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

NucPred

Fetching P12785 from www.uniprot.org...

The NucPred score for your sequence is 0.29 (see score help below)

   1  MEEVVIAGMSGKLPESENLQEFWANLIGGVDMVTDDDRRWKAGLYGLPKR    50
  51  SGKLKDLSKFDASFFGVHPKQAHTMDPQLRLLLEVSYEAIVDGGINPASL   100
 101  RGTNTGVWVGVSGSEASEALSRDPETLLGYSMVGCQRAMMANRLSFFFDF   150
 151  KGPSIALDTACSSSLLALQNAYQAIRSGECPAAIVGGINLLLKPNTSVQF   200
 201  MKLGMLSPDGTCRSFDDSGNGYCRAEAVVAVLLTKKSLARRVYATILNAG   250
 251  TNTDGCKEQGVTFPSGEAQEQLIRSLYQPGGVAPESLEYIEAHGTGTKVG   300
 301  DPQELNGITRSLCAFRQSPLLIGSTKSNMGHPEPASGLAALTKVLLSLEN   350
 351  GVWAPNLHFHNPNPEIPALLDGRLQVVDRPLPVRGGIVGINSFGFGGANV   400
 401  HVILQPNTQQAPAPAPHAALPHLLHASGRTMEAVQGLLEQGRQHSQDLAF   450
 451  VSMLNDIAATPTAAMPFRGYTVLGVEGHVQEVQQVPASQRPLWFICSGMG   500
 501  TQWRGMGLSLMRLDSFRESILRSDEALKPLGVKVSDLLLSTDEHTFDDIV   550
 551  HSFVSLTAIQIALIDLLTSMGLKPDGIIGHSLGEVACGYADGCLSQREAV   600
 601  LAAYWRGQCIKDANLPAGSMAAVGLSWEECKQRCPPGVVPACHNSEDTVT   650
 651  ISGPQAAVNEFVEQLKQEGVFAKEVRTGGLAFHSYFMEGIAPTLLQALKK   700
 701  VIREPRPRSARWLSTSIPEAQWQSSLARTSSAEYNVNNLVSPVLFQEALW   750
 751  HVPEHAVVLEIAPHALLQAVLKRGVKPSCTIIPLMKRDHKDNLEFFLTNL   800
 801  GKVHLTGIDINPNALFPPVEFPVPRGTPLISPHIKWDHSQTWDIPVAEDF   850
 851  PNGSSSSSATVYNIDASSESSDHYLVDHCIDGRVLFPGTGYLYLVWKTLA   900
 901  RSLSLSLEETPVVFENVTFHQATILPRTGTVPLEVRLLEASHAFEVSDSG   950
 951  NLIVSGKVYQWEDPDSKLFDHPEVPIPAESESVSRLTQGEVYKELRLRGY  1000
1001  DYGPHFQGVYEATLEGEQGKLLWKDNWVTFMDTMLQISILGFSKQSLQLP  1050
1051  TRVTAIYIDPATHLQKVYMLEGDTQVADVTTSRCLGVTVSGGVYISRLQT  1100
1101  TATSRRQQEQLVPTLEKFVFTPHVEPECLSESAILQKELQLCKGLAKALQ  1150
1151  TKATQQGLKMTVPGLEDLPQHGLPRLLAAACQLQLNGNLQLELGEVLARE  1200
1201  RLLLPEDPLISGLLNSQALKACIDTALENLSTLKMKVVEVLAGEGHLYSH  1250
1251  ISALLNTQPMLQLEYTATDRHPQALKDVQTKLQQHDVAQGQWDPSGPAPT  1300
1301  NLGALDLVVCNCALATLGDPALALDNMVAALKDGGFLLMHTVLKGHALGE  1350
1351  TLACLPSEVQPGPSFLSQEEWESLFSRKALHLVGLKKSFYGTALFLCRRL  1400
1401  SPQDKPIFLPVEDTSFQWVDSLKSILATSSSQPVWLTAMNCPTSGVVGLV  1450
1451  NCLRKEPGGHRIRCILLSNLSSTSHVPKLDPGSSELQKVLESDLVMNVYR  1500
1501  DGAWGAFRHFQLEQDKPEEQTAHAFVNVLTRGDLASIRWVSSPLKHMQPP  1550
1551  SSSGAQLCTVYYASLNFRDIMLATGKLSPDAIPGKWASRDCMLGMEFSGR  1600
1601  DKCGRRVMGLVPAEGLATSVLLSPDFLWDVPSSWTLEEAASVPVVYTTAY  1650
1651  YSLVVRGRIQHGETVLIHSGSGGVGQAAISIALSLGCRVFTTVGSAEKRA  1700
1701  YLQARFPQLDDTSFANSRDTSFEQHVLLHTGGKGVDLVLNSLAEEKLQAS  1750
1751  VRCLAQHGRFLEIGKFDLSNNHPLGMAIFLKNVTFHGILLDALFEGANDS  1800
1801  WREVAELLKAGIRDGVVKPLKCTVFPKAQVEDAFRYMAQGKHIGKVLVQV  1850
1851  REEEPEAMLPGAQPTLISAISKTFCPEHKSYIITGGLGGFGLELARWLVL  1900
1901  RGAQRLVLTSRSGIRTGYQAKHVREWRRQGIHVLVSTSNVSSLEGARALI  1950
1951  AEATKLGPVGGVFNLAMVLRDAMLENQTPELFQDVNKPKYNGTLNLDRAT  2000
2001  REACPELDYFVAFSSVSCGRGNAGQSNYGFANSTMERICEQRRHDGLPGL  2050
2051  AVQWGAIGDVGIILEAMGTNDTVVGGTLPQRISSCMEVLDLFLNQPHAVL  2100
2101  SSFVLAEKKAVAHGDGEAQRDLVKAVAHILGIRDLAGINLDSSLADLGLD  2150
2151  SLMGVEVRQILEREHDLVLPIREVRQLTLRKLQEMSSKAGSDTELAAPKS  2200
2201  KNDTSLKQAQLNLSILLVNPEGPTLTRLNSVQSSERPLFLVHPIEGSITV  2250
2251  FHSLAAKLSVPTYGLQCTQAAPLDSIPNLAAYYIDCIKQVQPEGPYRVAG  2300
2301  YSFGACVAFEMCSQLQAQQGPAPAHNNLFLFDGSHTYVLAYTQSYRAKLT  2350
2351  PGCEAEAEAEAICFFIKQFVDAEHSKVLEALLPLKSLEDRVAAAVDLITR  2400
2401  SHQSLDRRDLSFAAVSFYYKLRAADQYKPKAKYHGNVILLRAKTGGTYGE  2450
2451  DLGADYNLSQVCDGKVSVHIIEGDHRTLLEGRGLESIINIIHSSLAEPRV  2500
2501  SVREG                                               2505

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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