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

NucPred

Fetching Q8BML1 from www.uniprot.org...

The NucPred score for your sequence is 0.99 (see score help below)

   1  MGENEDEKQAQASQVFENFVQATTCKGTLQAFNILTCLLDLDPLDHRNFY    50
  51  SQLKSKVNTWKAKALWHKLDKRGSHKEYKRGKACSNTKCLIVGGGPCGLR   100
 101  TAIELAYLGAKVVVVEKRDTFSRNNVLHLWPFTIHDLRGLGAKKFYGKFC   150
 151  AGSIDHISIRQLQLILFKVALMLGVEVHVNVEFVRVLEPPEDQENQKVGW   200
 201  RAEFLPADHALSDFEFDVIIGADGHRNTLEGFRRKEFRGKLAIAITANFI   250
 251  NRNSTAEAKVEEISGVAFIFNQKFFQDLKEETGIDLENIVYYKDSTHYFV   300
 301  MTAKKQSLLDKGVILNDYIDTEMLLCSENVNQDNLLSYAREAADFATNYQ   350
 351  LPSLDFAINHNGQPDVAMFDFTSMYASENAALMRERQAHQLLVALVGDSL   400
 401  LEPFWPMGTGCARGFLAAFDTAWMVKSWDQGTPPLEVLAERESLYRLLPQ   450
 451  TTPENINKNFEQYTLDPATRYPNLNLHCVRPHQVKHLYITKEMDRFPLER   500
 501  WGSVRRSVSLSRRESDIRPNKLLTWCQQQTKGYQHVRVTDLTTSWRSGLA   550
 551  LCAIIHSFRPELINFDSLNEDDAVENNQLAFDVAKREFGILPVTTGKEMA   600
 601  STQEPDKLSMVMYLSKFYELFRGTPLRPMDSWRKNYGENADFGLGKTFIQ   650
 651  NNYLNLTLPRKRTPRVDTQTEENDMNKRRRQGFNHLEELPSFSSRSLGSS   700
 701  QEYAKESGSQNKVKHMANQLLAKFEENTRNPSVVKQDCRRVSGIGKPVLC   750
 751  SASRPPGTSCCPKLEESTPRLPPPLKRQFSSTVATGQVLRELNQVPASGE   800
 801  CPSRPWRARAKSDLQLGGVENLATLPRTCQGALALSGVLRRLQQVEEKVL   850
 851  QKRAQNLANREFHTKNIKEKAAHLASMFGHGDLPQDKLLSKRVPHAHPPS   900
 901  PPSCLPSPHPAAASSPPAADSVSPARKVVALNHRLPPPLHLTVGKVSSGI   950
 951  GAAAEVLVNLYLNDHRPKTQATSPDLESPRKAFPLSLGGRDTCYFCKKRV  1000
1001  YMIERLSAEGHFFHQECFRCSVCSATLRLAAYAFDCDEGKFYCKPHFVHC  1050
1051  KTSSKQRKRRAELNQQREEEGTWQEQEAPRRDVPTESSCAVAAISTPEGS  1100
1101  PPDEPISPKKPKSVPEPNPRDVEAEATSPRPSEWTSVRISPGEDTVRQDV  1150
1151  LAVRVLVTSEDSSSDTESDYGSITAPCAGAYEERPQLPESPPLSKPLTRH  1200
1201  ISLRENLTQPVSLLHEEPQALPALQRAHSLQSPTPSKYQNWRRRFQSNST  1250
1251  PMNQRAPSPPKEPPPPPSLSSSSSLPSSFSSASVPGHTADDSSSPQVTYN  1300
1301  LHSPQISRGDVSPTPIYLRRARAQGIVKEIPLYLPHSPMLESTEDCLVEP  1350
1351  GRESLRSPEEISSSEGCQEARALGNTRSIQHPILGKDQYLPNQNLALGAA  1400
1401  GNPGDPREESRMGQPGGPELSKERKLGLKKLVLTEEQKNKLLDWSDCTQE  1450
1451  HKTGEQLSQESAENIRGGSLKPTCSSTLSQAVKEKLLSQKKALGGMRTPA  1500
1501  VKAPQEREVPPPKSPLKLIANAILRSLLHNSEAGKKTSPKPESKTLPRGQ  1550
1551  PHARSFSLRKLGSSKDGDQQSPGRHMAKKASAFFSLASPTSKVAQASDLS  1600
1601  LPNSILRSRSLPSRPSKMFFSTTPHSKVEDVPTLLEKVSLQDATHSPKTG  1650
1651  ASHISSLGLKDKSFESFLQECKQRKDIGDFFNSPKEEGPPGNRVPSLEKL  1700
1701  VQPVGSTSMGQVAHPSSTGQDARKLEGGEGGSSLVSSLVLVSDPVAPVTE  1750
1751  ATSSPTSSSAEEEADSQLSLRIKEKILRRRRKLEKQSAKQEELKRLHKAQ  1800
1801  AIQRQLEEVEERQRTLAIQGVKLEKVLRGEAADSGTQDEAQLLQEWFKLV  1850
1851  LEKNKLMRYESELLIMAQELELEDHQSRLEQKLRQKMLKDEGQKDENDLK  1900
1901  EEQEIFEEMMQVIEQRNKLVDSLEEQRVKERTQDQHFENFVLSRGCQLSR  1950
1951  T                                                   1951

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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