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

NucPred

Fetching P19096 from www.uniprot.org...

The NucPred score for your sequence is 0.36 (see score help below)

   1  MEEVVIAGMSGKLPESENLQEFWANLIGGVDMVTDDDRRWKAGLYGLPKR    50
  51  SGKLKDLSKFDASFFGVHPKQAHTMDPQLRLLLEVSYEAIVDGGINPASL   100
 101  RGTNTGVWVGVSGSEASEALSRDPETLLGYSMVGCQRAMMANRLSFFFDF   150
 151  KGPSIALDTACSSSLLALQNAYQAIRSGECPAALVGGINLLLKPNTSVQF   200
 201  MKLGMLSPDGTCRSFDDSGSGYCRSEAVVAVLLTKKSLARRVYATILNAG   250
 251  TNTDGSKEQGVTFPSGEVQEQLICSLYQPAGLAPESLEYIEAHGTGTKVG   300
 301  DPQELNGITRSLCAFRQAPLLIGSTKSNMGHPEPASGLAALTKVLLSLEH   350
 351  GVWAPNLHFHNPNPEIPALLDGRLQVVDRPLPVRGGNVGINSFGFGGSNV   400
 401  HVILQPNTRQAPAPTAHAALPHLLHASGRTLEAVQDLLEQGRQHSQDLAF   450
 451  VSMLNDIAATPTAAMPFRGYTVLGVEGRVQEVQQVSTNKRPLWFICSGMG   500
 501  TQWRGMGLSLMRLDSFRESILRSDEAVKPLGVKVSDLLLSTDERTFDDIV   550
 551  HAFVSLTAIQIALIDLLTSVGLKPDGIIGHSLGEVACGYADGCLSQREAV   600
 601  LAAYWRGQCIKDAHLPPGSMAAVGLSWEECKQRCPAGVVPACHNSEDTVT   650
 651  ISGPQAAVNEFVEQLKQEGVFAKEVRTGGLAFHSYFMEGIAPTLLQALKK   700
 701  VIREPRPRSARWLSTSIPEAQWQSSLARTSSAEYNVNNLVSPVLFQEALW   750
 751  HIPEHAVVLEIAPHALLQAVLKRGVKSSCTIIPLMKRDHKDNLEFFLTNL   800
 801  GKVHLTGINVNPNALFPPVEFPAPRGTPLISPHIKWDHSQTWDVPVAEDF   850
 851  PNGSSSSSATVYSIDASPESPDHYLVDHCIDGRVIFPGTGYLCLVWKTLA   900
 901  RSLGLSLEETPVVFENVSFHQATILPKTGTVALEVRLLEASHAFEVSDTG   950
 951  NLIVSGKVYLWEDPNSKLFDHPEVPTPPESASVSRLTQGEVYKELRLRGY  1000
1001  DYGPQFQGICEATLEGEQGKLLWKDNWVTFMDTMLQVSILGSSQQSLQLP  1050
1051  TRVTAIYIDPATHRQKVYRLKEDTQVADVTTSRCLGITVSGGIHISRLQT  1100
1101  TATSRRQQEQLVPTLEKFVFTPHMEAECLSESTALQKELQLCKGLARALQ  1150
1151  TKATQQGLKAAMLGQEDPPQHGLPRLLAAACQLQLNGNLQLELGEALAQE  1200
1201  RLLLPEDPLISGLLNSQALKACVDTALENLSTLKMKVAEVLAGEGHLYSR  1250
1251  IPALLNTQPMLQLEYTATDRHPQALKDVQTKLQQHDVAQGQWNPSDPAPS  1300
1301  SLGALDLLVCNCALATLGDPALALDNMVAALKEGGFLLVHTVLKGHALGE  1350
1351  TLACLPSEVQPAPSLLSQEEWESLFSRKALHLVGLKRSFYGTALFLCRRA  1400
1401  IPQEKPIFLSVEDTSFQWVDSLKSTLATSSSQPVWLTAMDCPTSGVVGLV  1450
1451  NCLRKEPGGHRIRCILLSNLSNTSHAPKLDPGSPELQQVLKHDLVMNVYR  1500
1501  DGAWGAFRHFQLEQDKPKEQTAHAFVNVLTRGDLASIRWVSSPLKHTQPS  1550
1551  SSGAQLCTVYYASLNFRDIMLATGKLSPDAIPGKWASRDCMLGMEFSGRD  1600
1601  RCGRRVMGLVPAEGLATSVLLSSDFLWDVPSSWTLEEAASVPVVYTTAYY  1650
1651  SLVVRGRIQRGETVLIHSGSGGVGQAAISIALSLGCRVFTTVGSAEKRAY  1700
1701  LQARFPQLDDTSFANSRDTSFEQHVLLHTGGKGVDLVLNSLAEEKLQASV  1750
1751  RCLAQHGRFLEIGKFDLSNNHPLGMAIFLKNVTFHGILLDALFEEANDSW  1800
1801  REVAALLKAGIRDGVVKPLKCTVFPKAQVEDAFRYMAQGKHIGKVLVQVR  1850
1851  EEEPEAVLPGAQPTLISAISKTFCPAHKSYIITGGLGGFGLELARWLVLR  1900
1901  GAQRLVLTSRSGIRTGYQAKHIREWRRQGIQVLVSTSNVSSLEGARALIA  1950
1951  EATKLGPVGGVFNLAMVLRDAMLENQTPELFQDVNKPKYNGTLNLDRATR  2000
2001  EACPELDYFVAFSSVSCGRGNAGQTNYGFANSTMERICEQRRHDGLPGLA  2050
2051  VQWGAIGDVGIVLEAMGTNDTVIGGTLPQRISSCMEVLDLFLNQPHAVLS  2100
2101  SFVLAEKKAVAHGDGDTQRDLVKAVAHILGIRDLAGINLDSTLADLGLDS  2150
2151  LMGVEVRQILEREHDLVLPMREVRQLTLRKLQEMSSKTDSATDTTAPKSR  2200
2201  SDTSLKQNQLNLSTLLVNPEGPTLTQLNSVQSSERPLFLVHPIEGSTTVF  2250
2251  HSLAAKLSVPTYGLQCTQAAPLDSIPNLAAYYIDCIKQVQPEGPYRIAGY  2300
2301  SFGACVAFEMCSQLQAQQGPAPTHNNLFLFDGSHTYVLAYTQSYRAKMTP  2350
2351  GCEAEAEAEALCFFIKQFLDVEHSKVLEALLPLKSLEDRVAASVDLITKS  2400
2401  HHSLDRRELSFAAVSFYHKLRAADQYKPKAKYHGNVTLLRAKTGGTYGED  2450
2451  LGADYNLSQVCDGKVSVHIIEGDHRTLLEGSGLESIINIIHSSLAEPRVS  2500
2501  VREG                                                2504

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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