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

NucPred

Fetching P20054 from www.uniprot.org...

The NucPred score for your sequence is 0.37 (see score help below)

   1  MDILNRKKGCLVLEDGTKLSGYSFGSERSVAGECVFSTGMVGYNESISDP    50
  51  SYTGQILVFSFPLIGNYGVPSFRERDPESGLAVNFESDKAHVQAIICSEY   100
 101  CDEYSHWAAEKSLSEWLKESNIPGLYGIDTRALITKIREKGSLKGKVIIG   150
 151  DFDESKLEFEDINLRNLVAEVSTKEIKEYKAAENNKKTGEKRKNKKVIVL   200
 201  DCGIKNNQIRCLLNRGVDLKVVPWDYDVVANESINDYDGVFISNGPGDPS   250
 251  LCGKAIENIRKVLALPVAKAVFGVCMGNQLLGLAAGAQTHKMAFGNRGLN   300
 301  QPCVDQISGRCHITSQNHGFVIDSNSLPAGSGWKTYFINANDASNEGIYH   350
 351  ESKPWFSVQFHPEAMAGPTDTEYLFDNFVDNVCGEQQHKSPMNKSKIIDC   400
 401  PKGINKVLILGSGGLSIGQAGEFDYSGSQAIKALKEEGIKTILINPNIAT   450
 451  VQTSPGLADKVYFLPVNASSVQKVIENENPDGILVTFGGQTALNCGIELY   500
 501  KSGILEKYNCKVLGTPIETIIATEDRGIFAEKLSEINERIAPSMACNSLE   550
 551  ESLIEAEKIGYPVIVRAAYCLGGLGSGFADNKEQLTALVTEAMATSSQVL   600
 601  VEKSLKGWKEIEYEVLRDSKDNCITVCNMENFDPLGIHTGESIVVAPSQT   650
 651  LSDREYQMLRETAIKTVRHLGVIGECNIQYSLNPYSEEYCIIEVNARLSR   700
 701  SSALASKATGYPLAFISAKVALGYDLAALRNTITKKTTACFEPSLDYLVV   750
 751  KMPRWDLKKFTRVSNKISSSMKSVGEVMSIGRKFEEAIQKAIRMVMDGAV   800
 801  EGFQAGVFPTSDEELEHPTNNRILVLASAFKDGYSIDRVHQLTKIDKWFL   850
 851  TKLKAIIDLENHLSTYKEPSQIPSEILKFSKQQGFSDKQIARAVGTTELN   900
 901  VRDYRKKMGIIPCTKHIDTVAAEFPAQNNYLYMTYNGETNDVNINEKSYI   950
 951  TLGSGSYRIGSSVEFDWCAVSCIRTLRSLGLKSIMINFNPETVSTDYDEC  1000
1001  DYLYFEELSLERVLDIYERGGPNSNHGVILSVGGQIPNNLAIPLSRCNVK  1050
1051  VLGTHPDMIDSAENRYKFSRLLDTIGIDQPLWKELTSVSDTKDFCESVGF  1100
1101  PCLVRPSYVLSGAAMNVVHSSQDLETFLTEAAAVSRDHPVVISKFIQEAK  1150
1151  EIEIDAVADNGRIVLFAISEHVENAGVHSGDATIVCPAQDLDDATILKVE  1200
1201  ETARKIAEALNVSGPFNIQFIAKNNEIKVIECNLRCSRSFPFVSKTLNIN  1250
1251  FIELATKIIIKHQYDLPVVNPINYVGVKVPQFSFIRLKGADPVLGVEMAS  1300
1301  TGEVACFGNTREEAYVKGLISTGFKAPEKNVLLSIGSFKEKHEFLPSAHK  1350
1351  LIKLGYTLFGTQGTADFYSENGVPVTQLNWDEEDLGENVIQKKMTENTIH  1400
1401  LFINLPSKNKYRRPSSFMSRGYSLRRVAIDFQVPLITNIKCAKLFVDSLS  1450
1451  YMKGPMPIENVDWRTSNKIIRLPGLVDVHVHLREPGATHKEDWDSGTATA  1500
1501  LAGGFTMVGAMPNTNPAIMDDASFELCKSLAASKARCDYGIFIGATFTNT  1550
1551  TTAGKFASDAMGMKMYLEETFAPLPLKDDINVWRDHIMNWPGTTPICVHA  1600
1601  DGRNLAAILLLGWMYDKHMHVCHVSHKEEIDIIRDAKKRGMKLSCEVSPH  1650
1651  HLTLCDKDIPRIGAGQSEVRPKLGTEEDLNALWDNIDYIDMIATDHAPHT  1700
1701  WEEKCSAKPPPGFPGLETSLPLMLTAVHNGRITIEDLVMKMHTNPIRIFN  1750
1751  LPEQPDTYIEVDMEQEWTIPKKPLYSRCGWTPFEGLQVRGKVVKVVLRGQ  1800
1801  IAFIDGKIIAQKGFGLNLRSKEYQVEKERLLNTTKPIYDKIPTVQSTKNQ  1850
1851  TTNITSPSLISDSPNKAINKIKSTSTSTTPNTQEQSTQHLPLVGSNLASA  1900
1901  VLNKKEDTLQTAFNISDNSLAGKHIFSVKQFNRKQLHALFGIAHEMRILV  1950
1951  KRSGGSDLLKGKVLATLFYEPSTRTQCSFTAAMQRLGGSVVTVDNVSSSV  2000
2001  AKGESIADTIQTLESYCDAVCMRHPAVGSVESAIQVAKKPIINAGDGVGE  2050
2051  HPTQALLDVFTIREELGTVNGLTITVVGDLKHGRTVHSLVRLLANYQVKI  2100
2101  NYVSPSSLSMPTEIIKELNEKGIEQKEYTNIESILPTTNVLYVTRVQKER  2150
2151  FQSIEEYEKVKDSFIITPHTLTKASDNMIVMHPLPRINEISPEVDSDPRA  2200
2201  AYFRQMENGLYVRMSLLALVFGAGV                           2225

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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