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

NucPred

Fetching P34926 from www.uniprot.org...

The NucPred score for your sequence is 0.79 (see score help below)

   1  MDGVAEFSEYVSETVDVPSPFDLLEPPTSGGFLKLSKPCCYIFPGGRGDS    50
  51  ALFAVNGFNILVDGGSDRKSCFWKLVRHLDRIDSVLLTHIGADNLPGING   100
 101  LLQRKVAELEEEQSQGSSSYSDWVKNLISPELGVVFFNVPDKLRLPDASR   150
 151  KAKRSIEEACLTLQHLNRLGIQAEPLYRVVSNTIEPLTLFHKMGVGRLDM   200
 201  YVLNPVKDSKEMQFLMQKWAGNSKAKTGIVLANGKEAEISVPYLTSITAL   250
 251  VVWLPANPTEKIVRVLFPGNAPQNKILEGLEKLRHLDFLRYPVATQKDLA   300
 301  AGAVPANLKPSKIKHRADSKESLKAAPKTAVSKLAKREEVLEEGAKEARS   350
 351  ELAKELAKTEKKAKEPSEKPPEKPSKSERVRGESSEALKAEKRRLIKDKA   400
 401  GKKHLKEKISKLEEKKDKEKKEIKKERKELKKEEGRKEEKKDAKKDEKRK   450
 451  DTKPEVKKLSKPDLKPFTPEVRKTLYKAKAPGRVKVDKGRAARGEKELSS   500
 501  EPRTPPAQKGAAPPAAVSGHRELALSSPEDLTQDFEELKREERGLLAEQR   550
 551  DTGLGEKPLPADATEQGHPSAAIQVTQPSGPVLEGEHVEREKEVVPDSPG   600
 601  DKGSTNRGPDSGAEVEKEKETWEERKQREAELGPENTAAREESEAEVKED   650
 651  VIEKAELEEMEETHPSDEEGEETKAESFYQKHTQEALKASPKSREALGGR   700
 701  DLGFQGKAPEKETASFLSSLATPAGATEHVSYIQDETIPGYSETEQTISD   750
 751  EEIHDEPDERPAPPRFPTSTYDLSGPEGPGPFEASQAADSAVPASSSKTY   800
 801  GAPETELTYPPNMVAAPLAEEEHVSSATSITECDKLSSFATSVAEDQSVA   850
 851  SLTAPQTEETGKSSLLLDTVTSIPSSRTEATQGLDYVPSAGTISPTSSLE   900
 901  EDKGFKSPPCEDFSVTGESEKKGETVGRGLSGEKAVGKEEKYVVTSEKLS   950
 951  GQYAAVFGAPGHTLPPGEPALGEVEERCLSPDDSTVKMASPPPSGPPSAA  1000
1001  HTPFHQSPVEDKSEPRDFQEDSWGETKHSPGVSKEDSEEQTVKPGPEEGT  1050
1051  SEEGKGPPTRSPQAQDMPVSIAGGQTGCTIQLLPEQDKAIVFETGEAGSN  1100
1101  LGAGTLPGEVRTSTEEATEPQKDEVLRFTDQSLSPEDAESLSVLSVVSPD  1150
1151  TTKQEATPRSPCSLKEQQPHKDLWPMVSPEDTQSLSFSEESPSKETSLDI  1200
1201  SSKQLSPESLGTLQFGELNLGKEERGPVMKAEDDSCHLAPVSIPEPHRAT  1250
1251  VSPSTDETPAGTLPGGSFSHSALSVDRKHSPGEITGPGGHFMTSDSSLTK  1300
1301  SPESLSSPAMEDLAVEWEGKAPGKEKEPELKSETRQQKGQILPEKVAVVE  1350
1351  QDLIIHQKDGALDEENKPGRQQDKTPEQKGRDLDEKDTAAELDKGPEPKE  1400
1401  KDLDREDQGQRAGPPAEKDKASEQRDTDLQQTQATEPRDRAQERRDSEEK  1450
1451  DKSLELRDRTPEEKDRILVQEDRAPEHSIPEPTQTDRAPDRKGTDDKEQK  1500
1501  EEASEEKEQVLEQKDWALGKEGETLDQEARTAEQKDETLKEDKTQGQKSS  1550
1551  FVEDKTTTSKETVLDQKSAEKADSVEQQDGAALEKTRALGLEESPAEGSK  1600
1601  AREQEKKYWKEQDVVQGWRETSPTRGEPVGGQKEPVPAWEGKSPEQEVRY  1650
1651  WRDRDITLQQDAYWRELSCDRKVWFPHELDGQGARPRYCEERESTFLDEG  1700
1701  PDEQEITPLQHTPRSPWTSDFKDFQEPLPQKGLEVERWLAESPVGLPPEE  1750
1751  EDKLTRSPFEIISPPASPPEMTGQRVPSAPGQESPVPDTESTAPMRNEPT  1800
1801  TPSWLAEIPPWVPKDRPLPPAPLSPAPAPPTPAPEPHTPVPFSWGLAEYD  1850
1851  SVVAAVQEGAAELEGGPYSPLGKDYRKAEGEREGEGGAGAPDSSSFSPKV  1900
1901  PEAGESLATRDTEQTEPEQREPTPYPDERSFQYADIYEQMMLTGLGPACP  1950
1951  TREPPLGASGDWPPHLSTKEEAAGCNTSAEKETSSPASPQNLQSDTPAFS  2000
2001  YASLAGPAVPPRQEPDPGPNVEPSITPPAVPPRAPISLSKDLSPPLNGST  2050
2051  VSCSPDRRTPSPKETGRGHWDDGTNDSDLEKGAREQPEKETRSPSPHHPM  2100
2101  PMGHSSLWPETEAYSSLSSDSHLGSVRPSLDFPASAFGFSSLQPAPPQLP  2150
2151  SPAEPRSAPCGSLAFSGDRALALVPGTPTRTRHDEYLEVTKAPSLDSSLP  2200
2201  QLPSPSSPGGPLLSNLPRPASPALSEGSSSEATTPVISSVAERFPPGLEA  2250
2251  AEQSAEGLGSGKESAAHSLWDLTPLSPAPSASLDLAPAPAPAPAPAPGLP  2300
2301  GDLGDGTLPCRPECTGELTKKPSPFLSPSGDHEANGPGETSLNPPGFVTA  2350
2351  TAEKEEAEAPHAWERGSWPEGAERSSRPDTLLSSEQPLRPGKSSGGPPCS  2400
2401  LSSEVEAGPQGCATDPRPHCGELSPSFLNPPLPPSTDDSDLSTEEARLAG  2450
2451  KGGRRRVGRPGATGGPCPMADETPPTSASDSGSSQSDSDVPPETEECPSI  2500
2501  TAEAALDSDEDGDFLPVDKAGGVSGTHHPRPGHDPPPTPLPDPRPSPPRP  2550
2551  DVCMADPEGLSSESGRVERLREKGRPGRRAPGRAKPASPARRLDIRGKRS  2600
2601  PTPGKGPVDRTSRTVPRPRSTPSQVTSAEEKDGHSPMSKGLVNGLKAGST  2650
2651  ALGSKGGSGPPVYVDLAYIPNHCSGKTADQDFFRRVRASYYVVSGNDPAN  2700
2701  GEPSRAVLDALLEGKAQWGENLQVTLIPTHDTEVTREWYQQTHEQQQQLN  2750
2751  VLVLASSSTVVMQDESFPACKIEF                            2774

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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