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

NucPred

Fetching Q9JMH9 from www.uniprot.org...

The NucPred score for your sequence is 0.98 (see score help below)

   1  MFNLMKKDKDKDGGRKEKKEKKEKKERMSAAELRSLEEMSMRRGFFNLNR    50
  51  SSKRESKTRLEISNPIPIKVASGSDLHLTDIDSDSNRGSIILDSGHLSTA   100
 101  SSSDDLKGEEGSFRGSVLQRAAKFGSLAKQNSQMIVKRFSFSQRSRDESA   150
 151  SETSTPSEHSAAPSPQVEVRTLEGQLMQHPGLGIPRPGPRSRVPELVTKR   200
 201  FPADLRLPALVPPPPPALRELELQRRPTGDFGFSLRRTTMLDRAPEGQAY   250
 251  RRVVHFAEPGAGTKDLALGLVPGDRLVEINGQNVENKSRDEIVEMIRQSG   300
 301  DSVRLKVQPIPELSELSRSWLRTGEGHRREPADAKTEEQIAAEEAWYETE   350
 351  KVWLVHRDGFSLASQLKSEELSLPEGKARVKLDHDGAILDVDEDDIEKAN   400
 401  APSCDRLEDLASLVYLNESSVLHTLRQRYGASLLHTYAGPSLLVLSTRGA   450
 451  PAVYSEKVMHMFKGCRREDMAPHIYAVAQTAYRAMLMSRQDQSIVLLGSS   500
 501  GSGKTTSFQHLVQYLATIAGTSGTKVFSVEKWQALSTLLEAFGNSPTIMN   550
 551  GSATRFSQILSLDFDQAGQVASASIQTMLLEKLRVARRPASEATFNVFYY   600
 601  LLACGDATLRTELHLNHLAENNVFGIVPLSKPEEKQKAAQQFSKLQAAMK   650
 651  VLAISPEEQKTCWLILASIYHLGAAGATKEAAEAGRKQFARHEWAQKAAY   700
 701  LLGCSLEELSSAIFKHQLKGGTLQRSTSFRQGPEESGLGEGTKLSALECL   750
 751  EGMASGLYSELFTLLISLVNRALKSSQHSLCSMMIVDTPGFQNPEWGGSA   800
 801  RGASFEELCHNYAQDRLQRLFHERTFLQELERYKEDNIELAFDDLEPVAD   850
 851  DSVAAVDQASHLVRSLAHADEARGLLWLLEEEALVPGATEDALLDRLFSY   900
 901  YGPQEGDKKGQSPLLRSSKPRHFLLGHSHGTNWVEYNVAGWLNYTKQNPA   950
 951  TQNAPRLLQDSQKKIISNLFLGRAGSATVLSGSIAGLEGGSQLALRRATS  1000
1001  MRKTFTTGMAAVKKKSLCIQIKLQVDALIDTIKRSKMHFVHCFLPVAEGW  1050
1051  PGEPRSASSRRVSSSSELDLPPGDPCEAGLLQLDVSLLRAQLRGSRLLDA  1100
1101  MRMYRQGYPDHMVFSEFRRRFDVLAPHLTKKHGRNYIVVDEKRAVEELLE  1150
1151  SLDLEKSSCCLGLSRVFFRAGTLARLEEQRDEQTSRHLTLFQAACRGYLA  1200
1201  RQHFKKRKIQDLAIRCVQKNIKKNKGVKDWPWWKLFTTVRPLIQVQLSEE  1250
1251  QIRNKDEEIQQLRSKLEKVEKERNELRLSSDRLETRISELTSELTDERNT  1300
1301  GESASQLLDAETAERLRTEKEMKELQTQYDALKKQMEVMEMEVMEARLIR  1350
1351  AAEINGEVDDDDAGGEWRLKYERAVREVDFTKKRLQQELEDKMEVEQQSR  1400
1401  RQLERRLGDLQADSDESQRALQQLKKKCQRLTAELQDTKLHLEGQQVRNH  1450
1451  ELEKKQRRFDSELSQAHEETQREKLQREKLQREKDMLLAEAFSLKQQMEE  1500
1501  KDLDIAGFTQKVVSLEAELQDISSQESKDEASLAKVKKQLRDLEAKVKDQ  1550
1551  EEELDEQAGSIQMLEQAKLRLEMEMERMRQTHSKEMESRDEEVEEARQSC  1600
1601  QKKLKQMEVQLEEEYEDKQKALREKRELESKLSTLSDQVNQRDFESEKRL  1650
1651  RKDLKRTKALLADAQIMLDHLKNNAPSKREIAQLKNQLEESEFTCAAAVK  1700
1701  ARKAMEVEMEDLHLQIDDIAKAKTALEEQLSRLQREKNEIQNRLEEDQED  1750
1751  MNELMKKHKAAVAQASRDMAQMNDLQAQIEESNKEKQELQEKLQALQSQV  1800
1801  EFLEQSMVDKSLVSRQEAKIRELETRLEFEKTQVKRLENLASRLKETMEK  1850
1851  LTEERDQRAAAENREKEQNKRLQRQLRDTKEEMSELARKEAEASRKKHEL  1900
1901  EMDLESLEAANQSLQADLKLAFKRIGDLQAAIEDEMESDENEDLINSLQD  1950
1951  MVTKYQKKKNKLEGDSDVDSELEDRVDGVKSWLSKNKGPSKAPSDDGSLK  2000
2001  SSSPTSHWKPLAPDPSDDEHDPVDSISRPRFSHSYLSDSDTEAKLTETSA  2050

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.