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

NucPred

Fetching Q03640 from www.uniprot.org...

The NucPred score for your sequence is 0.56 (see score help below)

   1  MTGIKAQVHPPPDSTLFHEEEKKKVGGNLPQKVINQQERGSDHAPSGHHQ    50
  51  YHQLINHDANDTKTSNSVSDVSKGQKTADSNPEGKKQSSKDIFVASSAQK   100
 101  TNQLPGPNPQGSIGAVPLEGLRPKEFRSAPSRKPNKFDTSITKPGVLDDL   150
 151  GKLDEKDIKEKFHLDSDDKLFPWQNVGEFHASGKGSPNTKMSRVIKAYIL   200
 201  ENFYNDWYCNIATVLGTCFFSWLFAYIGFSWWSMIFIFLGTATVYNAEYT   250
 251  RFNRNIRDDLKRVTVEETLSDRVESTTWLNSFLSKFWVIYMPVLSQQVKD   300
 301  NVNPQLAGVAPGYGIDALAIDEFTLGSKAPTIKGIKSYTKTGKNTVEMDW   350
 351  SFAFTPSDVSDMTATEAREKINPKISLGVTLGKSFVSKTMPILVEDINVA   400
 401  GKMRIKVEFGKAFPNIKIVSLQLLEPPLIDFALKPIGGDTLGLDVMSFLP   450
 451  GLKSFVKNIINSNIGPMLFPPNHLDINVEDIMAAQSKEAIGVLAVTIASA   500
 501  DSLKGSDFITNTVDPYIVMTTEDAVPGTDEEVRTSIKSNVKNPRWNETKY   550
 551  LLLNTLEQKLNLKCFDFNDVRKDTVIGDLQLDLADLLQNPVLDNQTAELR   600
 601  SGTKSKGILHYSLHWFPVKEDKSEEKAVERAEAKAKGKKEDENEDTTEKE   650
 651  EDENEESSQTDVGIAKITLQKVKYLDTTSSMTGSLSPCAELFIDGQKVKS   700
 701  YRTLRRINEPSWNETIEVLVPSKSNSKFVLKIFDDRMNGKALICEYSSSL   750
 751  DDIMTTLDTAQEFVKGSPQGDIYLDVSWKSIEMTGAFAAANSVSEPIGCI   800
 801  KLDVKDAIIKGDLSGVGDVDPYYTVSLNRRVLYKSIYHSDTDHPIFDNST   850
 851  YVPIFSPNQILTLEFHDYQKIGKDRFIGSVQIPTSNVFKKDPKSGKYVGN   900
 901  NGKEEISKLKLKDHEHKVTESIVNVSTTFIPINLVYSPEELVNVEKLEKE   950
 951  LKEKKKKFEATQEENEQEMEKNPKEWEVAEIEDPFDSDEKKINRKAKLSL  1000
1001  NELIKQKSGILSMQILEGTLSPSSAYLEILADDISYPVFICMKPSQGKLN  1050
1051  SEMANIFIRDLNYSKLHFRVSKKHIAKDSDDVISETSYSTLKLLKQAYEE  1100
1101  PMWLNFNGSKMKVRFLYTPTSVKLPSSESVEDTGYLNIKLISGHGLKSAD  1150
1151  RNGYSDPFVHIFVNDKKVFKSNIKKKTLDPVWNEDAKIPILSRSKNQVIF  1200
1201  NVLDWDRAGDNDDLGQASLDVSSLEVGKTYNWNLNLNTQGSIKLQGSFNP  1250
1251  EYIKPSFDIVKGGITDKPMKIASGAAHATVGIAGTGIGAATGVATGGLKK  1300
1301  GGHLLKSLGGNPMKRSKSSNGNESNGAKKSSEKKSFDRRSPSNLNSTSVT  1350
1351  PRASLDYDPSVPNTSYAPVQSASPVVKPTDNTSSSSNKKDTPSSNSRGHS  1400
1401  RASSFARTLAPHGTYNGFITVVAAENVAKHVQIKISLTQGGRLKHIYKTK  1450
1451  SQKANNDGVAVFDEECSFKASPEANLVLGAISHQRLSRDKDLGIAQINLG  1500
1501  DPQIQQDGQISVKLGDGHLIVKINYGKDKNGQVPPVPEVPQEYTQ       1545

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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