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

NucPred

Fetching P70478 from www.uniprot.org...

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

   1  MAAASYDQLLKQVEALKMENSNLRQELEDNSNHLTELETEASNMKEVLKQ    50
  51  LQGSIEDETMTSGQIDLLERLKEFNLDSNFPGVKLRSKMSLRSYGSREGS   100
 101  VSSRSGECSPVPMGSFPRRAFVNGSRESTGYLEELEKERSLLLADLDKEE   150
 151  KEKDWYYAQLQNLTKRIDSLPLTENFSLQTDMTRRQLEYEARQIRAAMEE   200
 201  QLGTCQDMEKRAQRRIARIQQIEKDILRVRQLLQSQAAEAERSSQSKHET   250
 251  ASHEAERQLEGQGVAESNLATSGSGQSSAARVDHETAGVLSSSGTHSAPR   300
 301  RLTSHLGTKVEMVYSLLSMLGTHDKDDMSRTLLAMSSSQDSCISMRQSGC   350
 351  LPLLIQLLHGNDKDSVLLGNSRGSKEARARASAALHNIIHSQPDDKRGRR   400
 401  EIRVLHLLEQIRAYCETCWEWQEAHEQGMDQDKNPMPAPVEHQICPAVCV   450
 451  LMKLSFDEEHRHAMNELGGLQAIAELLQVDCEMHGLTDDHYSVTLRRYAG   500
 501  MALTNLTFGDVANKATLCSMKGCMRALVAQLKSESEDLQQVIASVLRNLS   550
 551  WRADVNSKKTLREVGSVKALMECALEVKKESTLKSVLSALWNLSAHCTEN   600
 601  KADICAVDGALAFLVGTLTYRSQTNTLAIIESGGGILRNVSSLIATNEDH   650
 651  RQILRENNCLQTLLQHLKSHSLTIVSNACGTLWNLSARNPKDQEALWDMG   700
 701  AVSMLKNLIHSKHKMIAMGSAAALRNLMANRPAKYKDANIMSPGSSLPSL   750
 751  HVRKQKALEAELDAQHLSETFDNIDNLSPKASHRSKQRHKQNLYGDYVFD   800
 801  ASRHDDNRSDNFNTGNMTVLSPYLNTTVLPSSSSSRGSLDSSRSEKDRSL   850
 851  ERERGIGLSTYHSATENPGTSSKRGLQLSATAAQIAKVMEEVSALHTSQD   900
 901  DRSPASAAELHCVAEERTAARRSSASHTHPNTHNFAKSESSNRTCSMPYA   950
 951  KVEYKRSSNDSLNSVTSSDGYGKRGQMKPSVESYSEDDEGKFCSYGQYPA  1000
1001  DLAHKIHSANHMDDNGGELDTPINYSLKYSDEQLNSGRQSPSQNERWARP  1050
1051  KHVIEDEIKQNEQRQSRSQNTNFPVYSENTDDKHLKFQQHFGQQECVSPY  1100
1101  RSRGTNGSETNRMGSSHAVNQNVNQSLCQEDDYEDDKPTNYSERYSEEEQ  1150
1151  HEEEERPTNYSIKYNEEKHHVDQPIDYSLKYATDISSSQKPSFSFSKTPS  1200
1201  VQGTKTEHNSPSSEAASAPSSNAKRQSQLHPSSAQRNGQTPKGTACKVPS  1250
1251  INQETMQTYCVEDTPICFSRCSSLSSLSSAEDEIGCDQTTQEADSANTLQ  1300
1301  IAEIKENDVTRSAQDPASDVPAVSQSTRTKPSRLQASGLASESARHKAVE  1350
1351  FSSGAKSPSKSGAQTPKSPPEHYVQETPLVFSRCTSVSSLDSFESRSIAS  1400
1401  SVQSEPCSGMVSGIVSPSDLPDSPGQTMPPSRSKTPPPPPPPQPVQTKRE  1450
1451  VPKTKVPAAEQREGGPKQTAVSAAVQRVQVLPDADTLLHFATESTPDGFS  1500
1501  CSSSLSALSLDEPFIQKDVELRIMPPVQENDNGNETEPEQPEESNENQDK  1550
1551  EVEKPDSEKDLLDDSDDDDIEILEECIISAMPTKSSRKAKKLAQTASKLP  1600
1601  PPVARKPSQLPVYKLLPSQSRLQAQKHVSFTPGDDVPRVYCVEGTPINFS  1650
1651  TATSLSDLTIESPPNELAAGDGVRASVQSGEFEKRDTIPTEGRSTDEAQR  1700
1701  GKVSSIAIPDLDGSKAEEGDILAECINSALPKGRSHKPFRVKKIMDQVQQ  1750
1751  ASMTSSGTNKNQIDTKKKKPTSPVKPMPQNTEYRTRVRKNTDSKVNVNTE  1800
1801  ETFSDNKDSKKQSLKNNPKDLNDKLPDNEDRVRGGFTFDSPHHYAPIEGT  1850
1851  PYCFSRNDSLSSLDFDDDDVDLSREKAELRKGKESKDSEAKVTCHTEPSS  1900
1901  SQQSARKAQASTKHPVNRGPSKPLLQEQPTFPQSSKDVPDRGAATDEKLQ  1950
1951  NFAIENTPVCFSRNSSLSSLSDVDQENNNNEETGPVRDAEPANAQGQPGK  2000
2001  PQASGYAPKSFHVEDTPVCFSRNSSLSSLSIDSEDDLLRECISSAMPKKR  2050
2051  RPSRLKGEGEWQSPRKVGSVLAEDLTLDLKDIQRPESEHGLSPDSENFDW  2100
2101  KAIQEGANSIVSSLHQAAAAAACLSRQASSDSDSILSLKSGVSLGSPFHL  2150
2151  TPDQEEKPFTSHKGPRILKPGEKSTLEAKKIESENKGIKGGKKVYKSLIT  2200
2201  GKIRSNSEISSQMKQPLQTNMPSISRGRTMIHIPGVRNSSSSTSPVSKKG  2250
2251  PPLKTPASKSPSEGPVATTSPRGTKPAVKSELSPITRQTSHISGSNKGPS  2300
2301  RSGSRDSTPSRPTQQPLSRPMQSPGRNSISPGRNGISTPNKLSQLPRTSS  2350
2351  PSTASTKSSGSGKMSYTSPGRQLSQQNLSKQTGLSKNASSIPRSESASKG  2400
2401  LNQMNNSNGSNKKVELSRMSSTKSSGSESDRSERPALVRQSTFIKEAPSP  2450
2451  TLRRKLEESASFESLSPSSRPDSPTRSQAQTPVLSPSLPDMSLSTHPSVQ  2500
2501  AGGWRKLPPNLSPTIEYSDGRPSKRHDIARSHSESPSRLPVNRAGTWKRE  2550
2551  HSKHSSSLPRVSTWRRTGSSSSILSASSESSEKAKSEDEKHVNSVPGPRQ  2600
2601  MKENQVPTKGTWRKIKESEISPTNTVSQTTSSGAASGAESKTLIYQMAPA  2650
2651  VSRTEDVWVRIEDCPINNPRSGRSPTGNTPPVIDSISEKGNPSIKDSKDT  2700
2701  QGKQSVGSGSPVQTVGLENRLNSFIQVEAPEQKGTETKAGQGSPAPVAET  2750
2751  GETCMAERTPFSSSSSSKHSSPSGTVAARVTPFNYNPSPRKSSADSTSAR  2800
2801  PSQIPTPVGSSTKKRDSKTDSTESSGAQSPKRHSGSYLVTSV          2842

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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