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

NucPred

Fetching O94851 from www.uniprot.org...

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

   1  MGENEDEKQAQAGQVFENFVQASTCKGTLQAFNILTRHLDLDPLDHRNFY    50
  51  SKLKSKVTTWKAKALWYKLDKRGSHKEYKRGKSCTNTKCLIVGGGPCGLR   100
 101  TAIELAYLGAKVVVVEKRDSFSRNNVLHLWPFTIHDLRGLGAKKFYGKFC   150
 151  AGSIDHISIRQLQLILFKVALMLGVEIHVNVEFVKVLEPPEDQENQKIGW   200
 201  RAEFLPTDHSLSEFEFDVIIGADGRRNTLEGFRRKEFRGKLAIAITANFI   250
 251  NRNSTAEAKVEEISGVAFIFNQKFFQDLKEETGIDLENIVYYKDCTHYFV   300
 301  MTAKKQSLLDKGVIINDYIDTEMLLCAENVNQDNLLSYAREAADFATNYQ   350
 351  LPSLDFAMNHYGQPDVAMFDFTCMYASENAALVRERQAHQLLVALVGDSL   400
 401  LEPFWPMGTGCARGFLAAFDTAWMVKSWNQGTPPLELLAERESLYRLLPQ   450
 451  TTPENINKNFEQYTLDPGTRYPNLNSHCVRPHQVKHLYITKELEHYPLER   500
 501  LGSVRRSVNLSRKESDIRPSKLLTWCQQQTEGYQHVNVTDLTTSWRSGLA   550
 551  LCAIIHRFRPELINFDSLNEDDAVENNQLAFDVAEREFGIPPVTTGKEMA   600
 601  SAQEPDKLSMVMYLSKFYELFRGTPLRPVDSWRKNYGENADLSLAKSSIS   650
 651  NNYLNLTFPRKRTPRVDGQTGENDMNKRRRKGFTNLDEPSNFSSRSLGSN   700
 701  QECGSSKEGGNQNKVKSMANQLLAKFEESTRNPSLMKQERRVSGIGKPVL   750
 751  CSSSGPPVHSCCPKPEEATPSPSPPLKRQFPSVVVTGHVLRELKQVSAGS   800
 801  ECLSRPWRARAKSDLQLGGTENFATLPSTRPRAQALSGVLWRLQQVEEKI   850
 851  LQKRAQNLANREFHTKNIKEKAAHLASMFGHGDFPQNKLLSKGLSHTHPP   900
 901  SPPSRLPSPDPAASSSPSTVDSASPARKEKKSPSGFHFHPSHLRTVHPQL   950
 951  TVGKVSSGIGAAAEVLVNLYMNDHRPKAQATSPDLESMRKSFPLNLGGSD  1000
1001  TCYFCKKRVYVMERLSAEGHFFHRECFRCSICATTLRLAAYTFDCDEGKF  1050
1051  YCKPHFIHCKTNSKQRKRRAELKQQREEEATWQEQEAPRRDTPTESSCAV  1100
1101  AAIGTLEGSPPDEPTSPKRPKSISEPQHSDAEGDAASPLPSEWTSVRISP  1150
1151  GEEAAGQDVLAVRVLVTSEDSSSDTESDYGGSEGSHTEPCEEKPWRPGSP  1200
1201  HLPHTSLGEALSRAVSPQCPEEPRAVHAALQRANSFQSPTPSKYQNWRRE  1250
1251  FWWSLTPVNKRTMSPPKDPSPSLPLPSSSSHSSSPPSSSSTSVSGNAPDG  1300
1301  SSPPQMTASEPLSQVSRGHPSPPTPNFRRRAVAQGAPREIPLYLPHHPKP  1350
1351  EWAEYCLVSPGEDGLSDPAEMTSDECQPAEAPLGDIGSNHRDPHPIWGKD  1400
1401  RSWTGQELSPLAGEDREKGSTGARKEEEGGPVLVKEKLGLKKLVLTQEQK  1450
1451  TMLLDWNDSIPESVHLKAGERISQKSAENGRGGRVLKPVRPLLLPRAAGE  1500
1501  PLPTQRGAQEKMGTPAEQAQGERNVPPPKSPLRLIANAIRRSLEPLLSNS  1550
1551  EGGKKAWAKQESKTLPAQACTRSFSLRKTNSNKDGDQHSPGRNQSSAFSP  1600
1601  PDPALRTHSLPNRPSKVFPALRSPPCSKIEDVPTLLEKVSLQENFPDASK  1650
1651  PPKKRISLFSSLRLKDKSFESFLQESRQRKDIRDLFGSPKRKVLPEDSAQ  1700
1701  ALEKLLQPFKSTSLRQAAPPPPPPPPPPPPPPTAGGADSKNFPLRAQVTE  1750
1751  ASSSASSTSSSSADEEFDPQLSLQLKEKKTLRRRKKLEKAMKQLVKQEEL  1800
1801  KRLYKAQAIQRQLEEVEERQRASEIQGVRLEKALRGEADSGTQDEAQLLQ  1850
1851  EWFKLVLEKNKLMRYESELLIMAQELELEDHQSRLEQKLREKMLKEESQK  1900
1901  DEKDLNEEQEVFTELMQVIEQRDKLVDSLEEQRIREKAEDQHFESFVFSR  1950
1951  GCQLSRT                                             1957

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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