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

NucPred

Fetching Q9UUG0 from www.uniprot.org...

The NucPred score for your sequence is 0.39 (see score help below)

   1  MVEAEQVHQSLRSLVLSYAHFSPSILIPASQYLLAAQLRDEFLSLHPAPS    50
  51  AESVEKEGAELEFEHELHLLAGFLGLIAAKEEETPGQYTQLLRIITLEFE   100
 101  RTFLAGNEVHAVVHSLGLNIPAQKDVVRFYYHSCALIGQTTKFHGSALLD   150
 151  ESSVKLAAIFGGQGYEDYFDELIELYEVYAPFAAELIQVLSKHLFTLSQN   200
 201  EQASKVYSKGLNVLDWLAGERPERDYLVSAPVSLPLVGLTQLVHFSVTAQ   250
 251  ILGLNPGELASRFSAASGHSQGIVVAAAVSASTDSASFMENAKVALTTLF   300
 301  WIGVRSQQTFPTTTLPPSVVADSLASSEGNPTPMLAVRDLPIETLNKHIE   350
 351  TTNTHLPEDRKVSLSLVNGPRSFVVSGPARSLYGLNLSLRKEKADGQNQS   400
 401  RIPHSKRKLRFINRFLSISVPFHSPYLAPVRSLLEKDLQGLQFSALKVPV   450
 451  YSTDDAGDLRFEQPSKLLLALAVMITEKVVHWEEACGFPDVTHIIDFGPG   500
 501  GISGVGSLTRANKDGQGVRVIVADSFESLDMGAKFEIFDRDAKSIEFAPN   550
 551  WVKLYSPKLVKNKLGRVYVDTRLSRMLGLPPLWVAGMTPTSVPWQFCSAI   600
 601  AKAGFTYELAGGGYFDPKMMREAIHKLSLNIPPGAGICVNVIYINPRTYA   650
 651  WQIPLIRDMVAEGYPIRGVTIAAGIPSLEVANELISTLGVQYLCLKPGSV   700
 701  EAVNAVISIAKANPTFPIVLQWTGGRAGGHHSFEDFHSPILLTYSAIRRC   750
 751  DNIVLIAGSGFGGADDTEPYLTGEWSAAFKLPPMPFDGILFGSRLMVAKE   800
 801  AHTSLAAKEAIVAAKGVDDSEWEKTYDGPTGGIVTVLSELGEPIHKLATR   850
 851  GIMFWKELDDTIFSLPRPKRLPALLAKKQYIIKRLNDDFQKVYFPAHIVE   900
 901  QVSPEKFKFEAVDSVEDMTYAELLYRAIDLMYVTKEKRWIDVTLRTFTGK   950
 951  LMRRIEERFTQDVGKTTLIENFEDLNDPYPVAARFLDAYPEASTQDLNTQ  1000
1001  DAQFFYSLCSNPFQKPVPFIPAIDDTFEFYFKKDSLWQSEDLAAVVGEDV  1050
1051  GRVAILQGPMAAKHSTKVNEPAKELLDGINETHIQHFIKKFYAGDEKKIP  1100
1101  IVEYFGGVPPVNVSHKSLESVSVTEEAGSKVYKLPEIGSNSALPSKKLWF  1150
1151  ELLAGPEYTWFRAIFTTQRVAKGWKLEHNPVRRIFAPRYGQRAVVKGKDN  1200
1201  DTVVELYETQSGNYVLAARLSYDGETIVVSMFENRNALKKEVHLDFLFKY  1250
1251  EPSAGYSPVSEILDGRNDRIKHFYWALWFGEEPYPENASITDTFTGPEVT  1300
1301  VTGNMIEDFCRTVGNHNEAYTKRAIRKRMAPMDFAIVVGWQAITKAIFPK  1350
1351  AIDGDLLRLVHLSNSFRMVGSHSLMEGDKVTTSASIIAILNNDSGKTVTV  1400
1401  KGTVYRDGKEVIEVISRFLYRGTFTDFENTFEHTQETPMQLTLATPKDVA  1450
1451  VLQSKSWFQLLDPSQDLSGSILTFRLNSYVRFKDQKVKSSVETKGIVLSE  1500
1501  LPSKAIIQVASVDFQSVDCHGNPVIEFLKRNGKPIEQPVEFENGGYSVIQ  1550
1551  VMDEGYSPVFVTPPTNSPYAEVSGDYNPIHVSPTFAAFVELPGTHGITHG  1600
1601  MYTSAAARRFVETYAAQNVPERVKHYEVTFVNMVLPNTELITKLSHTGMI  1650
1651  NGRKIIKVEVLNQETSEPVLVGTAEVEQPVSAYVFTGQGSQEQGMGMDLY  1700
1701  ASSPVARKIWDSADKHFLTNYGFSIIDIVKHNPHSITIHFGGSKGKKIRD  1750
1751  NYMAMAYEKLMEDGTSKVVPVFETITKDSTSFSFTHPSGLLSATQFTQPA  1800
1801  LTLMEKSAFEDMRSKGLVQNDCAFAGHSLGEYSALSAMGDVLSIEALVDL  1850
1851  VFLRGLTMQNAVHRDELGRSDYGMVAANPSRVSASFTDAALRFIVDHIGQ  1900
1901  QTNLLLEIVNYNVENQQYVVSGNLLSLSTLGHVLNFLKVQKIDFEKLKET  1950
1951  LTIEQLKEQLTDIVEACHAKTLEQQKKTGRIELERGYATIPLKIDVPFHS  2000
2001  SFLRGGVRMFREYLVKKIFPHQINVAKLRGKYIPNLTAKPFEISKEYFQN  2050
2051  VYDLTGSQRIKKILQNWDEYESS                             2073

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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