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

NucPred

Fetching Q61315 from www.uniprot.org...

The NucPred score for your sequence is 1.00 (see score help below)

   1  MAAASYDQLLKQVEALKMENSNLRQELEDNSNHLTKLETEASNMKEVLKQ    50
  51  LQGSIEDETMTSGQIDLLERLKEFNLDSNFPGVKLRSKMSLRSYGSREGS   100
 101  VSSRSGECSPVPMGSFPRRTFVNGSRESTGYLEELEKERSLLLADLDKEE   150
 151  KEKDWYYAQLQNLTKRIDSLPLTENFSLQTDMTRRQLEYEARQIRAAMEE   200
 201  QLGTCQDMEKRAQRRIARIQQIEKDILRVRQLLQSQAAEAERSSQSRHDA   250
 251  ASHEAGRQHEGHGVAESNTAASSSGQSPATRVDHETASVLSSSGTHSAPR   300
 301  RLTSHLGTKVEMVYSLLSMLGTHDKDDMSRTLLAMSSSQDSCISMRQSGC   350
 351  LPLLIQLLHGNDKDSVLLGNSRGSKEARARASAALHNIIHSQPDDKRGRR   400
 401  EIRVLHLLEQIRAYCETCWEWQEAHEQGMDQDKNPMPAPVEHQICPAVCV   450
 451  LMKLSFDEEHRHAMNELGGLQAIAELLQVDCEMYGLTNDHYSVTLRRYAG   500
 501  MALTNLTFGDVANKATLCSMKGCMRALVAQLKSESEDLQQVIASVLRNLS   550
 551  WRADVNSKKTLREVGSVKALMECALEVKKESTLKSVLSALWNLSAHCTEN   600
 601  KADICAVDGALAFLVGTLTYRSQTNTLAIIESGGGILRNVSSLIATNEDH   650
 651  RQILRENNCLQTLLQHLKSHSLTIVSNACGTLWNLSARNPKDQEALWDMG   700
 701  AVSMLKNLIHSKHKMIAMGSAAALRNLMANRPAKYKDANIMSPGSSLPSL   750
 751  HVRKQKALEAELDAQHLSETFDNIDNLSPKASHRSKQRHKQNLYGDYAFD   800
 801  ANRHDDSRSDNFNTGNMTVLSPYLNTTVLPSSSSSRGSLDSSRSEKDRSL   850
 851  ERERGIGLSAYHPTTENAGTSSKRGLQITTTAAQIAKVMEEVSAIHTSQD   900
 901  DRSSASTTEFHCVADDRSAARRSSASHTHSNTYNFTKSENSNRTCSMPYA   950
 951  KVEYKRSSNDSLNSVTSSDGYGKRGQMKPSVESYSEDDESKFCSYGQYPA  1000
1001  DLAHKIHSANHMDDNDGELDTPINYSLKYSDEQLNSGRQSPSQNERWARP  1050
1051  KHVIEDEIKQNEQRQARSQNTSYPVYSENTDDKHLKFQPHFGQQECVSPY  1100
1101  RSRGTSGSETNRMGSSHAINQNVNQSLCQEDDYEDDKPTNYSERYSEEEQ  1150
1151  HEEEEERPTNYSIKYNEEKHHVDQPIDYSLKYATDISSSQKPSFSFSKNS  1200
1201  SAQSTKPEHLSPSSENTAVPPSNAKRQNQLRPSSAQRNGQTQKGTTCKVP  1250
1251  SINQETIQTYCVEDTPICFSRCSSLSSLSSADDEIGCDQTTQEADSANTL  1300
1301  QTAEVKENDVTRSAEDPATEVPAVSQNARAKPSRLQASGLSSESTRHNKA  1350
1351  VEFSSGAKSPSKSGAQTPKSPPEHYVQETPLVFSRCTSVSSLDSFESRSI  1400
1401  ASSVQSEPCSGMVSGIISPSDLPDSPGQTMPPSRSKTPPPPPQTVQAKRE  1450
1451  VPKSKVPAAEKRESGPKQTAVNAAVQRVQVLPDVDTLLHFATESTPDGFS  1500
1501  CSSSLSALSLDEPFIQKDVELRIMPPVQENDNGNETESEQPEESNENQDK  1550
1551  EVEKPDSEKDLLDDSDDDDIEILEECIISAMPTKSSRKAKKLAQTASKLP  1600
1601  PPVARKPSQLPVYKLLPAQNRLQAQKHVSFTPGDDVPRVYCVEGTPINFS  1650
1651  TATSLSDLTIESPPNELATGDGVRAGIQSGEFEKRDTIPTEGRSTDDAQR  1700
1701  GKISSIVTPDLDDNKAEEGDILAECINSAMPKGKSHKPFRVKKIMDQVQQ  1750
1751  ASSTSSGANKNQVDTKKKKPTSPVKPMPQNTEYRTRVRKNTDSKVNVNTE  1800
1801  ETFSDNKDSKKPSLQTNAKAFNEKLPNNEDRVRGTFALDSPHHYTPIEGT  1850
1851  PYCFSRNDSLSSLDFDDDDVDLSREKAELRKGKESKDSEAKVTCRPEPNS  1900
1901  SQQAASKSQASIKHPANRAQSKPVLQKQPTFPQSSKDGPDRGAATDEKLQ  1950
1951  NLAIENTPVCFSRNSSLSSLSDIDQENNNNKESEPIKEAEPANSQGEPSK  2000
2001  PQASGYAPKSFHVEDTPVCFSRNSSLSSLSIDSEDDLLQECISSAMPKKK  2050
2051  RPSRLKSESEKQSPRKVGGILAEDLTLDLKDLQRPDSEHAFSPGSENFDW  2100
2101  KAIQEGANSIVSSLHQAAAAAACLSRQASSDSDSILSLKSGISLGSPFHL  2150
2151  TPDQEEKPFTSNKGPRILKPGEKSTLEAKKIESENKGIKGGKKVYKSLIT  2200
2201  GKIRSNSEISSQMKQPLPTNMPSISRGRTMIHIPGLRNSSSSTSPVSKKG  2250
2251  PPLKTPASKSPSEGPGATTSPRGTKPAGKSELSPITRQTSQISGSNKGSS  2300
2301  RSGSRDSTPSRPTQQPLSRPMQSPGRNSISPGRNGISPPNKLSQLPRTSS  2350
2351  PSTASTKSSGSGKMSYTSPGRQLSQQNLTKQASLSKNASSIPRSESASKG  2400
2401  LNQMSNGNGSNKKVELSRMSSTKSSGSESDSSERPALVRQSTFIKEAPSP  2450
2451  TLRRKLEESASFESLSPSSRPDSPTRSQAQTPVLSPSLPDMSLSTHPSVQ  2500
2501  AGGWRKLPPNLSPTIEYNDGRPTKRHDIARSHSESPSRLPINRAGTWKRE  2550
2551  HSKHSSSLPRVSTWRRTGSSSSILSASSESSEKAKSEDERHVSSMPAPRQ  2600
2601  MKENQVPTKGTWRKIKESDISPTGMASQSASSGAASGAESKPLIYQMAPP  2650
2651  VSKTEDVWVRIEDCPINNPRSGRSPTGNTPPVIDSVSEKGSSSIKDSKDS  2700
2701  KDTHGKQSVGSGSPVQTVGLETRLNSFVQVEAPEQKGTEAKPGQSNPVSI  2750
2751  AETAETCIAERTPFSSSSSSKHSSPSGTVAARVTPFNYNPSPRKSSADST  2800
2801  SARPSQIPTPVSTNTKKRDSKTDITESSGAQSPKRHSGSYLVTSV       2845

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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