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

NucPred

Fetching Q9SGG3 from www.uniprot.org...

The NucPred score for your sequence is 0.48 (see score help below)

   1  MARGRIRSKLRLSLLYTFGCLRPATLEGQDSQPIQGPGFSRTVFCNQPHM    50
  51  HKKKPLRYRSNYVSTTRYNLITFFPKSLYEQFHRAANLYFLVAAILSVFP   100
 101  LSPFNKWSMIAPLVFVVGLSMLKEALEDWRRFMQDVKINARKTCVHKSDG   150
 151  VFRQRKWKKVSVGDIVKVEKDEFFPADLLLLSSSYEDGICYVETMNLDGE   200
 201  TNLKVKRSLEVSLPLDDDESFKNFMATIRCEDPNPNLYTFVGNLEFERQT   250
 251  FPLDPSQILLRDSKLRNTTYVYGVVVFTGFDTKVMQNSTKSPSKRSRIER   300
 301  TMDYIIYTLLVLLILISCISSSGFAWETEFHMPKMWYLRPGEPIDFTNPI   350
 351  NPIYAGVVHLITALLLYGYLIPISLYVSIEVVKVWQASFINQDLHMYDDE   400
 401  SGVPANARTSNLNEELGQVHTILSDKTGTLTCNQMDFLKCSIAGTSYGVR   450
 451  SSEVEVAAAKQMAVDLEEHGEISSTPQSQTKVYGTWDSSRTQEIEVEGDN   500
 501  NYNTPRAPIKGFGFEDNRLMNGNWLRESQPNDILQFFRILAICHTAIPEL   550
 551  NEETGKYTYEAESPDEASFLAAAREFGFEFFKRTQSSVFIRERFSGSGQI   600
 601  IEREYKVLNLLEFTSKRKRMTVIVRDEEGQILLLCKGADSIIFERLAKNG   650
 651  KTYLGPTTRHLTEYGEAGLRTLALAYRKLDEDEYAAWNSEFLKAKTSIGS   700
 701  DRDELLETGADMIEKELILIGATAVEDKLQKGVPQCIDKLAQAGLKLWVL   750
 751  TGDKMETAINIGFACSLLRQGMRQICITSMNSEGGSQDSKRVVKENILNQ   800
 801  LTKAVQMVKLEKDPHAAFALIIDGKTLTYALEDDMKYQFLALAVDCASVI   850
 851  CCRVSPKQKALVVRLVKEGTGKTTLAIGDGANDVGMIQEADIGVGISGVE   900
 901  GMQAVMASDFSIAQFRFLERLLVVHGHWCYKRIAQMICYFFYKNIAFGLT   950
 951  LFYFEAFTGFSGQSVYNDYYLLLFNVVLTSLPVIALGVFEQDVSSEICLQ  1000
1001  FPALYQQGTKNLFFDWSRILGWMCNGVYASLVIFFLNIGIIYSQAFRDNG  1050
1051  QTADMDAVGTTMFTCIIWAANVQIALTMSHFTWIQHVLIWGSIGMWYLFV  1100
1101  AIYSMMPPSYSGNIYRILDEILAPAPIYWMATLLVTVAAVLPYVAHIAFQ  1150
1151  RFLNPLDHHIIQEIKYYGRDIEDARLWTRERTKAREKTKIGFTARVDAKI  1200
1201  RHLRSKLNKKQSNLSHFSAQDAMSPRSL                        1228

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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