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

NucPred

Fetching P49259 from www.uniprot.org...

The NucPred score for your sequence is 0.65 (see score help below)

   1  MPLLSLSLLLLLLQVPAGSAETAAWAVTPERLREWQDKGIFIIQSENLEK    50
  51  CIQASKSTLTLENCKPPNKYMLWKWVSNHRLFNIGGSGCLGLNVSSPEQP   100
 101  LSIYECDSTHVSLKWHCNKKTITGPLQYLVQVKQDNTLVASRKYLHKWVS   150
 151  YMSGGGGICDYLHKDLYTIKGNAHGTPCMFPFQYNQQWHHECTREGREDN   200
 201  LLWCATTSRYERDEKWGFCPDPTSTEVGCDAVWEKDLHSRICYQFNLLSS   250
 251  LSWSEAHSSCQMQGAALLSIADETEENFVRKHLGSEAVEVWMGLNQLDED   300
 301  AGWQWSDRTPLNYLNWKPEINFEPFVEYHCGTFNAFMPKAWKSRDCESTL   350
 351  PYVCKKYLNPTDHGVVEKDAWKYYATHCEPGWNPHNRNCYKLQKEKKTWN   400
 401  EALQSCQSNNSVLTDITSLAEVEFLVTLLGDENASETWIGLSSHKIPVSF   450
 451  EWSNGSSVTFTNWHTLEPHIFPNRSQLCVSAEQSEGHWKVKNCEETLFYL   500
 501  CKKTGLVLSDTESGCQKGWERHGKFCYKIDTVLRSFDHASSGYYCPPALI   550
 551  TITSRFEQAFITSLISSVVKTKDTYFWIALQDQNNTGEYTWKTAGQQLEP   600
 601  VKYTHWNTRQPRYSGGCVVMRGRSHPGRWEVRDCRHFKAMSLCKQPVENR   650
 651  EKTKQEEGWPFHPCYLDWESEPGLASCFKVFHSEKVLMKRTWRQAEEFCE   700
 701  EFGAHLASFAHIEEENFVNELLHSKFNRTEERQFWIGFNKRNPLNAGSWE   750
 751  WSDGTPVVSSFLDNSYFGEDARNCAVYKANKTLLPSYCGSKREWICKIPR   800
 801  DVRPKVPPWYQYDAPWLFYQDAEYLFHISASEWSSFEFVCGWLRSDILTI   850
 851  HSAHEQEFIHSKIRALSKYGVNWWIGLREERASDEFRWRDGSPVIYQNWD   900
 901  KGKERSMGLNESQRCGFISSITGLWASEECSISMPSICKRKKVWVIEKKK   950
 951  DIPKQHGTCPKGWLYFDYKCLLLKIPEGPSDWKNWTSAQDFCVEEGGTLV  1000
1001  AIENEVEQAFITMNLFGHTTNVWIGLQDDDYEKWLNGRPVSYSNWSPFDT  1050
1051  KNIPNHNTTEVQKRIPLCGLLSNNPNFHFTGKWYFEDCREGYGFVCEKMQ  1100
1101  DASGHSINTSDMYPIPNTLEYGNRTYKIINANMTWYTALKTCLMHGAELA  1150
1151  SITDQYHQSFLTVILNRVGYAHWIGLFTEDNGLSFDWSDGTKSSFTFWKD  1200
1201  DESSFLGDCVFADTSGRWSSTACESYLQGAICQVPTETRLSGRLELCSET  1250
1251  SIPWIKFKSNCYSFSTVLESTSFEAAHEFCKKKGSNLLTIKDEAENSFLL  1300
1301  EELLAFRSSVQMIWLNAQFDGDNETIKWFDGTPTDQSNWGIRKPEVYHFK  1350
1351  PHLCVALRIPEGVWQLSSCQDKKGFICKMEADIHTVKKHPGKGPSHSVIP  1400
1401  LTVALTLLVILAISTLSFCMYKHSHIIFGRLAQFRNPYYPSANFSTVHLE  1450
1451  ENILISDLEKNDQ                                       1463

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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