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

NucPred

Fetching P28290 from www.uniprot.org...

The NucPred score for your sequence is 0.96 (see score help below)

   1  MDRPLSSSAEAEEELEWQVASRRRKAWAKCRSSWQASETEDLSTEATTQD    50
  51  EEEDEEEDLPGAQLPAAGGRGNVPNEKIAIWLKDCRTPLGASLDEQSSST   100
 101  LKGVLVRNGGSFEDDLSLGAEANHLHESDAQIENCNNILAKERRLQFHQK   150
 151  GRSMNSTGSGKSSGTVSSVSELLELYEEDPEEILYNLGFGRDEPDIASKI   200
 201  PSRFFNSSSFAKGIDIKVFLSAQMQRMEVENPNYALTSRFRQIEVLTTVA   250
 251  NAFSSLYSQVSGTPLQRIGSMSSVTSNKETDPPPPLTRSNTANRLMKTLS   300
 301  KLNLCVDKTEKGESSSPSPSAEKGKILNVSVIEESGNKNDQKSQKIMKKK   350
 351  ESSSMLATVKEEVSGSSAAVTENADSDRISDEANSNFNQGTENEQSKETQ   400
 401  SHESKLGEESGIVESKLDSDFNISSHSELENSSELKSVHISTPEKEPCAP   450
 451  LTIPSIRNIMTQQKDSFEMEEVQSTEGEAPHVPATYQLGLTKSKRDHLLR   500
 501  TASQHSDSSGFAEDSTDCLSLNHLQVQESLQAMGSSADSCDSETTVTSLG   550
 551  EDLATPTAQDQPYFNESEEESLVPLQKGLEKAAAVADKRKSGSQDFPQCN   600
 601  TIENTGTKQSTCSPGDHIIEITEVEEDLFPAETVELLREASAESDVGKSS   650
 651  ESEFTQYTTHHILKSLASIEAKCSDMSSENTTGPPSSMDRVNTALQRAQM   700
 701  KVCSLSNQRMGRSLLKSKDLLKQRYLFAKAGYPLRRSQSLPTTLLSPVRV   750
 751  VSSVNVRLSPGKETRCSPPSFTYKYTPEEEQELEKRVMEHDGQSLVKSTI   800
 801  FISPSSVKKEEAPQSEAPRVEECHHGRTPTCSRLAPPPMSQSTCSLHSIH   850
 851  SEWQERPLCEHTRTLSTHSVPNISGATCSAFASPFGCPYSHRHATYPYRV   900
 901  CSVNPPSAIEMQLRRVLHDIRNSLQNLSQYPMMRGPDPAAAPYSTQKSSV   950
 951  LPLYENTFQELQVMRRSLNLFRTQMMDLELAMLRQQTMVYHHMTEEERFE  1000
1001  VDQLQGLRNSVRMELQDLELQLEERLLGLEEQLRAVRMPSPFRSSALMGM  1050
1051  CGSRSADNLSCPSPLNVMEPVTELMQEQSYLKSELGLGLGEMGFEIPPGE  1100
1101  SSESVFSQATSESSSVCSGPSHANRRTGVPSTASVGKSKTPLVARKKVFR  1150
1151  ASVALTPTAPSRTGSVQTPPDLESSEEVDAAEGAPEVVGPKSEVEEGHGK  1200
1201  LPSMPAAEEMHKNVEQDELQQVIREIKESIVGEIRREIVSGLLAAVSSSK  1250
1251  ASNSKQDYH                                           1259

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.)

Go back to the NucPred Home Page.