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

NucPred

Fetching P14381 from www.uniprot.org...

The NucPred score for your sequence is 0.76 (see score help below)

   1  MALSISTLNTNGCRNPFRMFQVLSFLRQGGYSVSFLQETHTTPELEASWN    50
  51  LEWKGRVFFNHLTWTSCGVVTLFSDSFQPEVLSATSVIPGRLLHLRVRES   100
 101  GRTYNLMNVYAPTTGPERARFFESLSAYMETIDSDEALIIGGDFNYTLDA   150
 151  RDRNVPKKRDSSESVLRELIAHFSLVDVWREQNPETVAFTYVRVRDGHVS   200
 201  QSRIDRIYISSHLMSRAQSSTIRLAPFSDHNCVSLRMSIAPSLPKAAYWH   250
 251  FNNSLLEDEGFAKSVRDTWRGWRAFQDEFATLNQWWDVGKVHLKLLCQEY   300
 301  TKSVSGQRNAEIEALNGEVLDLEQRLSGSEDQALQCEYLERKEALRNMEQ   350
 351  RQARGAFVRSRMQLLCDMDRGSRFFYALEKKKGNRKQITCLFAEDGTPLE   400
 401  DPEAIRDRARSFYQNLFSPDPISPDACEELWDGLPVVSERRKERLETPIT   450
 451  LDELSQALRLMPHNKSPGLDGLTIEFFQFFWDTLGPDFHRVLTEAFKKGE   500
 501  LPLSCRRAVLSLLPKKGDLRLIKNWRPVSLLSTDYKIVAKAISLRLKSVL   550
 551  AEVIHPDQSYTVPGRTIFDNVFLIRDLLHFARRTGLSLAFLSLDQEKAFD   600
 601  RVDHQYLIGTLQAYSFGPQFVGYLKTMYASAECLVKINWSLTAPLAFGRG   650
 651  VRQGCPLSGQLYSLAIEPFLCLLRKRLTGLVLKEPDMRVVLSAYADDVIL   700
 701  VAQDLVDLERAQECQEVYAAASSARINWSKSSGLLEGSLKVDFLPPAFRD   750
 751  ISWESKIIKYLGVYLSAEEYPVSQNFIELEECVLTRLGKWKGFAKVLSMR   800
 801  GRALVINQLVASQIWYRLICLSPTQEFIAKIQRRLLDFLWIGKHWVSAGV   850
 851  SSLPLKEGGQGVVCIRSQVHTFRLQQIQRYLYADPSPQWCTLASSFYRQV   900
 901  RNMGYDRQLFIIEPEGFLRNLSTLPAYYQDTLKTWSMVSVLRQGATEGED   950
 951  ILNEPLLYNPSFKTRMLESISIRRRLCQAQLTRVGDLLDFEKSDWVDSQA  1000
1001  VMQRMGFLTTRVPHRLLKEIKDTISPDSHTFIDGVLHAGEPRPPWNSSPP  1050
1051  DIIIAPKTRQSPQAPPSPNLSQLENFPLTRFHDITRKLLYSLMLHTVHFL  1100
1101  ALISRYDTIWRRVLNEGERPQWRAFYSSLVPRPTGDLSWKVLHGALSTGE  1150
1151  YLARFTDSPAACPFCGKGESVFHAYFTCARLQPLLALLRKLYLQFWLHFS  1200
1201  PHVYIFGRPVSRDNKEKDLLSNLLLALAKLVIHKSRKQCLEGGNPLPAEV  1250
1251  LFRVLVRSRIRAEYTQAVFTGRLKEFADQWAIDGVLCSVSPDLVSVQTIL  1300
1301  TLPYLSAL                                            1308

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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