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

NucPred

Fetching Q20EX1 from www.uniprot.org...

The NucPred score for your sequence is 0.79 (see score help below)

   1  MNIYLRQNSFLVPDFIAVQRNSFSQFLESGLIQEISKRNPITNSTKELEL    50
  51  CFYPQYYKLSPPELNAKQSILKNKTYSCRLYIPVKLTNKRTKTLKLQWVV   100
 101  LGNLPLMTKRGHFIINGSPRVIINQMVRSPGVYFKEVSHADQKLTYYADL   150
 151  IAYRGAWLRIELDKKADIWARMKKTPKLPMLILLQALGLNLPTILKSLNY   200
 201  PKFFENLGHDGNFMKQLKKGRVSSRSSSQELSGSFNLSEDVSLRLDDSSK   250
 251  NMGAENVQRAPLQKSTKKATLFGDFSRSSVYCKTQEEALWALYALTHPLK   300
 301  NPDEVTANLGKSFLYRKFMNSRVYDLSPLGRLRLNQKLNLSVNENITTIT   350
 351  AQDLLFITNTLINLNYGVGKVDDIDNLKNRRIRTAGELVQNQFGIGLLRL   400
 401  EKIIREKLKQQQTKLSIGSLINTKPINGALREFFGSSPLSQFMDQTNPLA   450
 451  EITHKRRLSSLGPGGVNRETAGMAIRGIHPTHYGRICPIETPEGQNAGLV   500
 501  NSLTIYSRVNPYGFIETPFYKVVKGQVQNSTRPIFFSAYQEEKKLLAPGD   550
 551  IYANKLKYLPKSELPIRKLAEFTRTTREKIDYISVSPLQMISIATSLIPF   600
 601  LEHDDANRALMGSNMQRQAVPLMTAEAPVVGTGLECRVASDSGHVLQAKK   650
 651  SGFVTYSSAEKITILSPVDSTPAVPKLSKGNNSPQHFHESVGGSCKESQS   700
 701  LQAAAEGYLSGVASSSSSKFTGSSFSTISALNDGVLRRALTQKVLTTGTN   750
 751  CSSMLKNQRFFVEPKAQLYTGAQTPVGRVETILQPNHAEGYLSEVETIQQ   800
 801  TQNKLPLQVRFGVEAPKSSFDSEATKISSTLNSIPQHPVLGEDSPSKQVG   850
 851  WALKDPQIQTMLKPKWHHSAQTMSRENWYQNLKGQNVKTFTQVESGRLVT   900
 901  KPTNTKMPMSSLAGTANSKKTGEALYKLASSESATKSMDFSTKTQLKPIT   950
 951  YELQKLFRSNQDTSIMHRPVVREGEWVNRGDLLADNSTTVGGELSLGKNL  1000
1001  LLAYMPWEGYNFEDAILISERLVSDDAYTSLHIERYEVEIRETKFGLEQI  1050
1051  TSQIPDEGKLSHLDHFGIAKPGTWVEEGDILIGKVAPMPQKNLSRYEKLL  1100
1101  YDVVGKKISTTRDTSLRVPRGVSGRVIHVEILNAENLPPEFVFEGPSRVN  1150
1151  LYIAEKRKIHVGDKMAGRHGNKGIISNILPRQDMPYLPDGTPLDMVLNPL  1200
1201  GVPSRMNVGQIYECLLGLAGRYLGQKFKVRPFDEIYGPQTSRSLVYSKLY  1250
1251  EARLRTGQRWLFNPASPGKTRLFDGRTGECFSQPVTVGQAYMLKLIHLVD  1300
1301  EKIHARSIGPYSLVTQQPLRGRSKHGGQRLGEMEVWALEGFGAAYTLQEL  1350
1351  LTVKSDDIKGREQVMESIQKNKTISLGTPESFKVLIRELQSLCLDVGVYA  1400
1401  VDGSGKIKQVDTMKLP                                    1416

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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