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

NucPred

Fetching Q9EQH7 from www.uniprot.org...

The NucPred score for your sequence is 0.51 (see score help below)

   1  MSFIMKPHRHFQRTLILLATFCMVSIIISAYYLYSGYKQESEVSGRASEV    50
  51  DCGDLQHIPSRLMEVRRTMISDASRTDPTVLVFVESQYSSLGQDIIMMLE   100
 101  SIRFHYHTEIAPGKGDLPALTDNVKGKYVLIIYENILKYINMDSWNRSLL   150
 151  DKYCIEYGVGIIGFHKTSEKNLQSFQFRGFPFSISGNLAVKDCCINPHSP   200
 201  LLRVTKSSKLDRGSLPGTDWTVFQINHSTYQPVIFAKVKTPENLSPPISK   250
 251  HAFYATIIHDLGLHDGIQRVLFGNNLNFWLHKLIFIDAISFLSGKRLTLS   300
 301  LDRYILVDIDDIFVGKEGTRMNTNDVKALLDTQNLLRTQITNFTFNLGFS   350
 351  GKFYHTGTEEEDEGDDCLLGSVDEFWWFPHMWSHMQPHLFHNESSLIEQM   400
 401  ILNKKFALEHGIPTDMGYAVSPHHSGVYPVHVQLYEAWKKVWNIKITSTE   450
 451  EYPHLKPARYRRGFIHKNIMVLPRQTCGLFTHTIFYKEYPGGPRELDKSI   500
 501  HGGELFFTVVLNPISIFMTHLSNYGNDRLGLYTFVNLANFVQTWTNLRLQ   550
 551  TLPPAQLAHKYFELFPDQKDPLWQNPCDDKRHRDIWSKEKTCDRLPKFLV   600
 601  IGPQKTGTTALCLFLIMHPSILSNSPSPKSFEEVQFFNRNNYHRGIDWYM   650
 651  DFFPVPSNVTTDFLFEKSANYFHSEDAPKRAASLVPKAKIITILIDPSDR   700
 701  AYSWYQHQRSHEDPAALKFSFYEVISAGPNAPWELRTLQKRCLVPGWYAN   750
 751  HIERWLVYFPPFQLLIIDGQHLRTTPATVMDEVQKFLGVSPHYNYSEALT   800
 801  FDSHKGFWCQLLEEGKTKCLGKSKGRKYPPMDSDSRAFLSSYYRDHNVEL   850
 851  SKLLHRLGQPLPSWLRQELQKVR                              873

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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