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

NucPred

Fetching O60522 from www.uniprot.org...

The NucPred score for your sequence is 0.40 (see score help below)

   1  MCSTPGMPAPGASLALRVSFVDVHPDVIPVQLWGLVGERRGEYLRLSREI    50
  51  QEAAATRGQWALGSASASPGELCLVQVGLLWHRCRVVSRQAQESRVFLLD   100
 101  EGRTITAGAGSLAPGRREFFNLPSEVLGCVLAGLVPAGCGAGSGEPPQHW   150
 151  PADAVDFLSNLQGKEVHGCVLDVLLLHRLVLLEVPDVFQQMRELGLARRV   200
 201  PDSLFRSLLERYLTAATASVGSGVPVLSRVPLKQKQPGLDYFYPQLQLGV   250
 251  TEAVVITQVCHPHRIHCQLRSVSQEIHRLSESMAQVYRGSTGTGDENSTS   300
 301  ATWEEREESPDKPGSPCASCGLDGHWYRALLLETFRPQRCAQVLHVDYGR   350
 351  KELVSCSSLRYLLPEYFRMPVVTYPCALYGLWDGGRGWSRSQVGDLKTLI   400
 401  LGKAVNAKIEFYCSFEHVYYVSLYGEDGINLNRVFGVQSCCLADRVLQSQ   450
 451  ATEEEEPETSQSQSPAEEVDEEISLPALRSIRLKMNAFYDAQVEFVKNPS   500
 501  EFWIRLRKHNVTFSKLMRRMCGFYSSASKLDGVVLKPEPDDLCCVKWKEN   550
 551  GYYRAIVTKLDDKSVDVFLVDRGNSENVDWYDVRMLLPQFRQLPILAVKC   600
 601  TLADIWPLGKTWSQEAVSFFKKTVLHKELVIHILDKQDHQYVIEILDESR   650
 651  TGEENISKVIAQAGYAKYQEFETKENILVNAHSPGHVSNHFTTESNKIPF   700
 701  AKTGEGEQKAKRENKTTSVSKALSDTTVVTNGSTELVVQEKVKRASVYFP   750
 751  LMQNCLEIKPGSSSKGELEVGSTVEVRVSYVENPGYFWCQLTRNIQGLKT   800
 801  LMSDIQYYCKNTAAPHQRNTLACLAKRTVNRQWSRALISGIQSVEHVNVT   850
 851  FVDYGDREMVSVKNIYSISEEFLKVKAQAFRCSLYNLIQPVGQNPFVWDV   900
 901  KAIQAFNEFIDNAWQKNLELKCTIFALASINEELFNIVDLLTPFQSACHF   950
 951  LVEKRLARPVKLQKPLESSVQLHSYFYSTHDMKIGSEELVYITHIDDPWT  1000
1001  FYCQLARNANILEQLSCSITQLSKVLLNLKTSPLNPGTLCLAKYTDGNWY  1050
1051  RGIVIEKEPKKVFFVDFGNIYVVTSDDLLPIPSDAYDVLLLPMQAVRCSL  1100
1101  SDIPDHIPEEVVVWFQETILDKSLKALVVAKDPDGTLIIELYGDNIQISA  1150
1151  SINKKLGLLSYKDRIRKKESEVLCSTTETLEEKNENMKLPCTEYLSKSVG  1200
1201  YKLPNKEILEESYKPQINSSYKELKLLQSLTKTNLVTQYQDSVGNKNSQV  1250
1251  FPLTTEKKEEISAETPLKTARVEATLSERKIGDSCDKDLPLKFCEFPQKT  1300
1301  IMPGFKTTVYVSHINDLSDFYVQLIEDEAEISHLSERLNSVKTRPEYYVG  1350
1351  PPLQRGDMICAVFPEDNLWYRAVIKEQQPNDLLSVQFIDYGNVSVVHTNK  1400
1401  IGRLDLVNAILPGLCIHCSLQGFEVPDNKNSKKMMHYFSQRTSEAAIRCE  1450
1451  FVKFQDRWEVILADEHGIIADDMISRYALSEKSQVELSTQVIKSASSKSV  1500
1501  NKSDIDTSVFLNWYNPEKKMIRAYATVIDGPEYFWCQFADTEKLQCLEVE  1550
1551  VQTAGEQVADRRNCIPCPYIGDPCIVRYREDGHYYRALITNICEDYLVSV  1600
1601  RLVDFGNIEDCVDPKALWAIPSELLSVPMQAFPCCLSGFNISEGLCSQEG  1650
1651  NDYFYEIITEDVLEITILEIRRDVCDIPLAIVDLKSKGKSINEKMEKYSK  1700
1701  TGIKSALPYENIDSEIKQTLGSYNLDVGLKKLSNKAVQNKIYMEQQTDEL  1750
1751  AEITEKDVNIIGTKPSNFRDPKTDNICEGFENPCKDKIDTEELEGELECH  1800
1801  LVDKAEFDDKYLITGFNTLLPHANETKEILELNSLEVPLSPDDESKEFLE  1850
1851  LESIELQNSLVVDEEKGELSPVPPNVPLSQECVTKGAMELFTLQLPLSCE  1900
1901  AEKQPELELPTAQLPLDDKMDPLSLGVSQKAQESMCTEDMRKSSCVESFD  1950
1951  DQRRMSLHLHGADCDPKTQNEMNICEEEFVEYKNRDAISALMPLFSEEES  2000
2001  SDGSKHNNGLPDHISAQLQNTYTLKAFTVGSKCVVWSSLRNTWSKCEILE  2050
2051  TAEEGTRVLNLSNGMEEIVNPENVWNGIPKLDKSPPEKRGLEVMEI      2096

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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