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

NucPred

Fetching Q71SP7 from www.uniprot.org...

The NucPred score for your sequence is 0.41 (see score help below)

   1  MEEVVITGMSGKLPESENLEEFWANLIGGVDMVTDDDRRWKAGLYGLPRR    50
  51  SGKLKDLSRFDASFFGVHPKQAHNMDPQLRLLLEVTYEAIVDAGINPASI   100
 101  RGTNTGVWVGVSGSEASEALSRDPETLVGYSMVGCQRAMLANRLSFFFDF   150
 151  KGPSITLDTACSSSLLALQRAYQAIQRGECAMAIVGGVNIRLKPNTSVQF   200
 201  MKLGMLSPEGTCKFFDASGNGYCRAKAVMAILLTKKSLARRVYATILNAG   250
 251  TNTDGCKEKGVTFPSGEAQEQLISSLYKPAGLDPETLEYVEAHGTGTKVG   300
 301  DPQELNGIVQALCGTRQSPLRIGSTKSNMGHPEPASGLAALAKVLLSLEH   350
 351  GLWAPNLHFHNPNPKIPALQDGRLQVVDRPLPVLGGNVGINSFGFGGSNV   400
 401  HVILQPNSQPLPPPAPHAALPRLLRASGRTLEGVQGLLELGLQHSQNLAF   450
 451  VSMLNDIATPSPAAMPFRGYAVLGSQGGSQKVQQVLAGKRPLWFICSGMG   500
 501  TQWRGMGLSLMRLSRFRDSILRSDEAVKPLGLQVSQLLLSTDEAIFDDMV   550
 551  ISFVSLTAIQIALIDLLTSMGLQPDGIIGHSLGEVACGYADGCISQEEAI   600
 601  LSAYWRGQCIKEANIPPGAMAAVGLTWEECKQRCPPGIVPACHNCIDTVT   650
 651  ISGPQASMLEFVQQLKQEGVFAKEVRTGGMAFHSYFMDAIAPMLLQQLKK   700
 701  VIREPQPRSPRWLSTSIPETQWQESLARTFSAEYNVNNLVSPVLFQEALW   750
 751  RVPEDAVVLEIAPHALLQAVLKRGLKSSCTIIPLMKKDHRDNLEFFLSNV   800
 801  GQLYLTGIDVNPNGLFPPVEFPAPRGTPLISPHIKWDHSQTWDVPTAEDF   850
 851  PSGSSSSSATIYKIDINPESPDHYLVDHCIDGRIIFPGTGYLCLVWKTLA   900
 901  RALDQNMEHTPVVFEDVTLHQAVILPKTGIVLLKVRLLEASCTFEVSENG   950
 951  NLIASGKVYQWEDPNPKLFDNRYGPDPATPVDPTTAIHLSRGDVYKELQL  1000
1001  QGFNYGPYFQGILEASSEGNTGQLLWKDNWVTFMDTMLQMSILAPSKRSL  1050
1051  RLPTRITAIYIHPATHQQKLYTLQDKTQVADVVINRCLDTTVAGGIYISR  1100
1101  IHTSVAPRHQQEQLVPILEKFCFTPHVETGCLAGNLALQEELQLCVGLAQ  1150
1151  ALQTRVAQQGIKMVVPGLDGAQAPQEAPQQGLPRLLATACQLQLNGNLQM  1200
1201  EMGQILAQERALLCDDPLLSGLLNSPALKACVTLALENMTSLKMKVVLAG  1250
1251  DGQLYSRIPTLLNTQPLLELDYTATDRHPQALEAAQAKLQQLDITQGQWD  1300
1301  PSDPAPSNLGGANLVVCNYALASLGDPATAVGNMVAALKEGGFLLLHTLL  1350
1351  RGHPLGETVTFLTCPEPQQGQRHLLSQDEWERLFAGASLHLVALKKSFYG  1400
1401  SVLFLCRRLAPLDSPIFLPVEDTSFQWVDSLKNILADSSSRAVWLMAVGC  1450
1451  TTSGVVGLVNCLRKEPDGHRIRCVLVSNLNSTSPIPETDPKSLELQKVLQ  1500
1501  SDLVMNVYRDGAWGAFRHFPLEQDKPEEQTEHAFINVLTRGDLSSIRWVC  1550
1551  SPLRHSQPTAPGFQLCTIYYASLNFKRNHAGHGQAVPRRHPRNWASRNCL  1600
1601  LGMEFSGRDASGKRVMGLVPAEGLATSTLVPQSFLWDVPSNWTLEEAASV  1650
1651  PVVYSTAYYALMVRGRMQPGETVLIHSGSGGVGQAAIAIALSLGCRVFPL  1700
1701  VGSAEKRAYLQSRFPQLNETSFANSRDTSFEQHVLWHTAGKGADLVLNSL  1750
1751  AEEKLQASVRCLAQHGRFLEIGKFDLSKNHPLGMAIFLKNVTFHGILLDS  1800
1801  LFEENNTMWQEVSTLLKAGIRKGVVQPLKRTVFPRTQAEDAFRYMAQGKH  1850
1851  IGKVVIQVREEEQEAVLHGTKPTQMVALCKTFCPAHKSYIITGGLGGFGL  1900
1901  ELAHWLVERGAQKLVLTSRSGIRTGYQARQVHEWRRQGVQVLVSTSDVST  1950
1951  LDGTRSLITEAAQLGPVGGIFNLAVVLRDAMLDNQTPEFFQDVNKPKYNG  2000
2001  TLNLDRVTREACPELDYFEVFSSVSCGRGNAGQTNYGFANSTMERICEKR  2050
2051  RHDGLPGLAVQWGAIADVGLLMELKGTKDKAIGGTLPQRITSCMEVLDLF  2100
2101  LNQPHPVLSSFVLAEKATSRGPSGSHQDLVKAVTHILGIRDLATVNLDSS  2150
2151  LSDLGLDSLMGVEVRQMLEREHNLLLSMREIRQLTIHKLQEISAQAGTAD  2200
2201  ELTDSTPKFGSPAQSHTQLNLSTLLVNPEGPTLTRLNSVQSSERPLFLVH  2250
2251  PIEGSTTVFHSLATKLSIPTYGLQCTGAAPLDSIQSLATYYIECIRQVQP  2300
2301  EGNYRIAGYSYGACVAFEMCSQLQAQQNAGPTNNSLFLFDGSHTFVMAYT  2350
2351  QSYRAKLNPGCEAEAEAEAMCFFMQQFTEAEHSRVLEALLPLGDLEARVA  2400
2401  ATVELIVQSHAGLDRHALSFAARSFYHKLRAAEEYTPRATYHGNVTLLRA  2450
2451  KMGSAYQEGLGADYNLSQVCDGKVSVHIIEGDHRTLLEGSGLESILSIIH  2500
2501  SSLAEPRVSVREG                                       2513

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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