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

NucPred

Fetching O60245 from www.uniprot.org...

The NucPred score for your sequence is 0.38 (see score help below)

   1  MLRMRTAGWARGWCLGCCLLLPLSLSLAAAKQLLRYRLAEEGPADVRIGN    50
  51  VASDLGIVTGSGEVTFSLESGSEYLKIDNLTGELSTSERRIDREKLPQCQ   100
 101  MIFDENECFLDFEVSVIGPSQSWVDLFEGQVIVLDINDNTPTFPSPVLTL   150
 151  TVEENRPVGTLYLLPTATDRDFGRNGIERYELLQEPGGGGSGGESRRAGA   200
 201  ADSAPYPGGGGNGASGGGSGGSKRRLDASEGGGGTNPGGRSSVFELQVAD   250
 251  TPDGEKQPQLIVKGALDREQRDSYELTLRVRDGGDPPRSSQAILRVLITD   300
 301  VNDNSPRFEKSVYEADLAENSAPGTPILQLRAADLDVGVNGQIEYVFGAA   350
 351  TESVRRLLRLDETSGWLSVLHRIDREEVNQLRFTVMARDRGQPPKTDKAT   400
 401  VVLNIKDENDNVPSIEIRKIGRIPLKDGVANVAEDVLVDTPIALVQVSDR   450
 451  DQGENGVVTCTVVGDVPFQLKPASDTEGDQNKKKYFLHTSTPLDYEATRE   500
 501  FNVVIVAVDSGSPSLSSNNSLIVKVGDTNDNPPMFGQSVVEVYFPENNIP   550
 551  GERVATVLATDADSGKNAEIAYSLDSSVMGIFAIDPDSGDILVNTVLDRE   600
 601  QTDRYEFKVNAKDKGIPVLQGSTTVIVQVADKNDNDPKFMQDVFTFYVKE   650
 651  NLQPNSPVGMVTVMDADKGRNAEMSLYIEENNNIFSIENDTGTIYSTMSF   700
 701  DREHQTTYTFRVKAVDGGDPPRSATATVSLFVMDENDNAPTVTLPKNISY   750
 751  TLLPPSSNVRTVVATVLATDSDDGINADLNYSIVGGNPFKLFEIDPTSGV   800
 801  VSLVGKLTQKHYGLHRLVVQVNDSGQPSQSTTTLVHVFVNESVSNATAID   850
 851  SQIARSLHIPLTQDIAGDPSYEISKQRLSIVIGVVAGIMTVILIILIVVM   900
 901  ARYCRSKNKNGYEAGKKDHEDFFTPQQHDKSKKPKKDKKNKKSKQPLYSS   950
 951  IVTVEASKPNGQRYDSVNEKLSDSPSMGRYRSVNGGPGSPDLARHYKSSS  1000
1001  PLPTVQLHPQSPTAGKKHQAVQDLPPANTFVGAGDNISIGSDHCSEYSCQ  1050
1051  TNNKYSKQMRLHPYITVFG                                 1069

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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