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

NucPred

Fetching P70039 from www.uniprot.org...

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

   1  MAAASYDQLVKQVEALTMENTNLRQELEDNSNHLTKLETEATNMKEVLKQ    50
  51  LQGSIEDEAMASSGPIDLLERFKDLNLDSSNIPAGKARPKMSMRSYGSRE   100
 101  GSLSGHSGECSPVPVGSFQRRGLLNGSRESAGYMEELEKERLLLIAEHEK   150
 151  EEKEKRWYYAQLQNLTKRIDSLPLTENFSMQTDMTRRQLEYEARQIRAAM   200
 201  EEQLGTCQDMEKRVQTRVGKIHQIEEEILRIRQLLQSQVAEAAERTPQSK   250
 251  HDAGSRDAEKLPDGQGTSEITASGNVGSGQGSSSRADHDTTSVMSSNSTY   300
 301  SVPRRLTSHLGTKVEMVYSLLSMLGTHDKDDMSRTLLAMSSSQDSCIAMR   350
 351  QSGCLPLLIQLLHGNDKDSVLLGNSRGSKEARASGSAALDNIIHSQPDDK   400
 401  RGRREIRVLHLLEQIRAYCETCWEWQEAHEQGMDQDKNPMPAPVDHQICP   450
 451  AVCVLMKLSFDEEHRHAMNELGGLQAIAELLQVDCEMYGLINDHYSVTLR   500
 501  RYAGMALTNLTFGDVANKATLCSMKSCMRALVAQLKSESEDLQQVIASVL   550
 551  RNLSWRADVNSKKTLREVGSVKALMECALDVKKESTLKSVLSALWNLSAH   600
 601  CTENKADICSVDGALAFLVSTLTYRSQTNTLAIIESGGGILRNVSSLIAT   650
 651  NEDHRQILRENNCLQTLLQHLKSHSLTIVSNACGTLWNLSARNAKDQEGL   700
 701  WDMGAVSMLKNLIHSKHKMIAMGSAAALRNLMANRPAKYKDANIMSPGSS   750
 751  VPSLHVRKQKALEAELDAQHLSETFDNIDNLSPKTTHRNKQRHKQNLCSE   800
 801  YALDSSRHDDSICRSDNFSIGNLTVLSPYINTTVLPGSSSPRPTMDGSRP   850
 851  EKDRERTAGLGNYHSTTESSGNSSKRIGIQLSTTAQISKVMDEVSNIHLV   900
 901  QENRSSGSASEMHCMSDERNSQRKPSSNHPQSNPFTFTKAESSTRGCPVA   950
 951  FMKMEYKMASNDSLNSVSSTEGYGKRGQVKPSVESYSEDDESKFFSYGQY  1000
1001  PAGLAHKIQSANHMDDNDTELDTPINYSLKYSDEQLNSGRQSPTQNERWS  1050
1051  RPKHIIDSEMKQSEQRQPRTTKTTYSSYTENKEEKHKKFPPHFNQSENVP  1100
1101  AYTRSRGANNQVDQSRVSSNLSNNSKASKPHCQVDDYDDDKTTNFSERYS  1150
1151  EEEQQEDETERQNKYNIKAYASEEHHGEQPIDYSRKYSTDVPSSAQKPSF  1200
1201  PYSNNSSKQKPKKEQVSSNSNTPTPSPNSNRQNQLHPNSAQSRPGLNRPK  1250
1251  QIPNKPPSINQETIQTYCVEDTPICFSRGSSLSSLSSAEDEIEGRERNSR  1300
1301  GQESNNTLQITEPKEISAVSKDGAVNETRSSVHHTRTKNNRLQTSNISPS  1350
1351  DSSRHKSVEFSSGAKSPSKSGAQTPKSPPEHYVQETPLMFSRCTSGSSLD  1400
1401  SFESHSIASSIASSVASEHMISGIISPSDLPDSPGQTMPPSRSKTPPPPQ  1450
1451  TVQAKKDGSKPIVPDEERGKVAKTAVHSAIQRVQVLQEADTLLHFATEST  1500
1501  PDGFSCASSLSALSLDEPYIQKDVQLKIMPPVLENDQGNKAEPEKEFIDN  1550
1551  KAKKEDKRSEQEKDMLDDTDDDIDILEECIISAMPRKPSRKNKKVPQPTP  1600
1601  GKPPPPVARKPSQLPVYKLLSSQNRLQTQKHVNFTHSDDMPRVYCVEGTP  1650
1651  INFSTATSLSDLTIESPPSEPTNDQPNTDSLSTDLEKRDTIPTEGRSTDD  1700
1701  TDASKPLNPTTVLDEDKAEEGDILAECIHSAMPKGKSHKPYRVKKIMDQI  1750
1751  NHTSAATSSGNSRSMQETDKNKPTSPVKPMPQSIGFKERLKKNTELKLNP  1800
1801  NSENQYCDPRKPSSKKPSKVANEKIPNNEERTKGFAFDSPHHYTPIEGTP  1850
1851  YCFSRNDSLSSLDFEDDDIDLSKEKAELRKEKGTKDTDQKVKYKHENRAI  1900
1901  NPMGKQDQTGPKSLGGRDQPKALVQKPTSFSSAAKGTQDRGGATDEKMEN  1950
1951  FAIENTPVCFSRNSSLSSLSDIDQENNNKETEPLKQTGTSETQLGLRRPQ  2000
2001  TSGYAPKSFHVEDTPVCFSRNSSLSSLSIDSEDDLLQECISSAMPKKRKP  2050
2051  SKIKNEVGKSRSNSVGGILAEEPDLTLDLRDIQSPDSENAFSPDSENFDW  2100
2101  KAIQEGANSIVSRLHQAAAAGSLSRQGSSDSDSILSLKSGISLGSPFHLT  2150
2151  LDKEEKTITSNKGPKILKPAEKSALENKKTEEEPKGIKGGKKVYKSLITG  2200
2201  KSRSSSDFSSHCKQSVQTNMPSISRGRTMIHIPGVRASSPSTSPVSKKGP  2250
2251  VFKNVPSKGSNENPSSSSSPKGTKPLKSELVYGSRPSSTPGGSSKGNSRS  2300
2301  GSRDSASSRPSPQPLSRPLQSPGRNSISPGKNGISPPNKFSQLPRTTSPS  2350
2351  TASTKSSGSGRMSYTSPGRQLSQPNLSKQSGLPKTHSSIPRSESASKSLN  2400
2401  QNVNTGSNKKVELSRMSSTKSSGSESDRSERPALVRQSTFIKEAPSPTLR  2450
2451  RKLEESASFESLSSSSRADSPPRSQTQTPALSPSLPDMALSTHSIQAGGW  2500
2501  RKMPPNLNPAAEHGDSRRRHDISRSHSESPSRLPITRSGTWKREHSKHSS  2550
2551  SLPRVSTWRRTGSSSSILSASSESSEKAKSEDEKQQVCSFPGPRSECSSS  2600
2601  AKGTWRKIKESEILETPSNGSSSTIAESNCSLESKTLVYQMAPAVSKTED  2650
2651  VWVRIEDCPINNPRSGRSPTGNSPPVIDNVLDQGQKEEAAKDCHTRHNSG  2700
2701  NGNVPLLENRQKSFIKVDGLDTKGTDPKSLINNQQETNENTVAERTAFSS  2750
2751  SSSSKHSSPSGTVAARVTPFNYNPSPRKSNGENSTSRPSQIPTPVTNSTK  2800
2801  KRDSKTETTDSSGSQSPKRHSGSYLVTSV                       2829

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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