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

NucPred

Fetching Q2QD30 from www.uniprot.org...

The NucPred score for your sequence is 0.97 (see score help below)

   1  MKGQQFKLWILEFREIKNSHYFLDSWTQFNSLGSFIHIFFHQERFIKLLD    50
  51  SRIWSILLSRNSQGSTSNRYFTIKGVVLFVVAVVLIYRINNRKMVERKNL   100
 101  YLTGFLPIPMNFIGPRNDTLEESFGSSNINRLIVLLLYLPTSFVQVTDSS   150
 151  QLKGSSDQSRDHFDSISNEDSEYHTLINQKEIQQPLPEEIEEFLGNPTRS   200
 201  IRSFFSDRWSELHMGSNPIERSTRDQKLLKKEQDVSFVPSRRSENKEIVN   250
 251  IFKIITYLQNTVSIHPISSDPGCDMVPKDELDMDSSNKISFLKKNPFIYL   300
 301  FHLFHDRNRRGYTLHHDFESEERFQEMADLFTLSITEPDLVYHKGFAFSI   350
 351  DSYGLDQKQFLNEVFNSRDESKKKYLLVLPPIFYEENDSFYRRIRKKWVR   400
 401  TSPGNDLEDPKQKIVVFASNNIMEAVNQYRLIRNLIQIQYYRYIRNVLNR   450
 451  FFLMNRSDRDLEYGIQRDQIGNDTLNHRTIMKYTINQHLSNFKKGQKKWF   500
 501  DPLILISRTERSMNRDPNAYRYKWSNGSKNFQEHFISEQKSHFHFQVVFD   550
 551  RLRINQYSIDWSEVIDKKDWSKSLRFFLSKLLVFLSKFLLFLSNSLPFFF   600
 601  VSFGNIPIHRSEIHIYELKGPNDRLCNQLLESIGLQIVHLKKLKPFLLDD   650
 651  HYTSQKSKFLINGGTISPFLFNKIPKWMIDSFDTRNNRRKSFDNTDSYFS   700
 701  MISHDQDNWLNPVKPFHRSSLISSFYKATRLRFLNNPHHFCFYCNKRFPF   750
 751  YVDYVEKARINNYDFTYGQFLNILFIRNKIFSLCGGKKKHAFLERDTISP   800
 801  IESQVSNIFIPNDFPQSGDERYNLYKSFHFPIRSNPFVRRAIYSIADISV   850
 851  TPLTEGQIVNFERTYCQPLSDMNLSDSEGKNLHQYLNFNSNMGLIHTPCS   900
 901  EKYLPSEKRKKQSLYRKKCLEKGQMYRTFQRDSAFSTLSKWNLFQTYMPW   950
 951  FFTSTGYKYLNLLFLDTFSDLLPILSSSPKFVSIFDDIMHRSDRSWRILR  1000
1001  KKLCLPQWNLISEISIKCLPNLLLSEEMIHRNNESPSISTHLRSPNVREF  1050
1051  LYSILFLLLIAVYLVRTHLLFVSRAYSELQTEFEKVKSLMIPSYMIELRK  1100
1101  LLDRYPTYERNSFWLKNLFLVALEQLGDSLEEIWGSASGGGPAYGVKSIR  1150
1151  SKKKDWNINLINLISIIPNPINRIAFSRNTRHLSHTSKEIYSLIRKNVNG  1200
1201  DWIDDKIQSWVWNSDSIDDKEREFLVQFSTLTTEKRIDQILLSLTHSDHL  1250
1251  SKNDSGYQMIEQPGVIYLRYLVDIQKKYLMNYKFNTSCLAERRTFLAHYQ  1300
1301  TITHSQTSCGANSFHFPSHGKLFSLRLALSPGILVIGSIGTGRSYLVKYL  1350
1351  ATNSYLPFITVFLNKFRDNKPKFIDDSDDDSDDIDDSGDIDDSDDIDRDL  1400
1401  DIDTELELLTMMNALTMEMKLEIDQFYITLQFELIKAMSPCIIWIPNIHD  1450
1451  LYVNKSSHLYFGLLVNYLYRDFERCSTTNILVIASTHIPQKVDPALIAPN  1500
1501  KLNTCIKIRRLLIPQQRKHFFTLSYTRGFHLEKKMFHTNGFGSITMGSNV  1550
1551  RDLVALTNEALSISITQRKSIIDTNIIRSALHRQTWDLRSQVRSVQDHGI  1600
1601  LFYQIGRALAQNVLLSNCSIDPISIYMKKKSCNEGGSYLYNWYFELETSM  1650
1651  KKLTILLYLLNCSAGSVVQDLWSLSGPDEKNGITSYVLVENDSHLVHGLL  1700
1701  EVEGALFGSSWTEKDCSRFDNDRVTLLLRPEPRNPLDMIQNGSSSIVDQI  1750
1751  FLYQKYESKFEEGEGVLDPQQIEEDLFNHIVWAPRIWSPWGFLFDCIERP  1800
1801  NELGVPYWARSFRGKRIIYDEEDELQENDSEFLQSGTVQYQTRDRSSKEQ  1850
1851  GFFLINQFIWDPADPLFFLFQDHPFVSVFSHREFFADEEMAKGLLTSQPA  1900
1901  FPTSLEKRWFINIKNTQEKYVELLIHRQRWLRTRTNSSLSKSNGFFRSNT  1950
1951  LSESYQYLSNLFLSNGTLLDQMTKTLLRKRWLFPDEMK              1988

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.)

Go back to the NucPred Home Page.