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

NucPred

Fetching P09976 from www.uniprot.org...

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

   1  MRGHQFKSWIFELREILREIKNSHHFLDSWTQFNSAGSFIHIFFHQERFL    50
  51  KLFDPRIWSILLSRNSQGSTSNRYFTIKGVILFVVAVLIYRINNRNMVER   100
 101  KNLYLIGLLPIPMNSIGPRNDTLEESVGSSNINRLIVSLLYLPKGKKISE   150
 151  SCFLNPKESTWVLPITKKCSMPESNWGSRWWRNWIGKKRDSSCKISNETV   200
 201  AGIEILFKEKDLKYLEFLFVYYMDDPIRKDHDWELFDRLSLRKSRNRINL   250
 251  NSGPLFEILVKHWISYLMSAFREKIPIEVEGFFKQQGAGSTIQSNDIEHV   300
 301  SHLFSRNKWAISLQNCAQFHMWQFRQDLFVSWGKNPPESDFLRNVSRENW   350
 351  IWLDNVWLVNKDRFFSKVQNVSSNIQYDSTRSSFVQVTDSSQLKGSSDQS   400
 401  RDHLDSISNEDSEYHTLINQREIQQRKERSILWDPSFLQTERKEIESGRF   450
 451  PKCLSGYSSMSRLFTEREKQMINHLFPEEIEEFLGNPTRSVRSFFSDRWS   500
 501  ELHLGSNPTERSTRDQKLLKKQQDLSFVPSKRSENKEMVNIFKIITYLQN   550
 551  TVSIHPISSDPGCDMVPKDEPDMDSSNKISFLNKNPFFDLFHLFHDRNRG   600
 601  GYTLHYDFESEERFQEMADLFTLSITEPDLVYHKGFAFSIDSCGLDQKQF   650
 651  LNEARDESKKKSLLVLPPIFYEENESFSRRIRKKWVRISCGNDLEDPKPK   700
 701  IVVFASNNIMEAVTQYRLIRNLIQIQYSTYGYIRNVLNRFFLMNRSDRNF   750
 751  EYGIQRDQIGKDTLNHRTIMKYTINQYLSNLKKSQKKWFEPLILISRTER   800
 801  SMNRDPDAYRYKWSNGSKNFQEHLEQSVSEQKSRFQVVFDRLRINQYSID   850
 851  WSEVIDKKDLSKPLRFFLSKSLLFLSKLLFFLSNSLPFFCVSFGNIPIHR   900
 901  SEIYIYELKGPNDQLCNQLLESIGLQIVHLKKWKPFLLDDHDTSQKSKFL   950
 951  INGGTISPFLFNKIPKWMIDSFHTRNNRRKSFDNPDSYFSMIFHDQDNWL  1000
1001  NPVKPFHRSSLISSFYKANRLRFLNNPHHFCFYWNTRFPFSVEKARINNS  1050
1051  DFTYGQFLNILFIRNKIFSLCVGKKKHAFWGRDTISPIESQVSNIFIPND  1100
1101  FPQSGDETYNLYKSFHFPSRSDPFVRRAIYSIADISGTPLTEGQIVNFER  1150
1151  TYCQPLSDMNLSDSEGKNLHQYLNFNSNMGLIHTPCSEKDLSSEKRKKRS  1200
1201  LCLKKCVEKGQMYRTFQRDSAFSTLSKWNLFQTYMPWFLTSTGYKYLNLI  1250
1251  FLDTFSDLLPILSSSQKFVPIFHDIMHGSGISWRILQKKLCLPQWNLISE  1300
1301  ISSKCLHNLLLSEEMIHRNNESPLISTHLRSPNAREFLYSILFLLLVAGY  1350
1351  LVRTHLLFVSRASSELQTEFEKVKSLMIPSSMIELRKLLDRYPTSEPNSF  1400
1401  WLKNLFLVALEQLGDSLEEIRGSASGGNMLGPAYGVKSIRSKKKDWNINL  1450
1451  IEIIDLIPNPINRITFSRNTRHLSHTSKEIYSLIRKRKNVNGDWIDDKIE  1500
1501  SWVANSDSIDDEEREFLVQFSTLTTENRIDQILLSLTHSDRLSKNDSGYQ  1550
1551  MIEQPGAIYLRYLVDIHKKHLMNYEFNPSCLAERRIFLAHYQTITYSQTS  1600
1601  CGENSFHFPSHGKPFSLRLALSPSRGILVIGSIGTGRSYLVKYLATNSYV  1650
1651  PFITVFLNKFLDNKPKGFLLDEIDIDDSDDIDDSDNLDASDDIDRDLDTE  1700
1701  LKLLTRMNGLTMDMMPEIDRFYITLQFELAKAMSPCIIWIPNIHDLDVNE  1750
1751  SNDLALGLLVNHLSRDCERCSTRNILVIASTHIPQKVDPALIAPNKLNTC  1800
1801  IKIRRLLLPQQRKHFFTLSYTRGFHLEKKMFHTNGFGSITMGSNARDLVA  1850
1851  LTNEVLSISITQKKSIIDTNTIRSALHRQTWDLRSQVRSVQDHGILFYQI  1900
1901  GRAVAQNVLLSNCPIDPISIYMKKKSCNEGDSYLYKWYFELGTSMKRLTI  1950
1951  LLYLLSCSAGSVAQDLWSLSGPDEKNGITSYGLVENDSDLVHGLLEVEGA  2000
2001  LVGSSRTEKDCSQFDNDRVTLLLRPEPRNPLDMMQNGSCSILDQRFLYEK  2050
2051  YESEFEEGEGEGALDPQEDLFNHIVWAPRIWRPWGFLFDCIERPNELGFP  2100
2101  YWSRSFRGKRIIYDEEDELQENDSEFLQSGTMQYQTRDRSSKEQGLFRIS  2150
2151  QFIWDPADPLFFLFKDQPPGSVFSHRELFADEEMSKGLLTSQTDPPTSIY  2200
2201  KRWFIKNTQEKHFELLINRQRWLRTNSSLSNGSFRSNTLSESYQYLSNLF  2250
2251  LSNGTLLDQMTKTLLRKRWLFPDEMKIGFM                      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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