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

NucPred

Fetching Q09796 from www.uniprot.org...

The NucPred score for your sequence is 0.55 (see score help below)

   1  MDGNEIAHAKKLVYDLYSGSLSPSAIAATEKELQKAQRSQQGWNIGLFML    50
  51  QSKDVYEQFFGALTLQMKINTQLETLSDKDLVQLFVQLLQKLLWDDGLPA   100
 101  LVERKVICTLASLTIKYELEKKEEASLKVIYCLFCNKLEFFNADMNAASV   150
 151  LNNLFPPASSRNAQLTASYINELLLELSFSIYTKENEDALFNNVFRPCSN   200
 201  IIVSVLVFIFTNYSLDLSKEKNVAALEEALNCMIAISSYLAKASVSVQSV   250
 251  LPAFTECMDLTVNCIALDEVSEKAMNCLADLLANYSNFITQPTIERLWTI   300
 301  LTGPWGETHLQQELEDPDSGEENDYSFLNIVIGFAEAMLPQIIDHIQEEK   350
 351  SIRLLYILASLLSFPGYAIVEEKVSWRTLEFWTTLIEDFSMSKAATDPSK   400
 401  DEIFKQIAFSVVEKAWWKMLLPSPEQWNSWPSSSRDSFNSYRRDLGDLLE   450
 451  SSYSIFGERLYAMYITTIENFFSDGTGSPQSLEVSFYCLCCILEYDTNDS   500
 501  DTLDAWLTRLFETSFAIKASAFQNPQLLKTCSQLLSSCSCFLQNHPQYLN   550
 551  ISLPVLFDALHISETSIQMTVSRSIHTLCTTCASHLLTEIDGFMAVVEEL   600
 601  TPKLVYVPSVLEKIYSSVGYVTQRIEDIELRISYLMRLLNCILAQLQPSL   650
 651  YPNLEIFENVLKSCLQSVAGVALSQSPIGESPIIDVEQSTQETTFWQQSC   700
 701  IAEFQAKLISFLTHSESMALQYSDVVGLICKIMIAGLNEVEPSPFSLPIV   750
 751  TTIQYFCDRFTEFPAAVLLTLGSAILTCPYGQTDIIDKVLIDMCSSIQNS   800
 801  VVIINEESFMNNIDITVELYHFFSIILQKHPSFLETMYPDFTQLILNRAI   850
 851  NLLGKPERLLESAAGQFIISFITSEKSDLLNTHTDFVNAIRSPLIAKILL   900
 901  GFGGNASRSSLPLLSDILGKLKAQNFSATRACLTQSLEEEGFPSRNVSNE   950
 951  IKRRFLTDLLKARIKDKVKQFWILCKGLESTPYGNSSWTF             990

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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