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

NucPred

Fetching Q3BAH3 from www.uniprot.org...

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

   1  MKRHQFKSWIFELREILREIKNSHYFLDSWIKFDSVGSFTHIFFHQERFM    50
  51  KLFDPRIWSILLSRDSQGATSNRYFTIKGLVLLVVVVLLSRINNRKMVER   100
 101  KNLYLMGLLPIPMNSIGPRKETLEESFWSSNRNRLIVSLLYLPKGKKISE   150
 151  SCFMDPQESTWVIPIKKKRIMPESNRGSRWWRNRIGKKRDSSCQISNETI   200
 201  AGIEISFKEKDSKYLEFLFLSYTDDPIRKDHDWELFDRLSPRKKRNIINL   250
 251  NSGQLFEILGKDLICYLMSAFREKRPIQGESFFKQQGAGATMQSNDIEHV   300
 301  SHLFSRNKWGLSLQNCAQFHMWQFRQDLFVSWGKNQHESDFLRNVSRENW   350
 351  IWLDNVWLVNKDRFFSKVRNVLSNIQYDSTRSIFVQVTDSSQWKGSSSDQ   400
 401  SRDHFDSVRNENSEYHTLIDQTEIQQLKERSILWDPSFLQTERTEIESDR   450
 451  FPKCLFGSSSMSWLFTEPEKRMNNHLLPEEIEEFLGNPTRSIRSFFSDRW   500
 501  SELHLGSNPTERSTRDHKLLKKKQDVSFVPSRRAEKKEMVDIFKIITYLQ   550
 551  DTVSIHPSEPYHIPDLVPKDEPDMDSSNKISFLNKNPFFDFFHLFHDRNK   600
 601  GGYALRHDFFESEERFPEMADLFTLSITEPDLVFHRGFAFYIDSYGLDQK   650
 651  RFLNEVFNSRDESKKKLVLPPLFYEENESFSRRIRKKSVRIYCGNELEDP   700
 701  KLKTAVFASNNIMEAVNQYRLIRNLQYYGYIRNVSNRFFLMNRSDRNFEY   750
 751  GIQRDQIGNDTLNHITIMKYTINQHLSNLKKSQKKWFDPLISRTERSMNQ   800
 801  DPDAYRYKGSDGSKNFQEHLEHFVSEQKNPFQVVQVVFDQLRIHQYSIDW   850
 851  SEVIDKEDLSKSLRFFLSKSLLFLSKSLRFFLSKSLPFFFVSIGNIPIHR   900
 901  SEIRIYELKGPNDQLCNQLLESIGVQIVHLKKLKPFLLDDHDTSQRPKFL   950
 951  INGGTILPFLFKKIPKRVIDSFHTRKNRRKSFDNTDSYFSMISHDRDNWL  1000
1001  NPVKAFHRSSLISSFYKANRLRFLNDPHHFWFYCNKRFPFDVEKTRINNY  1050
1051  DLTYGQFLNILSIRNKIFSLCVGKKGSLFLERETLSPIESQVSDIFIPND  1100
1101  FPQSGDETYNLYKLYKSFHFPIRSDPFVRGAIYSIADISATPLTEEQIVN  1150
1151  LEKTYCQPLSDMNLSDSEGNNLHQYLSFNSNMGLIHTPCSEKYLPSGKRK  1200
1201  KRSLCLKKCVEKGQMYRTFQRDSAFSNLSKWNLFQTYMPWFLTSTGCKYL  1250
1251  NFTLLDTLSNPLPILSSSQKFVSIFHDMMHGSDISWPIPQKILPQWTLIS  1300
1301  EISSQCLQNLLLSEEMIHRNNESPVPLIWAHLRSTNAREFLYSIFFLLLV  1350
1351  AGYLVRIHLLFVSRASSELQTELEKIKSLMIPSYMMEFRKLLDRYPTSEL  1400
1401  NPFWLKNLFLVVLEQLGDSLGEIRGSASGGNMLLGGGPAYGVKSIRSKKK  1450
1451  YWKINLIDLVSIIPNPINRIIFSRNTRHLSRTSKEIYSLIRKRKNVNGDW  1500
1501  IDDKIEFWVANSDSIDDEEREFLVQFSALTTEKRIDQILLSLTHSDHLSK  1550
1551  NDSGYQMIEQPGSISLRYLVDIHQKDLMNYEFNRSCLAERRIFLAHYHTI  1600
1601  TYSQTLCGANIFHSPSPHGKPFSLRLALSPSRGILVIGSIGTGRSCLVKY  1650
1651  LATNSYVPFITVFPNKFLDDKPKGYPIDDIDIDDSDDIDDSNDDLDIDKE  1700
1701  LLTMTNVLTMYMTTKIDRFDITLQFELAKAMSPCIIWIPNIHDLHVNESN  1750
1751  YLSLDLLENYLSRDCERCSTGKILVIASTHIPQKVDPALIAPNKLNTCIK  1800
1801  IRRLLLPQQLKHFFILSYTRGFHLEKKMFHTNGFGSITMGSNARDLVALI  1850
1851  NEALSISITQKKSIIETNTIRSALHRKTWDFRSQIRSVQDHGILFYQIGR  1900
1901  AVTQNVLLSNCPIDPISIYMKKKSCKGGDSYLYKWYFELGTSMKKLTILL  1950
1951  YLLSCSAGSVAQDLWSSSRHDEKNWITSYGFVENDSDLVHGLLLLLLLEV  2000
2001  EGALALAGSSRTEKDCSQFDNNRVTLLLRSEPRNQLDMMQNGSCSIVDQR  2050
2051  FLYEKYESEFEEGEGALDPQQIEEDLFNHIVWAPRIWRFDCIERPTELGF  2100
2101  PYWTGSFRGKWIIYHKEGELQENDSEFLQSGTMQYQTRDRSSKEQGFFRT  2150
2151  SQFIWDPADPSFSLFKDQPSVSVFSRREFFADEEMSKGLIASQTNPPTSI  2200
2201  YKRWFIKNTQEKHFELLIHRQRWFRTNSSLSNGSFRSNTLSESYQYLSNL  2250
2251  FLSNGTLLDQMTKTLLRKRWLFPDEMKHLIHVTGERFPIP            2290

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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