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

NucPred

Fetching Q8CJ11 from www.uniprot.org...

The NucPred score for your sequence is 0.65 (see score help below)

   1  MLFSGGQYSPVGRPEEVLLIYKIFLVIICFHAILVTSLKENAGNSSLLSP    50
  51  SAESSLVSLVPYSNGTPDAASEVLSTLNRTEKSKITILKTFNASGVKSQR   100
 101  NICNLSSICSDSVFFRGEIVFQHDDHYNVTQNQDIVNSTFAGVLSLSELK   150
 151  RTELNKTLQTLSETYFIVCATAEAQNTLNCTFTVKLNETMNVCAMMVTFK   200
 201  SVQIRPMEQCCCSPRTPCPSSPEELEKLQCDLQDPIVCLADQPHGPPVSS   250
 251  SSKPVPVVPQATIFSHVASDFSLAEPLDHALMTSSTPSLAQETRLPSPQP   300
 301  TISLTSSPAIDLPVQHVVASSSLPQTDLSHTLSPVQSSIPSPTTAAPSVP   350
 351  EKVVAISTPPGETVVNTSSVPDLEAQVSQMEKALSLGSLEPNLAGEMVNR   400
 401  VSKLLHSPLALLAPLAQRLLKVVDAIGLQLNFSSTTISLTSPSLALAVIR   450
 451  VNASNFNTTTFAAQDPANLQVSLEAQAPKNSIGAITLPSSLMSNLPASEV   500
 501  ELASRVQFNFFETPALFQDPSLENLSLISYVISSSVTNMTIKNLTRNVTV   550
 551  ALKHINPSQDDLTVKCVFWDLNRNGGRGGWSSDGCSVKEKRMNETICTCS   600
 601  HLTSFGILLDLSRTSLPPSQMMALTFITYIGCGLSSIFLSVTLVTYIAFE   650
 651  KIRRDYPSKILIQLCAALLLLNLVFLLDSWIALYNARGFCISVAVFLHYF   700
 701  LLVSFTWMGLEAFHMYLALVKVFNTYIRKYILKFCIVGWGIPAVVVSIVL   750
 751  TISPDNYGIGSYGKFPNGTPDDFCWINSSVVFYITVVGYFCVIFLLNVSM   800
 801  FIVVLVQLCRIKKKKQLGAQRKTSIQDLRSIAGLTFLLGITWGFAFFAWG   850
 851  PVNLTFMYLFAIFNTLQGFFIFIFYCAAKENVRKQWRRYLCCGKLRLAEN   900
 901  SDWSKTATNGLKKQTVNQGVSSSSNSLQSSCNSTNSTTLLVNSDCSVHAS   950
 951  GNGNASTERNGVSFSVQNGDVCLHDLTGKQHMFSDKEDSCNGKSRMALRR  1000
1001  TSKRGSLHFIEQM                                       1013

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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