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

NucPred

Fetching Q332R7 from www.uniprot.org...

The NucPred score for your sequence is 1.00 (see score help below)

   1  MTGHEFKSWILELREILREIKNSHYFLDSWTQFNSVGSFIHIFFHQERFI    50
  51  KLFDSRIWSILLSHNSQGSTSNRYFTIKGVILFGVAVLIYRINNRNMVER   100
 101  KNLYLIGLLPIPMNSIGPRNDTLEESVGSSNINRLIVSLLYLPKGKKIYE   150
 151  SSFLNPKESTWVLPITKKCSMPESNWGSRWWRDWIGKKRDSSCKISNETV   200
 201  AGIEILFKEKDLKYLEFFFVYYRDDPIRKDHDWELFDRLSLRKRQNRINL   250
 251  NSGPLFEILVKHWICYLMSAFREKIPIEVEGFFKQQGAGSTIKSNDIEHV   300
 301  SHLFSRNKSAISLQNCAQFHMWQFRQDLFVSWGKNPPESDLLRNVSRENL   350
 351  IWLDNVWLVNKDRFFRKVRNVSSNIQYDSTRSSFVQVRDSSQLKGSSDQS   400
 401  RDHFDSISNEDSEYHTLINQREIQQLKERSILWDPSFLQTEGTEIESNRF   450
 451  PKCLSGYSSMSRLFTEREKQMINHLLPEEIEEFLGNPTRSVRSFFSDRWS   500
 501  EFHLGSNPTERSTRDQKLLKKQQDLSFLRRSENKEMVNLFKIITYLQNTV   550
 551  SIHPISSDSGCDMVPKDEPDMDSSNKISFLNKNPFFDLFHLFHDRNRGGY   600
 601  TLHHDFESEERFQELADLFTLSITEPDLVYHKRFAFSIDSYGLDPKQFLN   650
 651  GVFNSRYEWKTTSLLVLLVLLPIFYEENESFYRRIRKKRVRISCGNDLEE   700
 701  PKPKIVVFASNNIMEAANQYRLIRNLIQIQHSTHRYIRNVLNRFFLMNRS   750
 751  DRNFKYGIQRDQIGKDTLNHRTLMKYMINQHLSNLKKSQKRWFDPLIFFS   800
 801  RTKRSMNRDPDAYRYKWSTGSKNFQEHFVSEQKSRFQVVFDRLRINQYSI   850
 851  DWSEVIDKKDLSKPLRFFLSKLLLFLSNSLPFLFVSFGNIPIHRSEIYIY   900
 901  ELKGPNDPQFLESIGLQIVHLKKLKPFLLDDHETCQKSKFLINGGTISPF   950
 951  LFNKIPKWMIDSFHTRNNRRKSFDNTDSYFSMIFHDQYNWLNPVKSFHRS  1000
1001  SLRSSFYKANQLRFLNNPHHFCFYCNKRFPFYVEKARINNYDFTYGQFLN  1050
1051  ILFIRNKIFSLCVGKKKHAFWGRDTISAIESQVSNIFIPKAFPQSGDETY  1100
1101  NLYKSFHFPSRSNPFVRRAIYSIADISGTPLTEGQIVNFERTYCQPLSDM  1150
1151  NLSDSEGKNLYQYLNFNSNMGLIHTPCYEKYLPSEKRKKRSLCLKKCVEK  1200
1201  GQMYRTFQRDSAYSTLSKWNLFQTYMPWFLTSTGYRYLKFLFLDTFSDLL  1250
1251  PILSSSQKFVSIFHDIMHGSNISWRILQKKFCLPQRNLISEISSKCLHNL  1300
1301  LLSEEMIHRNNESPLISTHLTNVREFLYAILFLLLVAAYLACTRLLFVFG  1350
1351  ASSELQTEFEKVKSLMIPSSMIELRKLLDRYPTSEPNSFWFLKQLGDSLG  1400
1401  GNMLLGGGPAYRVKSIRSKKKYLNINLIDIIDLISIIPNPINRITFSRNT  1450
1451  RHLSHTSKEIYSLIRKRKNVNGDWIDDKIESWVANSDSIDDEKREFLVQF  1500
1501  STLTTEKRIDQILLSLTHSDHFSKNDSGYQMIEQPGAIYLRYLVDIHKKY  1550
1551  LMNYEFNTSSLAERRIFLAHYQTITYSQTSCGANSLHFPSHGKPFSLRLA  1600
1601  LSLSRGTLVIGSIGTGRSYLVKYLAKNSYLPFITVFLNKSLDNKSQGFDN  1650
1651  IDVDASDDSDASDDIDASDDILDMELELLTSMNALTMDMMPEDEDLLYIT  1700
1701  LQFELAKAMSPCIIWIPNIHDLDVNESNYLSPGLLVNLLSRDYETRNILV  1750
1751  IASTHIPQKVDPALIAPNKLNTCIKIRRLLIPQQRKHFFTLSYTRGFHLE  1800
1801  KKMFHTNGFGSITMGSNARDLVALTNEALSISITQNKSIIDTNTIRSALH  1850
1851  RQIWDLRSQVRSVQDHGILFYKIGRAVAQNVLLSNCPIDPISIYMKKKSC  1900
1901  NEVDYYLYNWYFELGTSMKKLTILLYLLSCSAGSVTQDLWSLPGPDEKNG  1950
1951  ITPYGLVENDSGLVRGLLEVEGALVGSSRTCSQFDKDRVTLLLRPEPRNP  2000
2001  LDMMQNGSCSILDQRFLYEKDESEFEEGDERQQIEEDLFNHIVWAPRIWR  2050
2051  PWGFLFDCIERPNELGFPYWSRSFRGKRIVYDEEDELQENDSEFLQNGTV  2100
2101  QYQTRDISSKEQGLFRISQFIWDPADPLFFLFKAQPFVSVFSHRELFADE  2150
2151  EMSKGLLTPQKNRPTSLYKRWFIKKTQEKHFELLINRQRWLRTNRSLSNG  2200
2201  SFRSNTLSESYQYLSNLFLSNGTLLDQMTKALLRKRWLFPDEMQIGFMEQ  2250
2251  DKDFPFLSQKDMWP                                      2264

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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