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

NucPred

Fetching Q6E7D1 from www.uniprot.org...

The NucPred score for your sequence is 0.08 (see score help below)

   1  MSVWNYVVTAHKPTNVTHSCVGNFTGPQELNLIIAKCTRIEIHLLTPQGL    50
  51  QCICLQPMLDVPIYGRIATLELFRPHGETQDLLFIATERYKFCVLQWDTE   100
 101  ASEVITRAMGDVSDRIGRPTDNGQIGIIDPDCRLIGLHLYDGLFKVIPFD   150
 151  NKGQLKEAFNIRLEELQVLDIKFLYGCPKPTIVVLYQDNKDARHVKTYEV   200
 201  SLKDKDFIEGPWAQNNLDNGASLLIPVPPPLCGVLIIGEETIVYCSASAF   250
 251  KAIPIRPSITRAYGRVDADGSRYLLGDHNGLLHLLVITHEKEKVTGLKIE   300
 301  LLGETSIASTISYLDNAFVFIGSSYGDSQLVKLNLQPDTKGSYVEVLERY   350
 351  VNLGPIVDFCVVDLERQGQGQVVTCSGAYKDGSLRIVRNGIGINEQASVE   400
 401  LQGIKGMWSLRSATDDPYDTFLVVSFISETRVLAMNLEDELEETEIEGFN   450
 451  SQVQTLFCHDAVYNQLVQVTSNSVRLVSSTSRDLKNEWFAPVGYSVNVAT   500
 501  ANATQVLLATGGGHLVYLEIGDGVLNEVKYAKLDYDISCLDINPIGENPN   550
 551  YSNIAAVGMWTDISVRIYSLPDLNLITKEQLGGEIIPRSVLMCSFEGISY   600
 601  LLCALGDGHLLNFVLSMSTGELTDRKKVSLGTQPITLRTFSSKDTTHVFA   650
 651  ASDRPTVIYSSNKKLLYSNVNLKEVSHMCPFNVAAFPDSLAIAKEGELTI   700
 701  GTIDEIQKLHIRSIPLGEHARRISHQEQTRTFALCSVKYTQSNADDPEMH   750
 751  FVRLLDDQTFEFISTYPLDQFEYGCSILSCSFSDDSNVYYCIGTAYVMPE   800
 801  ENEPTKGRILVFIVEDGKLQLIAEKETKGAVYSLNAFNGKLLAAINQKIQ   850
 851  LYKWASREDGGSRELQTECGHHGHILALYVQTRGDFIVVGDLMKSISLLI   900
 901  FKHEEGAIEERARDYNANWMSAVEILDDDIYLGAENNFNLFTVRKNSEGA   950
 951  TDEERSRLEVVGEYHLGEFVNRFRHGSLVMRLPDSDVGQIPTVIFGTVNG  1000
1001  VIGVIASLPHDQYLFLEKLQTNLRKVIKGVGGLSHEQWRSFYNEKKTVDA  1050
1051  KNFLDGDLIESFLDLSRNRMEEISKAMSVPVEELMKRVEELTRLH       1095

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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