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

NucPred

Fetching Q4KKX4 from www.uniprot.org...

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

   1  MSSSGYPPNQGAFSTEQGRYSSHPVQYTFPSSRHQQEFPVPEYRSSHLEA    50
  51  SQLLQQQQLRRRPSLLSEFHPVSDRPQDRRQGYEQQYHSVTQNEHEALES   100
 101  KRPRLDVSDSHYRVGAASVVPLVPTIQEGVRVQSEVKKEQGLPSKHETTS   150
 151  SPLSGQPGEEQEASPSKLSKEELIQSMDRVDREIAKVEQQILKLKKKQQQ   200
 201  LEEEAAKPPEPEKPVSPPPVEQKHRSIVQIIYDENRKKAEEAHKILEGLG   250
 251  PKVELPLYNQPSDTKVYHENIKTNQVMRKKLILFFKRRNHARKLREQNIC   300
 301  QRYDQLMEAWEKKVDRIENNPRRKAKESKTREYYEKQFPEIRKQREQQER   350
 351  FQRVGQRGAGLSATIARSEHEISEIIDGLSEQENNEKQMRQLSVIPPMMF   400
 401  DAEQRRVKFINMNGLMEDPMKVYKDRQFMNVWTDHEKEIFKEKFVQHPKN   450
 451  FGLIASYLERKTVSDCVLYYYLTKKNENFKALVRRNYPKRRGRNQQQITR   500
 501  PAQEEKEIEKVEEEKAERNDKKEEERREEEEKEEKEELRDGTKDRTDAIA   550
 551  EDGEDKEQSTPRGRKTANSQGRRKGRITRSMASEAAAAANAASTATTAPA   600
 601  TTTSTTATTTTAALVPVAPPPEEPTPPPTQEQSLVEHGRNWGAIAKMVGS   650
 651  KSESQCKNFYFNYKRRHNLDNLLQQHKQKSSRRPREERDVSQCESVASTV   700
 701  SAQEDEENEASNEEENAEDSEGAENSSDTESAPSPSPAEAAKLGDDAVDR   750
 751  TTSSVSIEAPPEQDAASKSVSDSSPTPTVENIKPPETQYTELKVKEEIST   800
 801  ETEEAMEVEERSQGAEIKSTLSLPVQTKAEPDEVESKPSESAEVKIEEDT   850
 851  KDQDMERLMDRAEATDMVYAPPLHISRGRQESQSDNDSSATCSADEEVDG   900
 901  EPERPRIYTLDSKPSLLNPAGTILISSSMKQGPMDLQQLQHRAAVIPPMA   950
 951  SCSPCNITTGTSNFSMYQRHLYENNLLEEQRQRQEQLSLESRMSASPGNM  1000
1001  SKSPNMDWEGKSVYMPYTEVKRAFEHEAQMQNVARSVSPYRLSPREVSRA  1050
1051  SPQVDMNPARYCVPPVLQPAPHQVITSLSDGARLPVTRPTRPPPPLIPSS  1100
1101  KTSATSSDKPSFITGGSISQGTPGTYLTSLSQSYSQETVKPSVGSISLGL  1150
1151  PRQQESAKTGSVTYIKQEEFSPRGQSSQPEGLLVRAQHEGVVRGTMTAIQ  1200
1201  EGSITRGTPATKVPIEAVSTLRGSITQGTPALSQSGIAADVLLKTTITRL  1250
1251  ATEDIGSPERCRDETSAKGHVIYEGKSGHIVSYDTAIKNMREGTRSPRTA  1300
1301  PEVTLKRTFDTMEGNIKQAMSVREAAVSGPMEGLICRTLPKGSTHAEIKD  1350
1351  RQVLSGSIMKGTPRTTSDSFEDGLKYAKQIKLESPPIRSFEGAISKGKPY  1400
1401  ECVTTIKEMGRSIHEIPRQDLGSQESRKTPESSRQIIEGSISQGTPIKYE  1450
1451  GTSGQSAIKHNVKSLITGPSNLSRGLPQMEVMPENLKMGERSKYEDTKSS  1500
1501  EAIRSRHTSVVSSGPSVLRSTLHEASKSQLSPGVYEDNNARRTPVNYPSP  1550
1551  MSRSSPMARSAEVGLTPGKSSSHERKSTLTPTQRENIVVKSPVPGVDPTA  1600
1601  AHSPFDPHLRGAPPGDVYRTHLPPHLDPALQFHRPLDPAAAAAYLFQRQL  1650
1651  SPTPGYPSQYQLYAMENTRQTILNDYITSQQMQVNLRPDVARGLSPRDQG  1700
1701  LAIPYPGARGIIDLTNMPPAILVPHPGGTSTPPMDRITYIPGTQLAFPPR  1750
1751  PYNPASMSPGHPTHLAAANSVSAERERERERDRERDREREKEQRERERDR  1800
1801  ERERERLAAAPSDHYLRPVSEQPGRPGSHGFVRSPSPSVRAQESIMQQRP  1850
1851  SIFQGTNGKSVITPLDAAQLRIMPPTPGAASITQGIPASRYSTAADALAA  1900
1901  LVDAAASAPQMEVVKPKEMKHDPARSEESLSRRNVLEQQQQQQQIDCERR  1950
1951  VMQSPYTSSSFSGSKSQGQPSPAVYSEAGKEKTAHTKSRYVEELRMRGKT  2000
2001  TITAANFIDVIITQQIASDKDGRDRNSQSSDSSSSHSSHRYDAPRDTIEV  2050
2051  ISPANSPVQEKESYPPEIPKSSQTESESSRKYEGQPNRYRQQQESPSPQQ  2100
2101  TIPGHVPQTHRLITLADHICQIITQDFARNQPVNQALQQPPASTFQSTNP  2150
2151  SSTPVRTKASSRFSPESQVQPVHNQRPASRVSPENVLDRPRGRPGKSPDR  2200
2201  GHISEPYEPISPPQAPLLHAKQDSMLLLSQRQEPPEQRNDSRSPGNISYL  2250
2251  PSFFTKLENTSPMVMYKKQEIFRKLNSSGGGDSEMAAAQPGTEIFNLPAV  2300
2301  TTSGAISSRGHSFADPASNLGLEDIIRKALMGNFDDKSEDHSVLVGVAQG  2350
2351  NPSGTQNSEARREEANPSPNSGGGTHKQKLISKYGSRKTKSPISGSQTYL  2400
2401  GAERPSSVSSVHSEGDYRQASAWAWEDRPSSTGSTQFPYNPLTMGMLNST  2450
2451  PPSSMSCAPTSMTQTSAHQQSRIWEREPAPLLSEQYETLSDSDE        2494

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.