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

NucPred

Fetching Q9WU60 from www.uniprot.org...

The NucPred score for your sequence is 0.48 (see score help below)

   1  MVAVAAAAATEARLRGSTTATAAPAGRKGRQHRPCTATGAWRPGPRARLC    50
  51  LPRVLSRALPPPPLLPLLFSLLLLPLPREAEAAAVAAAVSGSAAAEAKEC   100
 101  DRPCVNGGRCNPGTGQCVCPTGWVGEQCQHCGGRFRLTGSSGFVTDGPGN   150
 151  YKYKTKCTWLIEGQPNRIMRLRFNHFATECSWDHLYVYDGDSIYAPLIAA   200
 201  FSGLIVPERDGNETAPEVTVTSGYALLHFFSDAAYNLTGFNITYNFDMCP   250
 251  NNCSGRGECKSSNSSSAVECECSENWKGESCDIPHCTDNCGFPHRGICNA   300
 301  SDTRGCSCFPHWQGPGCSIPVPANQSFWTREEYSDLKLPRASHKAVVNGN   350
 351  IMWVVGGYMFNHSDYSMVLAYDLTSREWLPLNHSVNSVVVRYGHSLALHK   400
 401  DKIYMYGGKIDSTGNVTNELRVFHIHNESWVLLTPKAKDQYAVVGHSAHI   450
 451  VTLASGRVVMLVIFGHCPLYGYISVVQEYDLEKNTWSILHTQGALVQGGY   500
 501  GHSSVYDDRTKALYVHGGYKAFSANKYRLADDLYRYDVDTQMWTILKDSR   550
 551  FFRYLHTAVIVSGTMLVFGGNTHNDTSMSHGAKCFSSDFMAYDIACDRWS   600
 601  VLPRPELHHDVNRFGHSAVLYNSTMYVFGGFNSLLLSDVLVFTSEQCDAH   650
 651  RSEAACVAAGPGIRCLWDTQSSRCTSWELATEEQAEKLKSECFSKRTLDH   700
 701  DRCDQHTDCYSCTANTNDCHWCNDHCVPVNHSCTEGQISIAKYESCPKDN   750
 751  PMYYCNKKTSCRSCALDQNCQWEPRNQECIALPENICGNGWHLVGNSCLK   800
 801  ITTAKENYDNAKLSCRNHNAFLASLTSQKKVEFVLKQLRLMQSSQSMSKL   850
 851  TLTPWVGLRKINVSYWCWEDMSPFTNSLLQWMPSEPSDAGFCGILSEPST   900
 901  RGLKAATCINPLNGSVCERPANHSAKQCRTPCALRTACGECTSSSSECMW   950
 951  CSNMKQCVDSNAYVASFPFGQCMEWYTMSSCPPENCSGYCTCSHCLEQPG  1000
1001  CGWCTDPSNTGKGKCIEGSYKGPVKMPSQASAGNVYPQPLLNSSMCLEDS  1050
1051  RYNWSFIHCPACQCNGHSKCINQSICEKCEDLTTGKHCETCISGFYGDPT  1100
1101  NGGKCQPCKCNGHASLCNTNTGKCFCTTKGVKGDECQLCEVENRYQGNPL  1150
1151  KGTCYYTLLIDYQFTFSLSQEDDRYYTAINFVATPDEQNRDLDMFINASK  1200
1201  NFNLNITWATSFPAGTQTGEEVPVVSKTNIKEYKDSFSNEKFDFRNHPNI  1250
1251  TFFVYVSNFTWPIKIQIAFSQHSNFMDLVQFFVTFFSCFLSLLLVAAVVW  1300
1301  KIKQSCWASRRREQLLREMQQMASRPFASVNVALETDEEPPDLIGGSIKT  1350
1351  VPKPIALEPCFGNKAAVLSVFVRLPRGLGGIPPPGQSGLAVASALVDISQ  1400
1401  QMPIVYKEKSGAVRNRKQQPPAQPGTCI                        1428

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.