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

NucPred

Fetching P35658 from www.uniprot.org...

The NucPred score for your sequence is 0.82 (see score help below)

   1  MGDEMDAMIPEREMKDFQFRALKKVRIFDSPEELPKERSSLLAVSNKYGL    50
  51  VFAGGASGLQIFPTKNLLIQNKPGDDPNKIVDKVQGLLVPMKFPIHHLAL   100
 101  SCDNLTLSACMMSSEYGSIIAFFDVRTFSNEAKQQKRPFAYHKLLKDAGG   150
 151  MVIDMKWNPTVPSMVAVCLADGSIAVLQVTETVKVCATLPSTVAVTSVCW   200
 201  SPKGKQLAVGKQNGTVVQYLPTLQEKKVIPCPPFYESDHPVRVLDVLWIG   250
 251  TYVFAIVYAAADGTLETSPDVVMALLPKKEEKHPEIFVNFMEPCYGSCTE   300
 301  RQHHYYLSYIEEWDLVLAASAASTEVSILARQSDQINWESWLLEDSSRAE   350
 351  LPVTDKSDDSLPMGVVVDYTNQVEITISDEKTLPPAPVLMLLSTDGVLCP   400
 401  FYMINQNPGVKSLIKTPERLSLEGERQPKSPGSTPTTPTSSQAPQKLDAS   450
 451  AAAAPASLPPSSPAAPIATFSLLPAGGAPTVFSFGSSSLKSSATVTGEPP   500
 501  SYSSGSDSSKAAPGPGPSTFSFVPPSKASLAPTPAASPVAPSAASFSFGS   550
 551  SGFKPTLESTPVPSVSAPNIAMKPSFPPSTSAVKVNLSEKFTAAATSTPV   600
 601  SSSQSAPPMSPFSSASKPAASGPLSHPTPLSAPPSSVPLKSSVLPSPSGR   650
 651  SAQGSSSPVPSMVQKSPRITPPAAKPGSPQAKSLQPAVAEKQGHQWKDSD   700
 701  PVMAGIGEEIAHFQKELEELKARTSKACFQVGTSEEMKMLRTESDDLHTF   750
 751  LLEIKETTESLHGDISSLKTTLLEGFAGVEEAREQNERNRDSGYLHLLYK   800
 801  RPLDPKSEAQLQEIRRLHQYVKFAVQDVNDVLDLEWDQHLEQKKKQRHLL   850
 851  VPERETLFNTLANNREIINQQRKRLNHLVDSLQQLRLYKQTSLWSLSSAV   900
 901  PSQSSIHSFDSDLESLCNALLKTTIESHTKSLPKVPAKLSPMKQAQLRNF   950
 951  LAKRKTPPVRSTAPASLSRSAFLSQRYYEDLDEVSSTSSVSQSLESEDAR  1000
1001  TSCKDDEAVVQAPRHAPVVRTPSIQPSLLPHAAPFAKSHLVHGSSPGVMG  1050
1051  TSVATSASKIIPQGADSTMLATKTVKHGAPSPSHPISAPQAAAAAALRRQ  1100
1101  MASQAPAVNTLTESTLKNVPQVVNVQELKNNPATPSTAMGSSVPYSTAKT  1150
1151  PHPVLTPVAANQAKQGSLINSLKPSGPTPASGQLSSGDKASGTAKIETAV  1200
1201  TSTPSASGQFSKPFSFSPSGTGFNFGIITPTPSSNFTAAQGATPSTKESS  1250
1251  QPDAFSSGGGSKPSYEAIPESSPPSGITSASNTTPGEPAASSSRPVAPSG  1300
1301  TALSTTSSKLETPPSKLGELLFPSSLAGETLGSFSGLRVGQADDSTKPTN  1350
1351  KASSTSLTSTQPTKTSGVPSGFNFTAPPVLGKHTEPPVTSSATTTSVAPP  1400
1401  AATSTSSTAVFGSLPVTSAGSSGVISFGGTSLSAGKTSFSFGSQQTNSTV  1450
1451  PPSAPPPTTAATPLPTSFPTLSFGSLLSSATTPSLPMSAGRSTEEATSSA  1500
1501  LPEKPGDSEVSASAASLLEEQQSAQLPQAPPQTSDSVKKEPVLAQPAVSN  1550
1551  SGTAASSTSLVALSAEATPATTGVPDARTEAVPPASSFSVPGQTAVTAAA  1600
1601  ISSAGPVAVETSSTPIASSTTSIVAPGPSAEAAAFGTVTSGSSVFAQPPA  1650
1651  ASSSSAFNQLTNNTATAPSATPVFGQVAASTAPSLFGQQTGSTASTAAAT  1700
1701  PQVSSSGFSSPAFGTTAPGVFGQTTFGQASVFGQSASSAASVFSFSQPGF  1750
1751  SSVPAFGQPASSTPTSTSGSVFGAASSTSSSSSFSFGQSSPNTGGGLFGQ  1800
1801  SNAPAFGQSPGFGQGGSVFGGTSAATTTAATSGFSFCQASGFGSSNTGSV  1850
1851  FGQAASTGGIVFGQQSSSSSGSVFGSGNTGRGGGFFSGLGGKPSQDAANK  1900
1901  NPFSSASGGFGSTATSNTSNLFGNSGAKTFGGFASSSFGEQKPTGTFSSG  1950
1951  GGSVASQGFGFSSPNKTGGFGAAPVFGSPPTFGGSPGFGGVPAFGSAPAF  2000
2001  TSPLGSTGGKVFGEGTAAASAGGFGFGSSSNTTSFGTLASQNAPTFGSLS  2050
2051  QQTSGFGTQSSGFSGFGSGTGGFSFGSNNSSVQGFGGWRS            2090

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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