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

NucPred

Fetching P46530 from www.uniprot.org...

The NucPred score for your sequence is 0.78 (see score help below)

   1  MNRFLVKLTLLTAASLATVAQGQRCSEYCQNGGICEYKPSGEASCRCPAD    50
  51  FVGAQCQFPNPCNPSPCRNGGVCRPQMQGNEVGVKCDCVLGFSDRLCLTP   100
 101  VNHACMNSPCRNGGTCSLLTLDTFTCRCQPGWSGKTCQLADPCASNPCAN   150
 151  GGQCSAFESHYICTCPPNFHGQTCRQDVNECAVSPSPCRNGGTCINEVGS   200
 201  YLCRCPPEYTGPHCQRLYQPCLPSPCRSGGTCVQTSDTTHTCSCLPGFTG   250
 251  QTCEHNVDDCTQHACENGGPCIDGINTYNCHCDKHWTGQYCTEDVDECEL   300
 301  SPNACQNGGTCHNTIGGFHCVCVNGWTGDDCSENIDDCASAACSHGATCH   350
 351  DRVASFFCECPHGRTGLLCHLDDACISNPCQKGSNCDTNPVSGKAICTCP   400
 401  PGYTGSACNQDIDECSLGANPCEHGGRCLNTKGSFQCKCLQGYEGPRCEM   450
 451  DVNECKSNPCQNDATCLDQIGGFHCICMPGYEGVFCQINSDDCASQPCLN   500
 501  GKCIDKINSFHCECPKGFSGSLCQVDVDECASTPCKNGAKCTDGPNKYTC   550
 551  ECTPGFSGIHCELDINECASSPCHYGVCRDGVASFTCDCRPGYTGRLCET   600
 601  NINECLSQPCRNGGTCQDRENAYICTCPKGTTGVNCEINIDDCKRKPCDY   650
 651  GKCIDKINGYECVCEPGYSGSMCNINIDDCALNPCHNGGTCIDGVNSFTC   700
 701  LCPDGFRDATCLSQHNECSSNPCIHGSCLDQINSYRCVCEAGWMGRNCDI   750
 751  NINECLSNPCVNGGTCKDMTSGYLCTCRAGFSGPNCQMNINECASNPCLN   800
 801  QGSCIDDVAGFKCNCMLPYTGEVCENVLAPCSPRPCKNGGVCRESEDFQS   850
 851  FSCNCPAGWQGQTCEVDINECVRNPCTNGGVCENLRGGFQCRCNPGFTGA   900
 901  LCENDIDDCEPNPCSNGGVCQDRVNGFVCVCLAGFRGERCAEDIDECVSA   950
 951  PCRNGGNCTDCVNSYTCSCPAGFSGINCEINTPDCTESSCFNGGTCVDGI  1000
1001  SSFSCVCLPGFTGNYCQHDVNECDSRPCQNGGSCQDGYGTYKCTCPHGYT  1050
1051  GLNCQSLVRWCDSSPCKNGGSCWQQGASFTCQCASGWTGIYCDVPSVSCE  1100
1101  VAARQQGVSVAVLCRHAGQCVDAGNTHLCRCQAGYTGSYCQEQVDECQPN  1150
1151  PCQNGATCTDYLGGYSCECVPGYHGMNCSKEINECLSQPCQNGGTCIDLV  1200
1201  NTYKCSCPRGTQGVHCEIDIDDCSPSVDPLTGEPRCFNGGRCVDRVGGYG  1250
1251  CVCPAGFVGERCEGDVNECLSDPCDPSGSYNCVQLINDFRCECRTGYTGK  1300
1301  RCETVFNGCKDTPCKNGGTCAVASNTKHGYICKCQPGYSGSSCEYDSQSC  1350
1351  GSLRCRNGATCVSGHLSPRCLCAPGFSGHECQTRMDSPCLVNPCYNGGTC  1400
1401  QPISDAPFYRCSCPANFNGLLCHILDYSFSGGQGRDIAPPVEVEIRCEIA  1450
1451  QCEGRGGNAICDTQCNNHACGWDGGDCSLNFDDPWQNCSAALQCWRYFND  1500
1501  GKCDEQCATAGCLYDGFDCQRLEGQCNPLYDQYCRDHYADGHCDQGCNNA  1550
1551  ECEWDGLDCADDVPQKLAVGSLVLVVHIPPDELRNRSSSFLRELSSLLHT  1600
1601  NVVFRRDANGEALIFPYYGSEHELSKHKRSDWTDPGQLMQRARRSLTSFL  1650
1651  KPRTRRELDHMEVKGSIVYLEIDNRQCFQQSDECFQSATDVAAFLGALAS  1700
1701  SGNLNVPYIIEAVTSEGGPPKTGEMYPMFLVLLALAVLALAAVGVVVSRK  1750
1751  RKREHGQLWFPEGFKVNEPKKKRREPVGEDSVGLKPLKNSDSSLMDEQLS  1800
1801  EWAEDDTNKRFRFEGQSILEMSGQLDHRQWTQQHLDAADLRLNSMAPTPP  1850
1851  QGQIENDCMDVNVRGPDGFTPLMIASCSGGGLENENGEAEEDPSADVITD  1900
1901  FIYHGANLHNQTDRTGETALHLAARYARSDAAKRLLESCADANVQDNMGR  1950
1951  TPLHAAVAADAQGVFQILIRNRATDLDARMHDGTTPLILATRLAVEGMVE  2000
2001  ELINCHADPNAVDDSGKSALHWAAAVNNVDAAVVLLKNGANKDLQNNKEE  2050
2051  TPLFLAAREGSYETAKVLLDHLANRDIADHLDQLPRDIAHERMHHDIVRL  2100
2101  LEEYNLVRSPPLPLSPPLCCPNTYLGIKPSPGNNNNTAKKTRKPGGKGVG  2150
2151  GKDSGKDIRTKKKKSGDGKNGGIMEVGVLSPVDSLESPHGYLSDVSSPPM  2200
2201  MTSPFQQSPPISLNQLQGLADSHMGGALQGLGKPFDSAPRLSHLPVANNV  2250
2251  GGAQAGACDWLQRVQQQQQQQQQQQQAGMLMPTMLSATNMPQVMGYPTMQ  2300
2301  SSHLGAPSHMIAHQNMAPMQHQNISHHFLGDLSGLDLQSSSGHAPIQTIL  2350
2351  PQDSQRMAPPISSTQFLTPPSQHSYSNPMDNTPNHQQVPDHPFLTPSAGS  2400
2401  PDQWSSSSPHSNLSDWSEGISSPPTSMQMNHIPEAFK               2437

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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