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

NucPred

Fetching Q68RU4 from www.uniprot.org...

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

   1  MKGHQFKSWIFELREILREIKNSHYFLDSRTQFNSVGSFSHIFFHQERFI    50
  51  KLFDPRIWSILLSRNSQGSTSNRYFTIKGVILFVVAVLIYRINSRNMVER   100
 101  KNLYLIGLLPIPMNSIGPRNDTLEESVGSSNINRLIVSLLYLPKGKKISE   150
 151  SCFLNPKESTWVLPITKKCSMPESNWGSRWWRNWIGKKRDSSQLKGSSDQ   200
 201  SRDPLDSISNEDSEYHTLINQREIQQLKERSILWDPSFLQTERTEIESDR   250
 251  FPKCLSVYSSMSRLFTEREKQMINHLLPEEIEEFLGNPTRSVRSFFSDRW   300
 301  SELHLGSNPTERSTRDQKLLKKQQDLSFVPSRRSEKKEMVNIFKIITYLQ   350
 351  NTVSIHPISSYPGCDMVPKDEPDMDSSNKISFLNKNPFFDLFHLFHDRNR   400
 401  GGYTLHHDFESEERFQEMADLFTLSITEPDLVYHKGFAFSIDSYGLDQKQ   450
 451  FLNEVFDSRDESKKKYLLALPPFFYEENESFYRRIRKKWVRISCGNDLED   500
 501  PKPKIVVFASNNIMEAVNQYRLIRNLIQIQYSTYGYIRNVLNRFFLMNRS   550
 551  DRNFEYGIQRDQIGKDTLNHRTIMKYTINQHFSNLKKSQKRWFDPLILIS   600
 601  RTERSMNRDPDAYRYKWSNGSKNFQEHLEHFVSEQKSRFQVVFDRLRINQ   650
 651  YSIDWSEVIDKKGLSKPFRFFLSKLLFFLSNSLPFFFVSFGNIPIHRSEI   700
 701  YIYELKGPNDQLCNQLLESIGLQIVHLKKWKPFLLDLLDDHDTSQKSKFL   750
 751  INGGTISPFLFNKIPKWMIDSFHTRNNRRKSFDNTDSYFSTIFHDQDNWL   800
 801  NPVKPFHRSSLISSFYKANRLRFLNNPHHFCFYCNKRFPFYVEKARINNS   850
 851  DFTYGQFLNILFIHNKIFSLCVGKKKHAFWGRDTISPIESQVSNIFIPND   900
 901  FPQSGGDETYNLYKSFHFPSRSDPFVRRAIYSIADISGTPLTEGQIVNFE   950
 951  RTYCQPLSDMNLSDSEGKNSHQYLNFNSNMGLIHTPCSEKYLPSEKRKKR  1000
1001  SLCLKKCVEKGQMYRTFQRDSAFSTLSKWNLFQTYMPWFLTSTGYKYLNF  1050
1051  IFLDTFSDLLPILSLSSSQKFVSIFHDIMHGSDISWRILQKKLCLLQWKW  1100
1101  NLISEISSKCFHNLLLSEERIHRNNESPLISTHLRSPNVREFLYSILFLL  1150
1151  LVAGYLVCTHLLFVSWASSELQTEFEKVKSLMIPSSMIELRKLLDRYPTS  1200
1201  EPNSFWLKNLFLVALEQLGDSLEEIRGSASGGNMLLGGDPAYGVKSIRSK  1250
1251  KKYLNINLIDIIDLISIIPNPINRITFSRNTRHLSHTSKEIYSLIRKRKN  1300
1301  VNGDWIDDKIESWVANSDSIDDEEREFLVQFSTLTTEKRIDQILLSLTHS  1350
1351  DHLSKNDSGYQMIEQPGAIYLRYLVDIHKKYLMNYEFNTSCLAERRIFLA  1400
1401  HYQTITYSQTSCGANSLNFPSHGKPFSLRLALSPSRGILVIGSIGTGRSY  1450
1451  LVKYLATNSYVPFITVFLNKFLDNKPKGFLIDDIDIDASDDIDASDDIDA  1500
1501  SDDIDASDDIDRDLHTELELLTMDMMPEIDRFYITLQFELAKAMSPCIIW  1550
1551  IPNIHDLDVNESNYFSLGLLVNHLSRDCERCSTRNILVIASTHIPQKVDP  1600
1601  ALIAPNKLNTCIKIRRLLIPQQRKHFFTLSYTRGFRLENKMFHTNGFGSI  1650
1651  TMGSNARDLVALTNEALSISITQKKSIIDTNTIRSALHRQTWDLRSQVRS  1700
1701  VQDHGILFYQIGRAVAQNVLLSNCPIDPISIYMKKKSCNEGDSYLYKWYF  1750
1751  ELGTSMKKLTILLYLLSCSAGSVAQDLWSLPRPDEKNGITSYGLVENDSD  1800
1801  LVHGLLEVEGALVGSSRTEKDCSQFDNDRVTLLLRPEPRNPLDMMQNGSC  1850
1851  SILDQRFLYEKNESEFEEGEGEGALDPQQIEEDLFNHIVWAPRIWRPWGF  1900
1901  LFDCIERPNELGFPYWSRSFRGKRILYDEEDELQENDSEFLQSGTMQYQT  1950
1951  RDRSSKEQGLFRISQFIWDPADPLFFLFKDQPFVSVFSHRELFADEEMSK  2000
2001  GLLTSPTDPPTSIYKRWFIKKTQEKHFELLINRQRWFRTNSSLSNGSFRS  2050
2051  NTLSESYQYLSNLFLSNGTLLDQMTKTLLRKRWLFPDEMKIGFMEQEKDF  2100
2101  PFLSRKDMWP                                          2110

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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