQGSTTRMDHETASVLSSSSTHSA   300
 301  PRRLTSHLGTKVEMVYSLLSMLGTHDKDDMSRTLLAMSSSQDSCISMRQS   350
 351  GCLPLLIQLLHGNDKDSVLLGNSRGSKEARARASAALHNIIHSQPDDKRG   400
 401  RREIRVLHLLEQIRAYCETCWEWQEAHEPGMDQDKNPMPAPVEHQICPAV   450
 451  CVLMKLSFDEEHRHAMNELGGLQAIAELLQVDCEMYGLTNDHYSITLRRY   500
 501  AGMALTNLTFGDVANKATLCSMKGCMRALVAQLKSESEDLQQVIASVLRN   550
 551  LSWRADVNSKKTLREVGSVKALMECALEVKKESTLKSVLSALWNLSAHCT   600
 601  ENKADICAVDGALAFLVGTLTYRSQTNTLAIIESGGGILRNVSSLIATNE   650
 651  DHRQILRENNCLQTLLQHLKSHSLTIVSNACGTLWNLSARNPKDQEALWD   700
 701  MGAVSMLKNLIHSKHKMIAMGSAAALRNLMANRPAKYKDANIMSPGSSLP   750
 751  SLHVRKQKALEAELDAQHLSETFDNIDNLSPKASHRSKQRHKQSLYGDYV   800
 801  FDTNRHDDNRSDNFNTGNMTVLSPYLNTTVLPSSSSSRGSLDSSRSEKDR   850
 851  SLERERGIGLGNYHPATENPGTSSKRGLQISTTAAQIAKVMEEVSAIHTS   900
 901  QEDRSSGSTTELHCVTDERNALRRSSAAHTHSNTYNFTKSENSNRTCSMP   950
 951  YAKLEYKRSSNDSLNSVSSSDGYGKRGQMKPSIESYSEDDESKFCSYGQY  1000
1001  PADLAHKIHSANHMDDNDGELDTPINYSLKYSDEQLNSGRQSPSQNERWA  1050
1051  RPKHIIEDEIKQSEQRQSRNQSTTYPVYTESTDDKHLKFQPHFGQQECVS  1100
1101  PYRSRGANGSETNRVGSNHGINQNVSQSLCQEDDYEDDKPTNYSERYSEE  1150
1151  EQHEEEERPTNYSIKYNEEKRHVDQPIDYSLKYATDIPSSQKQSFSFSKS  1200
1201  SSGQSSKTEHMSSSSENTSTPSSNAKRQNQLHPSSAQSRSGQPQKAATCK  1250
1251  VSSINQETIQTYCVEDTPICFSRCSSLSSLSSAEDEIGCNQTTQEADSAN  1300
1301  TLQIAEIKEKIGTRSAEDPVSEVPAVSQHPRTKSSRLQGSSLSSESARHK  1350
1351  AVEFSSGAKSPSKSGAQTPKSPPEHYVQETPLMFSRCTSVSSLDSFESRS  1400
1401  IASSVQSEPCSGMVSGIISPSDLPDSPGQTMPPSRSKTPPPPPQTAQTKR  1450
1451  EVPKNKAPTAEKRESGPKQAAVNAAVQRVQVLPDADTLLHFATESTPDGF  1500
1501  SCSSSLSALSLDEPFIQKDVELRIMPPVQENDNGNETESEQPKESNENQE  1550
1551  KEAEKTIDSEKDLLDDSDDDDIEILEECIISAMPTKSSRKAKKPAQTASK  1600
1601  LPPPVARKPSQLPVYKLLPSQNRLQPQKHVSFTPGDDMPRVYCVEGTPIN  1650
1651  FSTATSLSDLTIESPPNELAAGEGVRGGAQSGEFEKRDTIPTEGRSTDEA  1700
1701  QGGKTSSVTIPELDDNKAEEGDILAECINSAMPKGKSHKPFRVKKIMDQV  1750
1751  QQASASSSAPNKNQLDGKKKKPTSPVKPIPQNTEYRTRVRKNADSKNNLN  1800
1801  AERVFSDNKDSKKQNLKNNSKVFNDKLPNNEDRVRGSFAFDSPHHYTPIE  1850
1851  GTPYCFSRNDSLSSLDFDDDDVDLSREKAELRKAKENKESEAKVTSHTEL  1900
1901  TSNQQSANKTQAIAKQPINRGQPKPILQKQSTFPQSSKDIPDRGAATDEK  1950
1951  LQNFAIENTPVCFSHNSSLSSLSDIDQENNNKENEPIKETEPPDSQGEPS  2000
2001  KPQASGYAPKSFHVEDTPVCFSRNSSLSSLSIDSEDDLLQECISSAMPKK  2050
2051  KKPSRLKGDNEKHSPRNMGGILGEDLTLDLKDIQRPDSEHGLSPDSENFD  2100
2101  WKAIQEGANSIVSSLHQAAAAACLSRQASSDSDSILSLKSGISLGSPFHL  2150
2151  TPDQEEKPFTSNKGPRILKPGEKSTLETKKIESESKGIKGGKKVYKSLIT  2200
2201  GKVRSNSEISGQMKQPLQANMPSISRGRTMIHIPGVRNSSSSTSPVSKKG  2250
2251  PPLKTPASKSPSEGQTATTSPRGAKPSVKSELSPVARQTSQIGGSSKAPS  2300
2301  RSGSRDSTPSRPAQQPLSRPIQSPGRNSISPGRNGISPPNKLSQLPRTSS  2350
2351  PSTASTKSSGSGKMSYTSPGRQMSQQNLTKQTGLSKNASSIPRSESASKG  2400
2401  LNQMNNGNGANKKVELSRMSSTKSSGSESDRSERPVLVRQSTFIKEAPSP  2450
2451  TLRRKLEESASFESLSPSSRPASPTRSQAQTPVLSPSLPDMSLSTHSSVQ  2500
2501  AGGWRKLPPNLSPTIEYNDGRPAKRHDIARSHSESPSRLPINRSGTWKRE  2550
2551  HSKHSSSLPRVSTWRRTGSSSSILSASSESSEKAKSEDEKHVNSISGTKQ  2600
2601  SKENQVSAKGTWRKIKENEFSPTNSTSQTVSSGATNGAESKTLIYQMAPA  2650
2651  VSKTEDVWVRIEDCPINNPRSGRSPTGNTPPVIDSVSEKANPNIKDSKDN  2700
2701  QAKQNVGNGSVPMRTVGLENRLNSFIQVDAPDQKGTEIKPGQNNPVPVSE  2750
2751  TNESSIVERTPFSSSSSSKHSSPSGTVAARVTPFNYNPSPRKSSADSTSA  2800
2801  RPSQIPTPVNNNTKKRDSKTDSTESSGTQSPKRHSGSYLVTSV         2843

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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