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

NucPred

Fetching Q9S7P5 from www.uniprot.org...

The NucPred score for your sequence is 0.97 (see score help below)

   1  MEARIEGEVEGHSLEYGFSGKRSVEWDLNDWKWNGDLFVATQLNHGSSNS    50
  51  SSTCSDEGNVEIMERRRIEMEKKKKRRAVTVVAMEEDNLKDDDAHRLTLN   100
 101  LGGNNIEGNGVKKTKLGGGIPSRAICCQVDNCGADLSKVKDYHRRHKVCE   150
 151  IHSKATTALVGGIMQRFCQQCSRFHVLEEFDEGKRSCRRRLAGHNKRRRK   200
 201  ANPDTIGNGTSMSDDQTSNYMLITLLKILSNIHSNQSDQTGDQDLLSHLL   250
 251  KSLVSQAGEHIGRNLVGLLQGGGGLQASQNIGNLSALLSLEQAPREDIKH   300
 301  HSVSETPWQEVYANSAQERVAPDRSEKQVKVNDFDLNDIYIDSDDTTDIE   350
 351  RSSPPPTNPATSSLDYHQDSRQSSPPQTSRRNSDSASDQSPSSSSGDAQS   400
 401  RTDRIVFKLFGKEPNDFPVALRGQILNWLAHTPTDMESYIRPGCIVLTIY   450
 451  LRQDEASWEELCCDLSFSLRRLLDLSDDPLWTDGWLYLRVQNQLAFAFNG   500
 501  QVVLDTSLPLRSHDYSQIITVRPLAVTKKAQFTVKGINLRRPGTRLLCTV   550
 551  EGTHLVQEATQGGMEERDDLKENNEIDFVNFSCEMPIASGRGFMEIEDQG   600
 601  GLSSSFFPFIVSEDEDICSEIRRLESTLEFTGTDSAMQAMDFIHEIGWLL   650
 651  HRSELKSRLAASDHNPEDLFSLIRFKFLIEFSMDREWCCVMKKLLNILFE   700
 701  EGTVDPSPDAALSELCLLHRAVRKNSKPMVEMLLRFSPKKKNQTLAGLFR   750
 751  PDAAGPGGLTPLHIAAGKDGSEDVLDALTEDPGMTGIQAWKNSRDNTGFT   800
 801  PEDYARLRGHFSYIHLVQRKLSRKPIAKEHVVVNIPESFNIEHKQEKRSP   850
 851  MDSSSLEITQINQCKLCDHKRVFVTTHHKSVAYRPAMLSMVAIAAVCVCV   900
 901  ALLFKSCPEVLYVFQPFRWELLEYGTS                          927

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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