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

NucPred

Fetching P55141 from www.uniprot.org...

The NucPred score for your sequence is 0.07 (see score help below)

   1  MSSSRPANSSSNPGRANQNARVVLTTLDAKIHADFEESGNSFDYSSSVRV    50
  51  TSAVGENSSIQSNKLTTAYLHHIQKGKLIQPVGCLLAVDEKSFKIMAYSE   100
 101  NAPEMLTMVSHAVPSVGEHPVLGIGTDVRTIFTAPSAAALQKAVGFTDIN   150
 151  LLNPILVHCKTSGKPFYAIAHRVTGSLIIDFEPVKPYEVPMTAAGALQSY   200
 201  KLASKAVNRLQALPGGSMERLCDTMVQEVFELTGYDRVMAYKFHDDDHGE   250
 251  VTAEVTKPGLEPYFGLHYPATDVPQAARFLFLKNKVRMICDCRANSAPVL   300
 301  QDEKLPFELTLCGSTLRAPHSCHLQYMENMNSIASLVMAVVINDSDEVVE   350
 351  SSDRNSVKSKKLWGLVVCHNTSPRFVPFPLRYACEFLAQVFAIHVSKELE   400
 401  LENQIVEKNILRTQTLLCDLLMRDAPLGIVSQSPNMMDLVKCDGAALLYK   450
 451  NKVYRLGATPSDYQLRDIVSWLTEYHTDSTGLSTDSLYDAGYPGALALGD   500
 501  VVCGMAVVKITSHDMLFWFRSHAAGHIRWGGAKAEPDENHDGRKMHPRSS   550
 551  FKAFLEVVKTRSTTWKEFEMDAIHSLQLILRKALSVEKAVAAQGDEIRSN   600
 601  TDVIHTKLNDLKIEGIQELEAVTSEMVRLIETATVPIFAVDADEIVNGWN   650
 651  TKIAELTGLPVDQAMGKHLLTLVEDSSVGTVVFLLALALQGKEEQGIPFE   700
 701  FKTYGSREDSVPITVVVNACATRGLHDNVVGVCFVAQDVTSQKTIMDKFT   750
 751  RIQGDYKAIVQNPNPLIPPIFGTDEFGWCSEWNQAMTELSGWRREDVMNK   800
 801  MLLGEIFGIQTSCCHLKSKEAFVNLGVVLNNALTGQISEKICFSFFATDG   850
 851  KYVECLLCASKKLHGEGTVTGIFCFLQLASQELQQALHIQRLTEQTAMKR   900
 901  LKTLSYLRRQAKNPLCGINFVREKLEEIGMGEEQTKLFRTSVHCQRHVNK   950
 951  ILDDTDLDSIIDGYLDLEMSEFRLHDVYVASRSQVSMRSNGKAIQVVDNF  1000
1001  SEEMMSETLYGDSLRLQKVLADFMSVCVNLTPVGGHLGISVTLTEDNLGQ  1050
1051  SVQLVHLEFRITHTGAGVPEEAVSQMFGSDSETSEEGISLLISRKLVKLM  1100
1101  NGDVHYLREAGKSTFIITVELAAASKRES                       1129

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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