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

NucPred

Fetching Q9QYR6 from www.uniprot.org...

The NucPred score for your sequence is 0.77 (see score help below)

   1  MDGVAEFSEYVSETVDVPSPFDLLEPPTSGGFLKLSKPCCYIFPGGRGDS    50
  51  ALFAVNGFNILVDGGSDRKSCFWKLVRHLDRIDSVLLTHIGADNLPGING   100
 101  LLQRKVAELEEEQSQGSSSYSDWVKNLISPELGVVFFNVPDKLRLPDASR   150
 151  KAKRSIEEACLTLQHLNRLGIQAEPLYRVVSNTIEPLTLFHKMGVGRLDM   200
 201  YVLNPVKDSKEMQFLMQKWAGNSKAKTGIVLANGKEAEISVPYLTSITAL   250
 251  VVWLPANPTEKIVRVLFPGNAPQNKILEGLEKLRHLDFLRYPVATQKDLA   300
 301  AGAVPANLKPSKIKHRADSKESLKAAPKTAMSKLAKREEVLEEGAKEARS   350
 351  ELAKELAKSEKKAKEPSEKPPEKPSKPERVRTESSEALKAEKRKLIKDKV   400
 401  GKKHLKEKISKLEEKRDKEKKEIKKERKELKKEEGRKEEKKDAKKDEKRK   450
 451  DTKPELKKFSKPDLKPFTPEVRKTLYKAKAPGRLKVDKGRAARGEKELSS   500
 501  EPRTPPAQKGAAPPPAASGHRELALSSPEDLTQDFEELKREERGLLAEPR   550
 551  DTELGEKPLPADASEQGRPSTAIQVTQPPASVLEQEQVEREKEVVPDFPE   600
 601  DKGSKNRAPDSGAEVEREKETWEERKPREAELTPENIAAAREESEPEVKE   650
 651  DVIEKAELEEMEEVHPSDEEEEETKAESFYQKHMQEALKVIPKGREALGG   700
 701  RELGFQGKAPEKETASFLSSLATPAGAAEHVSYIQDETIPGYSETEQTIS   750
 751  DEEIHDEPDERPAPPRFPTSTYDLSGPEGPGPFEASQSAESAVPASSSKT   800
 801  YGAPETELTYPPNMVAAPLAEEEHVSSATSITECDKLSSFATSVAEDQSV   850
 851  ASLTAPQTEETGKSSLLLDTVTSIPSSRTEATQGLDYVPSAGTISPTSSL   900
 901  EEDKGFKSPPCEDFSVTGESEKKGESVGRGLTGEKAVGKEEKNVTTSEKL   950
 951  SSQYAAVFGAPGHALHPGEPALGEVEERCLSPDDSTVKMASPPPSGPPSA  1000
1001  AHTPFHQSPVEEKSEPQDFQEDSWGDTKHAPGVSKEDAEEQTVKPGPEEA  1050
1051  MSEEGKVPLSRSPQAQDTLGSLAGGQTGCTIQLLPEQDKAVVFETGEAGA  1100
1101  ASGAGSLPGEVRTQEPAEPQKDELLGFTDQSFSPEDAESLSVLSVVSPDT  1150
1151  AKQEATPRSPCTPKEQQLHKDLWPMVSPEDTQSLSFSEESPSKETSLDIS  1200
1201  SKQLSPESLGTLQFGELSLGKEEKGPLVKAEDNSCHLAPVSIPEPHTATV  1250
1251  SPPTDEAAGEAGLTDESPAGNLPGSSFSHSALSGDRKHSPGEITGPGGHF  1300
1301  MTSDSSLTKSPESLSSPAMEDLAMEWGGKAPGSEDRATEQKEKELERKSE  1350
1351  TLQQKDQILSEKAALVQRDSVMHQKDEALDEENKPGGQQDKTSEQKGRDL  1400
1401  DKKDTAVELGKGPEPKGKDLYLEDQGLAEKDKALEQRGAALQQTQAPEPR  1450
1451  ARAQEHRDLEQKDEHLELRDKTPEEKDKVLVLEDRAPEHIIPQPTQTDRA  1500
1501  PEHRSKVDKEQKDEASEEKEQVLEQKDWAREKEGAALDQDNRAAGQKDGT  1550
1551  LKEDKTQGQKSSFLEDKSTTPKEMTLDQKSPEKAKGVEQQDGAVPEKTRA  1600
1601  LGLEESPEEEGKAREQEEKYWKEQDVVQGWRETSPTRGEPVPAWEGKSPE  1650
1651  QEVRYWRDRDITLQQDAYWKELSCERKVWFPHELDGQGARPRYSEEREST  1700
1701  FLDEGPNEQEITPLQHTPRSPWASDFKDFQEPLPQKGLEVERWLAESPVG  1750
1751  LPPEEEDKLTRSPFEIISPPASPPEMTGQRVPSAPGQESPVPDTKSTPPT  1800
1801  RNEPTTPSWLAEIPPWVPKDRPLPPAPLSPAPAPPTPAPDPHAPAPFSWG  1850
1851  IAEYDSVVAAVQEGAAELEGGPYSPLGKDYRKAEGEREGEGGAGAPDSSS  1900
1901  FSSKVPEVTESHTTRDAEQTEPEQREPTPYPDERSFQYADIYEQMMLTGL  1950
1951  GPACPTREPPLGASGDWPPHLSTKEEAAGRNKSAEKELSSAVSPPNLHSD  2000
2001  TPTFSYASLAGPTIPPRQEPEPGPNVEPSFTPPAVPPRAPISLSQDPSPP  2050
2051  LNGSTTSCGPDRRTPSPKEAGRSHWDDGTNDSDLEKGAREQPEKETQSPS  2100
2101  PHHPMPVGHPSLWPETEAHSSLSSDSHLGPVRPSLDFPASAFGFSSLQPA  2150
2151  PPQLPSPAEPRSAPCGSLAFSGDRALALVPGTPTRTRHDEYLEVTKAPSL  2200
2201  DSSLPQLPSPSSPGAPLLSNLPRPASPALSEGSSSEATTPVISSVAERFP  2250
2251  PGLEVAEQSSGELGPGNEPAAHSLWDLTPLSPAPLASRDLAPAPAPAPAP  2300
2301  SLPGNLGDGTLSCRPECSGELTKKPSPFLSHSGDHEANGPGETSLNPPGF  2350
2351  ATATAEKEEAEALHAWERGSWPEGAERSSRPDTLLSSEQRPGKSSGGPPC  2400
2401  SLSSEVEAGPQGCATDPRPHCGELSPSFLNPPLPPSTDDSDLSTEEARLA  2450
2451  GKGGRRRAGRPGATGGPCPMADETPPTSASDSGSSQSDSDVPPETEECPS  2500
2501  ITAEAALDSDEDGDFLPVDKAGGVSGTHHPRPGHDPPPAPLPDPRPPPPR  2550
2551  PDVCMADPEGLSSESGRVERLREKVQGRPGRKAPGRAKPASPARRLDIRG  2600
2601  KRSPTPGKGPVDRTSRALPRPRSTPSQVTSEEKDGHSPMSKGLVNGLKAG  2650
2651  STALGSKGSSGPPVYVDLAYIPNHCSGKTADQDFFRRVRASYYVVSGNDP  2700
2701  ANGEPSRAVLDALLEGKAQWGENLQVTLIPTHDTEVTREWYQQTHEQQQQ  2750
2751  LNVLVLASSSTVVMQDESFPACKIEF                          2776

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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