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

NucPred

Fetching Q27RY7 from www.uniprot.org...

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

   1  MRGHQFKSWIFELREILREIKNSHHFLDSWTQFNSVGSFIHIFFHQERFL    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  ELHLGSNPTERSTRDQKLLKKQQDLSFVPSRRSEKKEMVNIFKIITYLQN   550
 551  TVSIHPISSDPGCDMVPKDEPDMDSSNKISFLNKNPFFDLFHLFHDRNRG   600
 601  GYTLHYDFASEERFQEMADLFTLSITEPDLVYHKGFAFSIDSCGLDQKQF   650
 651  LNEARDESKKKSLLVLPPIFYEENESFSRRIRKKWVRISCGNDLEDPKPK   700
 701  IVVFASNNIMEAVTQYRLIRNLIQIQYSTYGYIRNVLNRFFLMNRSDRNF   750
 751  EYGIQRDQIGKDTLNHRTIMKYTINQYLSNLKKSQKKWFEPLILISRTER   800
 801  SMNRDPDAYRYKWSNGSKSFQEHLEQSVSEQKSRFQVVFDRLRINQYSID   850
 851  WSEVIDKKDLSKSLRFFLSKSLLFLSKLLLFLSNSLPFFCVSFGNIPIHR   900
 901  SEIYIYEELKGPNDQLCNQLLESIGLQIVHLKKLKPFLLDDHDTSQKSKF   950
 951  LINGGTISPFLFNKIPKWMIDSFHTRNNRRKSFDNPDSYFSMIFHDQDNW  1000
1001  LNPVKPFHRSSLISSFYKANRLRFLNNPHHFCFYWNTRFPFSVEKARINN  1050
1051  SDFTYGQFLNILFIRNKIFSLCVGKKKHAFWGRDTISPIESQVSNIFIPN  1100
1101  DFPQSGDETYNLYKSFHFPSRSDPFVRRAIYSIADISGTPLTEGQIVNFE  1150
1151  RTYCQPLSDMNLSDSEGKNLHQYLNFNSNMGLIHTPCSEKDLSSEKRKKW  1200
1201  SLCLKKCVEKGQMYRTFQRDSAFSTLSKWNLFQTYMPWFLTSTGYKYLNL  1250
1251  IFLDTFSDLLPILSSSQKFVSIFPDIMHGSGISWRILQKKLCLPQWNLIS  1300
1301  EISSKCLHNLLLSEEMIHRNNESPLISTHLRSPNAREFLYSILFLLLVAG  1350
1351  YLVRTHLLFVSRASSELQTEFEKVKSLMIPSSMIELRKLLDRYPTSEPNS  1400
1401  FWLKNLFLVALEQLGDSLEEIRGSASGGNMLGPAYGVKSIRSKKKDWNIN  1450
1451  LIEIIDLIPNPINRITFSRNTRHLSHTSKEIYSLIRKRKNVNGDWIDEKI  1500
1501  ESWVANSDSIDDEEREFLVQFSTLTTENRIDQILLSLTHSDHLSKNDSGY  1550
1551  QMIEQPGAIYLRYLVDIHKKHLMNYEFNPSCLAERRIFLAHYQTITYSQT  1600
1601  SCGENSFHFPSPGKPFSLRLALSPSRGILVIGSIGTGRSYLVKYLATNSY  1650
1651  VPFITVFLNKFLDNKSKGFLLDEIDIDDSDDIDDSDNLDASDDIDRDLDT  1700
1701  ELELLTRMNGLTVDMMPEIDRFYITLQFELAKAMSPCIIWIPNIHDLDVN  1750
1751  ESNDLSLGLLVNHLSRDCERCSTRNILVIASTHIPQKVDPALIAPNKLNT  1800
1801  CIKIRRLLIPQQRKHFFTLSYTRGFHLEKKMFHTNGFGSITMGSNARDLV  1850
1851  ALTNEVLSISITQKKSIIDTNTIRSALHRQTWDLRSQVRSVQDHGILFYQ  1900
1901  IGRAVAQNVLLSNCPIDPISIYMKKKSCNEGDSYLYKWYFELGTSMKRLT  1950
1951  ILLYLLSCSAGSVAQDLWSLSVPDEKNGITSYGLVENDSDLVHGLLEVEG  2000
2001  ALVGSSRTEKDCSQFDNDRVTLLLRPEPRNPLDMMQKGSWSILDQRFLYE  2050
2051  KYESEFEEGEGEGALDPQEDLFNHIVWAPRIWRPWGFLFDCIERPNELGF  2100
2101  PYWSRSFRGKRIIYDEEDELQENDSGFLQSGTMQYQTRDRSQGLFRISQF  2150
2151  IWDPADPLFFLFKDQPPGSVFSHRELFADEEMSKGLLTSQTDPPTSIYKR  2200
2201  WFIKNTQEKHFELLINRQRWLRTNSSLSNGSFRSNTLSESYQYLSNLFLS  2250
2251  NGTLLDQMPKTLLRKRWLFPDEMKIGFM                        2278

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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