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

NucPred

Fetching Q84TX2 from www.uniprot.org...

The NucPred score for your sequence is 0.66 (see score help below)

   1  MIRYQIRNEYGLSDPELYAPGEKDDPEALLEGVAMAGLVGVLRQLGDLAE    50
  51  FAAEIFHDLHEDVMATASRGHGLMLRLRQLEAEFPAVEKAIISQSDHSNY   100
 101  PHDDGVEWHTNLQIDQNMITQGDMPRFILDSYEECRGPPRLFTLDKFDVA   150
 151  GAGASLKRYSDPSFFKTEHSSDMIETDAVIEKKPRKIKKKALRWRKGETL   200
 201  ESLLIANSESHTTSKDRSSRKVPPRTTKLKYRYPRESDHKNISRICREHL   250
 251  QEIISSQQKIFSNYSSRYYHPKFRLTESSETASSFGEIDNFSARAQSSAK   300
 301  LELTKVVPINEFDTKGIAPTHINGSDCLEALEADDRQLQATQHEPDKVED   350
 351  VCKRSLVEQNAMLSNSDRMQSVQEENLLSAMVPADQNDDRCRPDDTGSDQ   400
 401  ENFVDALNNMESEGEAHAEMKIKKDPGAKMELDELNFHRDEGENERHTEF   450
 451  SELGHVIDSSPWLNDSYNGGEPNHAISSNTNFSGVDCTNDEEPSNDVDLM   500
 501  EMDVSSSSSVFSDDNDVFRTNGNMNGFQQYQEASLSNDHHAVIAHSSDKQ   550
 551  SSQKSSGLDGSSIESNDFIEKPFHSLEDDKNFAPDGTSVILGRPNDVSQC   600
 601  EEEIEVGNADDSLLQPTISNQEVHRSNNQLEGVAMHASISSGKVASFPDM   650
 651  DPGMCTKDLELDNVLVPKETVANTPPTGLGTDHIHEHVDELDSGVAPINS   700
 701  SIQSDSTYESDDDDMAEDLNSLPEDDLYKHDVEDLYKHVLEDDGIIALGK   750
 751  GPCSTRANMHQEDPMEVSDVRGDFSNGQELPVLTETASPQGELVGGGELP   800
 801  LLTETASPQGGEEDLADEVVVISSRDLNDEKKPSLAEVPLACGDASLLDS   850
 851  SASCLEHDESTETGEIAKSDEVLVNVEVAEESITGRFTDDMTPFQEDLPD   900
 901  GAKYSEDAEFLANPRVDNSRHDVQLQSSSPCREELETVKAPCENLCALDE   950
 951  SREHIFEKSVLQINNLPQHIETKNTGEACSDIDDIQHLSALHCPKNPVCQ  1000
1001  EELPDETNLSADVQYHCDVEKGGAVILNSKMVEEQPENIDLVREPRAQDS  1050
1051  FGTNPFMDPGYKANHALADPCPSYQPCFSEEEQDFISELLIPHGNMGIED  1100
1101  LNPVPVADSLWEPATPPDEVPLPSEVMTEEDFRSFCHEYHEMDLTATPES  1150
1151  IDDKPASDSNVVSSSLVTSESEFLYCVSAVRTGVDQEESRDAPDDTLMHF  1200
1201  SAKADPDDKAANSDLKSDEPFIDEKIHELGVPSVPMELEVEQHALHEVDS  1250
1251  HGDSQLLDNDMIDETCSSPSGNSIAVKDKQETCANLVSRAFINERTDELE  1300
1301  VPVSNSVLLEPSEEVHDSDEYNYQDVPWSSTDEGRDEVDAHPLSKRIQTQ  1350
1351  GSEALVLGELDSRAVPSCSVNEMADHVDAPPLSTVLEAEQEPEDCISGEH  1400
1401  NSQVTKSSLVDEKIGELDDASPLSNTLLAEMEREVCVPGKSASQIASCSP  1450
1451  TPSNEKIDELNAPPLSSSGLIELESEDSVSGDLDSQIIPCSSPNDKTNEP  1500
1501  DGATSTHVLPVELEQEVCSFPELDSLVAPCSLNDDKVCELDEPPCKQLES  1550
1551  ENGSYCLPQVDCQIEPCYSESVVLSEASTMSSANAMPSTEETYRLSSPVP  1600
1601  PPNEPFSNVSYEDPQKPPPLPPLLWRLGKPRLGIASTKGHMLEPERGKGP  1650
1651  VLHTSDAGMDNMPGCLSGMTESIEPVSSQEIKERHLDPILDNNERGVEFR  1700
1701  RLATPPTANDVAVTEHVQLFSDACENIKHQERVSSSETEAEEHQNGTGIT  1750
1751  DVMDSHPPKPLFLVPSISQQGLQGSVFPSDTSDNGEHSSYTSRAVSEDEK  1800
1801  TVDDHNAACAMDLHITSSSASSHVSENGCNQQSHGESLPVTSVDKVHTSD  1850
1851  ASCEDNKLKNHFITSEVCSDATNLSASGLLTEEENIHNVEDQYEGPLPSE  1900
1901  ESSGCLDYPHDDHNSEKEDIHQPDGYAASPGNNNHFDSSHEGGYLHAEQP  1950
1951  PVMGWTVRPQMLHPNYGISMEENQFEPKVEDHLLIKKPVSIRNIPRNPLV  2000
2001  DAVAAHDRSTMRKVSELVAPTDKSKPNERNLLLEQIRNKTFNLKPVSSAK  2050
2051  QPTIRTPPRASTRNLKVAAIIEKANAIRQAVGSDDEDGDNWSESSDT     2097

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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