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

NucPred

Fetching Q3UHC2 from www.uniprot.org...

The NucPred score for your sequence is 0.81 (see score help below)

   1  MAGTSQRPPSMYWCVGTEGLAVCPGPAMETHNGAEDMGSKLSLPGGSSTV    50
  51  QCPSMEEIHTAYKQRNLSRARDLLRGVCEESESSQEKGQLLSIAAAHGDL   100
 101  ETVQFLLTEKRVELPTEPTDDNPAVVAAHFGHAEVVRELLESLPGPCTPQ   150
 151  RLLNWMLALACQRGHLEVVKLLVLTHGADPENYAVRKNEFPVIVRLPLYA   200
 201  AIKAGNEDIAIFLLRHGAYFCSYILLDSPEPSKHLLRKYFIEASALPSSY   250
 251  PGKIALRVKWSHLKLPWVDLDWLLDISCQITELDLSANCLPSLPSIIPWG   300
 301  LINLKKLNLSNNQLGELPCVQSSDEIICSRLLEIDISSNKLSHLPPGFLH   350
 351  LSKLQKLTASKNYLERLFEEENATNWIGLRKLQELDLADNRLTELPVQFM   400
 401  HSFKSLTSLNVSRNNLKSFPDPWSCPLKCCKASKNALESLPDKMAVFWKS   450
 451  HLRDADFSENSLKEVPLGLFQLDALMFLRLQGNQLLSLPPQEKWTCTQLK   500
 501  TLDLSRNQLGKNEDGLKTKRISLFTTRGRQRSGTETASMLEFPAFLSESL   550
 551  EVLCLNDNHLDAVPPSVCLLKNLSELYLGNNPGLRELPPELGQLGNLWQL   600
 601  DIEDLNISNVPAEVRKEGPKATLSFLRAQLRKAEKCKLMKMILVGPPRQG   650
 651  KSTLLEILQTGKAPQLAHSEATIRTTKWELQRPAGSKAKVESVEFNVWDI   700
 701  GGPASMATVNQCFFTDKALYVVVWNLALGEEAVANLQFWLLNIEAKAPNA   750
 751  VVLVVGTHLDLIEAKFRVERIATLRAYVLALCRSPSGSRATGFPDITFKH   800
 801  LHEISCKNLEGQEGLRQLIFHVTCNMKDVGSTIGCQKLAGRLIPRSYISL   850
 851  QEAVLAEQQRRSLGDQVQYLTDRQLDQLVEQTPGNDIKDYEDLQSAISFL   900
 901  IETGTLLHFPDTSHGLRNLYFLDPIWLSECLQRIFNIKGSRSVAKNGVIQ   950
 951  AEDLRMLLVGTGFTQQTEEQYFQFLAKFEIALPVANDSYLLPHLLPSKPG  1000
1001  LDTHSMRHPMANTIQRVFKMSFVPVGFWQRFIARMLISLAEMDLQLFENK  1050
1051  KNTKSRNRKVTIYSFTGSQRNRCSTFRVRRNQTIYWQEGLLVTFDGGYLS  1100
1101  VESSDVNWKKKKSGGIKIICQSEMRDFSAMAFITDHVNSLIDQWFPALTA  1150
1151  TESDGTPLMEQYVPCPVCEASWAQHADPNERSESVQYFDMEDCVLTAIER  1200
1201  DFISCPRHPDLPVPLQELVPELFMTDFPARLFLENSKLEHTEGENSILGQ  1250
1251  GGSGTVIYQARYQGQPVAVKRFHIKKFKNSANAPADTMLRHLRAMDAMKN  1300
1301  FSDFRQEASMLHALQHPCIVSLIGISIHPLCFALELAPLGSLNTVLSENA  1350
1351  KDSSFMPLGHMLTQKIAYQIASGLAYLHKKNIIFCDLKSDNILVWSLSAK  1400
1401  EHINIKLSDYGISRQSFHEGALGVEGTPGYQAPEIRPRIVYDEKVDMFSY  1450
1451  GMVLYELLSGQRPALGHHQLQIVKKLSKGIRPVLGQPEEVQFHRLQALMM  1500
1501  ECWDTKPEKRPLALSVVSQMKDPTFATFMYMLPCGKQSAFFSSQSQEYTV  1550
1551  VFWDGKEESRNYTVVNTEKGLLEVQRMTCPGMKLSCQLKVQSSVWIATED  1600
1601  QKIYIYSLKGMCPLSVPQQALDTPAVVTCFLAVPVIKKNSFLVLAGLADG  1650
1651  LVAVFPVARGTPKESCSYLCSHTANRSKFCIPDEDARQNPYPVKAMEVVN  1700
1701  SGSEVWYSNGPGLLVIDCTILDISRRLEPYAAPSMVTSLVCSSDCRGEEM  1750
1751  VWCLDDKANCLVMYHSATYQLCARYFCGDPNPLRDTFSVQPSVLETPGSH  1800
1801  KTTSKGPVEECIADVSIMYSEELGTQILTHQDSLTDYCSMSSYSSSPPHQ  1850
1851  DPRSPSSLPSSLTSYSSVPFSANYEDSDRLQEPSVTSDRTEHDLSPMDGE  1900
1901  TFSQHLQAVKVLAVKDLIWVPRHGGDIIVIGLEKDSGAQRGRVIAVLKAR  1950
1951  ELNRHGVLVDAAVVAKDTVVCSFANENTEWCLAVWRGWGAREFDIFYQSY  2000
2001  EELGRLEACTRKRR                                      2014

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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