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

NucPred

Fetching Q9BY66 from www.uniprot.org...

The NucPred score for your sequence is 0.87 (see score help below)

   1  MEPGCDEFLPPPECPVFEPSWAEFQDPLGYIAKIRPIAEKSGICKIRPPA    50
  51  DWQPPFAVEVDNFRFTPRVQRLNELEAQTRVKLNYLDQIAKFWEIQGSSL   100
 101  KIPNVERKILDLYSLSKIVIEEGGYEAICKDRRWARVAQRLHYPPGKNIG   150
 151  SLLRSHYERIIYPYEMFQSGANHVQCNTHPFDNEVKDKEYKPHSIPLRQS   200
 201  VQPSKFSSYSRRAKRLQPDPEPTEEDIEKHPELKKLQIYGPGPKMMGLGL   250
 251  MAKDKDKTVHKKVTCPPTVTVKDEQSGGGNVSSTLLKQHLSLEPCTKTTM   300
 301  QLRKNHSSAQFIDSYICQVCSRGDEDDKLLFCDGCDDNYHIFCLLPPLPE   350
 351  IPRGIWRCPKCILAECKQPPEAFGFEQATQEYSLQSFGEMADSFKSDYFN   400
 401  MPVHMVPTELVEKEFWRLVSSIEEDVTVEYGADIHSKEFGSGFPVSNSKQ   450
 451  NLSPEEKEYATSGWNLNVMPVLDQSVLCHINADISGMKVPWLYVGMVFSA   500
 501  FCWHIEDHWSYSINYLHWGEPKTWYGVPSLAAEHLEEVMKMLTPELFDSQ   550
 551  PDLLHQLVTLMNPNTLMSHGVPVVRTNQCAGEFVITFPRAYHSGFNQGYN   600
 601  FAEAVNFCTADWLPAGRQCIEHYRRLRRYCVFSHEELICKMAAFPETLDL   650
 651  NLAVAVHKEMFIMVQEERRLRKALLEKGVTEAEREAFELLPDDERQCIKC   700
 701  KTTCFLSALACYDCPDGLVCLSHINDLCKCSSSRQYLRYRYTLDELPTML   750
 751  HKLKIRAESFDTWANKVRVALEVEDGRKRSFEELRALESEARERRFPNSE   800
 801  LLQRLKNCLSEVEACIAQVLGLVSGQVARMDTPQLTLTELRVLLEQMGSL   850
 851  PCAMHQIGDVKDVLEQVEAYQAEAREALATLPSSPGLLRSLLERGQQLGV   900
 901  EVPEAHQLQQQVEQAQWLDEVKQALAPSAHRGSLVIMQGLLVMGAKIASS   950
 951  PSVDKARAELQELLTIAERWEEKAHFCLEARQKHPPATLEAIIRETENIP  1000
1001  VHLPNIQALKEALTKAQAWIADVDEIQNGDHYPCLDDLEGLVAVGRDLPV  1050
1051  GLEELRQLELQVLTAHSWREKASKTFLKKNSCYTLLEVLCPCADAGSDST  1100
1101  KRSRWMEKALGLYQCDTELLGLSAQDLRDPGSVIVAFKEGEQKEKEGILQ  1150
1151  LRRTNSAKPSPLAPSLMASSPTSICVCGQVPAGVGVLQCDLCQDWFHGQC  1200
1201  VSVPHLLTSPKPSLTSSPLLAWWEWDTKFLCPLCMRSRRPRLETILALLV  1250
1251  ALQRLPVRLPEGEALQCLTERAIGWQDRARKALASEDVTALLRQLAELRQ  1300
1301  QLQAKPRPEEASVYTSATACDPIREGSGNNISKVQGLLENGDSVTSPENM  1350
1351  APGKGSDLELLSSLLPQLTGPVLELPEAIRAPLEELMMEGDLLEVTLDEN  1400
1401  HSIWQLLQAGQPPDLDRIRTLLELEKFEHQGSRTRSRALERRRRRQKVDQ  1450
1451  GRNVENLVQQELQSKRARSSGIMSQVGREEEHYQEKADRENMFLTPSTDH  1500
1501  SPFLKGNQNSLQHKDSGSSAACPSLMPLLQLSYSDEQQL             1539

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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