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

NucPred

Fetching Q7Y667 from www.uniprot.org...

The NucPred score for your sequence is 0.99 (see score help below)

   1  MKRHQFKSWIFELREIKNSHYFLDSWTKFDSVGSFTHIFFHQERFMKLFD    50
  51  PRIWSILLSRDSQGSTSNRYFTIKGVVLLVVVVLIYRINNRNMVERKNLY   100
 101  LMGLLPIPMNSIGPRNDTLEESFWSSNLNRLIVSLLYLPKGKKISESCFM   150
 151  DPKESTWVLPITKKCIMPESNWGSRWWRNRIGKKRDSSCKISNETVAGIE   200
 201  ISFKEKDIKYLEFLFVSYTDDPIRKDHDWEFFDRLSPRKKRNIINLNSGQ   250
 251  LFEILVKHLICYLMSAFREKRPIEVEGFFKQQGAEATIQSNDIEHVSHLF   300
 301  SRNKRGISLQNCAQFHMWQFRQDLFVSWGKNRHELDFLRNVSRENLIWLD   350
 351  NVWLVNKDRFFSKVRNVSSNIQYDSTRSIFVQVTDSSQLKGSSDQSRDPF   400
 401  DSISNEDSEYHTLINQTEIQQLKERSILWGPSFLQTERTEIESDRLLKCL   450
 451  SGYSSMSRLFTEREKQMNNHLLPEEIEEFLGNPTRSIRSFFSDRWSELHL   500
 501  GSNPTERSTRDHKLLKKQQDVSFVPSRRSENQEIVDIFKIITYLQNTVSI   550
 551  HPISSDPGCDMVPKDEPDMDSSNKISFLNKNPFLDLFHLFHDRNKGGYRL   600
 601  HHDFESEERFQEMADLFTLSITEPGLVDHKGFAFSIDSYGLDQKKFLNEV   650
 651  FNSRDESKKKSLLVLPPIFYEENESFYRRIRKKSVRISCGNDLEDPKPKI   700
 701  VVFANNNIMEAVNQYRLIRNLMQIQYSTYGYIRNVSNRFFLMNRSDRNFE   750
 751  YGIQRDQIGNDTLNHLTIIKYTINQHLSNLKKSQKKWFDPLISRTERSMN   800
 801  RDPDAYRYKWSNGSKNFQEHLEHFVSEQKHRFQVVFDRLRINQYSIDWSE   850
 851  VIDKQDLSKSLRFFLSKSLLFLSKSLLFLSKSLPFFFVSIGNIPIHRSEI   900
 901  HIYELKGPNDQLCNQLLESIGVQIVHLNKLKPFLLDDHDTSQRSKFLING   950
 951  GTISPNKIPKWMIDSFHTRNNRRKSFENTDSYFSMISHDRDNWLNPVKPF  1000
1001  HRSSLISSFYKANRLRFLNHPHHFWFYCNKGFPFYVEKTRINNYDLTYGQ  1050
1051  FLNILFIRNKIFSLCVGKKKHVFLERDTISPIESQVSDIFIPNDFPQSGD  1100
1101  ETYNLYKSFHFPIRSDPFVRRAIYSIADISGTPLTEEQIVNFERTYCQPL  1150
1151  SDMNLSDSEGKNLHQYLSFNSNMGLIHTPCSEKYLPSGKRKKRSLCLKKC  1200
1201  VEKRQMDRTFQRDSAFSNLSKWNLFQTYMPWFLTSTGCKYLNLTLLDTFS  1250
1251  DPLPILSSSQKFVSIFHDIMHGSDISWPIPQKKLWAILPQWNLISESSSK  1300
1301  CLQNLLLSEEMIHRNNESPVPLIWTHLRSPNAWEFLYSILFLFLVAGYLV  1350
1351  RTHLLFVSRASSELQTGLERIKSLMIPSYMIELRKLLDRYPTSEPNSFWL  1400
1401  KNLFLVALEQLGDSLEKIRGSASGGNMLLGGGPAYGVKSIRSKKKYLNIN  1450
1451  LIDLISIIPNPINRITFSRNTRHLSRTSKEIYSLIRKRKNVNGDWIDDKI  1500
1501  ESWVANSDSIDDEEREFLVQFSTLTTEKGIDQILLSLTHSDHLSKNDSGY  1550
1551  QMIEQPGSIYLRYLVDIHKKYLMNYEFNRSCLAERRIFLAHYQTITYSQT  1600
1601  SCGANSSHFPSHGKPFSLRLALSPSRGILVIGSIGTGRSYLVKYLATNSY  1650
1651  VPFITVFPNKFLDDKPKGYRIDDIDIDDSDDIDIDDSDDIDDDLDTELLT  1700
1701  MTNVLTMYMTPKIDRFDITLQFELAKAMSPCIIWIPNIHDLYVNESNYLS  1750
1751  LGLLVNYLSRDCERCSTRNILVIASTHIPQKVDPALIAPNKSNTCIKIRR  1800
1801  LLIPQQRKHFFILSYTRGFHLEKKMFHTNGFGSITMGSNARDLVALTNEA  1850
1851  LSISITQKKSIIDTNTIRSALHRQTWDLRSQVRSVQDHGILFYQIGRAVA  1900
1901  QNVLLSNCPIDPISIYMKKKSCKEGDSYLYKWYFELGTSMKKLTILLYLL  1950
1951  SCSAGSVAQDLWSPPGPDEKNWITSYGFVENDSDLVHGLLEVEGALLGSS  2000
2001  RTEKDCSQFDNDRVTLFLRSEPRNPLDMMQNGSCSIVDQRFLYEKYESEF  2050
2051  EEGEREGALDPQQIEEDLFNHIVWAPRIWRPCGNLFDCIERTNELGFPYW  2100
2101  ARSFRGKRIIYHKEDELQENDSEFLQSGTMQYQTRDRSSKEQGFFRISQF  2150
2151  IWDPADPFFFLFKDQPFVSVFSRREFFADEEMSKGLITSQTNPPTSIYKR  2200
2201  WFIKNTQEKHFELLIHRQRWLRTNSSLSNGSFRSNTPSESYQYLSNLFLS  2250
2251  NGTLLDQIAKALLRKRWLFPDEMKHLIHVTGERFPIP               2287

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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