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

NucPred

Fetching Q49KT6 from www.uniprot.org...

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

   1  MKGHQFKSWIFELREILREIKNSHHFLDSWTQFNSVGSFIHIFFHQERFI    50
  51  KLLDPRIWSILLSRNSQGSTSNRYFTIKGVVLFVVAVLLYRINNRNMVER   100
 101  KNLYLTGLLPIPMNSIGPRNDTLEESFGSSNINRLIVSLLYLPKGKKISE   150
 151  SCFLDPKESTWVLPITKKCIMPESNWGSRWWRNWIGKKRDSSCKISNETV   200
 201  AGIEISFKEKDIKYLEFLFVYYMDDPICKDHDWEFLDRLSPSKRRNIINL   250
 251  NSRQLFEILVKDWICYLMFAFREKIPIEVEGFFKQQGAGSTIQSNDIEPI   300
 301  SHLFSRKKWAISLQNCAQFHMWQFRQDLFVSWGKNPPESDFLRNISRENW   350
 351  IWLDNVWLVNKDRFFSKVRNVSSNIQYDSTRSSFVQVTDSSQLKGSSDQS   400
 401  RDHFDSISNEDSEYHTLINQREIQQLKERSILWDPSFLQTERTELESDRF   450
 451  SKCLSGYSRLFTEREKEMKNHLLPEEIEEFLGNPTRSILSFFSDRWSELH   500
 501  LGSNPTERSTRDQKLLKKEQDVSFVPSRRSENKEIVNIFKIITYLQNTVS   550
 551  IHPISSDPGCDMVPKDELDMHSSHKISFLNKNTFFDLFHLFHDRNRGGYT   600
 601  LHHDFESEERFQEMADLFTLSISEPDLVYHKGFAFSMDSYVLDQKQFLNE   650
 651  VFNSRDESKKKSLLVLPPLFYEENESFYRRIRKKWVRISCGNDLEDPKPK   700
 701  IVVFASNNIMEAVNQYRWIRNLIQIQYSTYGYIRNVWNRFFLMNRSDRNF   750
 751  EYGIQRDQIGNDTLNHRTIMKYTINQHLSNLKKSQKKWFNPLIFISRTER   800
 801  SVNRDPNAYRYKWSNGSKNFQEHLEHFVSKQKSRFQVVFDRLRINQYSID   850
 851  WSEVIDKKDLSKSLRFVLSKLLLFLSKFLLFLSNSLPFFFVSFGNTPIHR   900
 901  SEIHVYELKGPNDQLCNQLLESIGLQIVHLKKWKPLLLDDHDTSQKSKLL   950
 951  INGGTISPFFFNKIPKWMIDSFHTRNNRRKSFDNTDSYFSMISHDQDNWL  1000
1001  NPVKPFHRSSLISSFYKANRLRFLNNPHHFCFYCNKRFPFYVERARINNS  1050
1051  DFTYGQFLNILFIRNKIFSLCGGKKKYAFLERDTISPIESQVSNIFIPND  1100
1101  FPQSGDERSNLYKSFHFAIRSDPLVRRAIYSIADISGTPLTEGQIVNFER  1150
1151  TYCQPLSDMNLSDSEGKNLYQYLNFNSNMGLIHTPCSEKYLPSEKRKKRS  1200
1201  LCLKKCVEKGQMYRTFQRDSAFSTLSKWNLFQTYMPWFLTSTGYKYLNWI  1250
1251  FLDTFSDLLPILSSSQKFVSIFHDIMHGSDISWQILQKKFCLPQWNLISE  1300
1301  ISSKCLHNLLLSEEMIHRNNESPLISTHLRSPNVREFLYSILFLLLVATY  1350
1351  IVRTHLLFVSRAYSELQTEFEKVKSWMIPSYMMELRKLLDRYPTSELNSF  1400
1401  WLKNLFLVALEKLGDSLEEIRGSASGGNMLWGGGPAYGFKSIRSKKKYWN  1450
1451  INLIDLISIIPNPIHRITFSKKTRHLSHTSKEIYSLIRKRKNVNGDWIDD  1500
1501  KIESWVANSDSIDDKEREFLVQFSTLTTEKGIDQILLSLTHSDHLSKNDS  1550
1551  GYQMIEQPGAIYLRYLVDIHKKYLMNYEFNTFCLAERRIFLAHYQTITYS  1600
1601  QTSCGTNSFHFTSHGKPFSLRLALSPSRGILVIGSIGTGRSYLVKYLATN  1650
1651  SYVPFITVFLNKFLDNKPKGFLIDDIDIEDSDDIEDSDNIDRDLDTELEL  1700
1701  LTRMNALTMDMMPEIDRFYITLQFELAKAMSPCIIWIPNIHDLDVNESNY  1750
1751  LSLGLLVNYLSRDCERCSTQNILVIASTHIPQKVDPALIAPNKLNTCIKI  1800
1801  RRLLIPQQRKHFFTLSYTRGFHLEKKMFHTNGFGSITMGSNVRDLVALTN  1850
1851  EALSISITQKKSILDTNTIRSALHRQTWDLRSQVRSVQDHGILFYQIGRA  1900
1901  VAQNVLLSNCPIDPISIYMKKKSCNEGDSYLYKWYFELGTSMKKLTILLY  1950
1951  LLSCSAGSIAQDLWSLPGPDEKNEITSYGLVENDSDLVHGLLEVEGALVG  2000
2001  SSRTEKDYSQFDNDRVTLLLRPKPRNPLDMMQNGSCSIVDQRFLYEKYES  2050
2051  EFEEGEGEGVLDPQQIEEDLFNHIVWAPRIWRPWGFLFDCIERPNSLGFP  2100
2101  YWARSFRGKRIIYDEKEELQENDSEFLQSGTMQYQTRDRSSKEQGFFRIS  2150
2151  QFIWDPADPLFFLFKDQPFVSVFSHREFFADEEMSKGLLTSQTDSPTSIY  2200
2201  KRWFIKNTQEKHFELLIHRQRWLRTNSSLSNGFFRSNTPSESYQYLSNLF  2250
2251  LSNGRLLDQMTKTLLRKRWLFPDEMKIGFM                      2280

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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