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

NucPred

Fetching Q67C55 from www.uniprot.org...

The NucPred score for your sequence is 0.84 (see score help below)

   1  MNISIIQNNNPLSMMSSVYRQNQSQDTNLPSALTIYNSLTGAKVVASAYQ    50
  51  FHNLEALKQFIGMSFNVATENLFLLTPFGIKLKFSMIVHEEISEIYVFDR   100
 101  RYFNVNNIEASGNMDNVNDLLAELNQTDFINMIKPLASPLLSEELSVFVE   150
 151  KLTLVLENTTQIKAVDINLNMLRMLLNSLKRNSGWASALLSDFKKTVAFD   200
 201  ECTPEDNDLETILTSLNVLIQYVGLVFKTLEKKFNDSIDALVLLQSNSLV   250
 251  DQWRDQYALLKRIPFEFKSGSSNVPEKLFLSQLVNESHLDKCAEESRRLN   300
 301  KSMNERLVMLRSKIEADVIKPRQELLQEYNGYMSQYIRPETDATQKTQKI   350
 351  QDCKRILAELEVHVSKLIQSSSSLPSFEELITTASQTSTTLSASSIANIK   400
 401  KLTQLYKYQESELVPYIFQLANNLYDIQINKLNARKELQTKLICSTLINI   450
 451  TKIQLNIMRLSTVLNTEVAKNIASIKENELQLSVVSDLPLMFGIFVIANL   500
 501  NNLKFGISLNNIVKKANEIFEMLRFMESRNRAKWLKEFLASSGADKVEFL   550
 551  HLDEEARERFINENMLSYKLEQVDAIRSKKSPSPVDHPASPVSGQEKHYL   600
 601  TSINRLLHNINGFPAPRPTATELPKQRETNIMTNLARNISVKSIVSYINT   650
 651  LRKEGIDLNIVNRLEECLKDFGITYGAIERKAIETEDGEEIVVKGKNAGD   700
 701  LGTFDVNDVNYMRLFKKFIKSFESEGIVININVNQQDSVSNDELIKGYER   750
 751  RIRKLENVLHTRNFQQFNEQWSRHRPVHTLPNPVSRRQSDMSQEPAVHEN   800
 801  TILFNENVVLGRKTIDLPPSHYGERIERLEKENERYRGEIEELKKGTDLA   850
 851  ELDRLKKEIEDLQKADMEKDKRLAALEEENKNLKESNEELTNSNKELVNM   900
 901  CEELKSMKSDLLENMTQKESEFGKEAKVNQQEINELKLRIEELEEDESNL   950
 951  VNVNKTLNERLAIKDGLLCQLYELVQGAYGKLNQMSGEIFSNLTRVCLLL  1000
1001  ESIGLLLIRETPSFDNHPGTLTIKRVKGLRSRKRQIKQASDSTHNGNLQN  1050
1051  DTFEDSEHIDNALMEVVSSEVVPEAEQYLHWVDTNVLNYTISSDLGIEDE  1100
1101  IEHKKNESSLIDMSLCEESSIEKKVKKLLANYESFNVEQGFQNFLRFNHV  1150
1151  DNELVIERVFRRFSDVETLARKLQKDKTQQKQELKMLTAELDGKIAFRNF  1200
1201  KVGDLVLFLKTLTPANEELGGGDEQPWAAFNVGCPNYYLKNTKGEGYIEL  1250
1251  SDRDWLVGRVSKIEPRQVTEQNFHSKTENPFRLAKSVVWYYVEAREVKE   1299

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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