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

NucPred

Fetching O00874 from www.uniprot.org...

The NucPred score for your sequence is 0.92 (see score help below)

   1  MSGGNDGASWRLSRKPNAPNFDETQEDQWRSLREEVLQSDEDENIPESGD    50
  51  LTIPQLPSAKKAAKKLRKPPSGAKPTPKPKQQTLAQSMSDMDMERLLKRY   100
 101  RIDEDIDIAEDIDMSHLLQLHSDSDDGGDAQEATLTADEFLARLARAEAA   150
 151  PAASIAKEKRESGENVTVVALKDELFNVERDQSAKPPRPRPTPGAGGGAG   200
 201  YRNEETPKQAIELTATLAPQMDAAQFVSPAVPYKSGEMTEGLFYWFDARE   250
 251  QPHTLSVDPGSLFLFGKMAVEKNGRTSYLSCCVRVRNMYRSVFVLPKAGS   300
 301  SQEDVVKEINDICRNQGIEQRRIKFVERYYAFEVPGVPHEKTQWAKLRYP   350
 351  GRYPPLNAKGPFRHILIIMGASSSLLELFLIKRKLKGPSFLRISGLVASA   400
 401  NRISHCALEFSVESPKNLRAEDTKLPVPPFTLASIQIHTQLDSKGACNEI   450
 451  LIASVAIYKDVNIENTIRYIPDNILTGVRPASMSTPLPIDLESYCSAKGL   500
 501  PGVRRFANERALLDWLAQQLGKIDADMMIGHNFLGFTLDILLRRYQELSI   550
 551  SSWSTIGRLDLKRLPRFQGTATNVNQEKETCIGRLVVDSYSLSREHYKTV   600
 601  NYRLLSLADQMQLQGITKGSNNFEPGTSVLTPAMLSASRDIYDVLLQVCN   650
 651  CAVLSTAVVSHLDVIRLTKRLTTIAGNLWSRTLFGARSERIEYLLLHTFH   700
 701  DLKFITPDRYVQNFKRGRDDEEEEDGKRKAKYQGGMVLDPKCGLYSDYIL   750
 751  LLDFNSLYPSLIQEFNICFTTVDRESGSEIDVPPPENLICASCAAAGLSA   800
 801  PCLHKCVLPKVIKSLVDSRREVKRLMKIEKDANNLALLEIRQKALKLTAN   850
 851  SMYGCLGFEYSRFHAQPLAELVTRQGRLALQSTVDLIPQLNPSLRVIYGD   900
 901  TDSVMIQTGIKNDIKAVRDLGLDLKAKINKRYQSLEIDIDGVFRAILLLK   950
 951  KKKYAALTVTDWQGEGKTYKKEVKGLDMVRRDWCPLSKCVCDSVLSRVLN  1000
1001  AEGSEDILDYVMNYMRDVSEKVRAGRYTLDNFVISKSLTKEPEAYRGNSF  1050
1051  PHATVALRMKQRKELVRVGDLIPYVICTGDRLSDKAFHVEEVRQNSQLQI  1100
1101  DSEWYLSVQIYPPVMRLCEHIQGFSNAQLSEAMGIACHTGAKLEEEEAET  1150
1151  MNDFSHSSLFQSRNLEECFPAALSLQVACTHCRLMTPINPHTRVMEVLAD  1200
1201  QERQRDRFDLYVCVSCRKSLPVDYVANCFTQTCYGIIRQFYQCGSAAAVK  1250
1251  AVRTQFTYYRALFDVPHAPGCPARVKDAHYYQARRCLGVDRRLYTLAEAA  1300
1301  DPAVQEVADPVDPLNAAAETIYKRIDHLFINLDSLFAGI             1339

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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