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

NucPred

Fetching Q09291 from www.uniprot.org...

The NucPred score for your sequence is 0.88 (see score help below)

   1  MGDEFPFHHLGYVCLNEIYKHLTLKEIFQLSFSSNQIKRSLGIASIPVKS    50
  51  IFVNFDSQYPKIKLIGESSQLEWVFGIPDGLEYTDVGVYKIGHFKFQCKT   100
 101  SGTAFYTEHYDLENAMLVVIRYMISIFKCSNSIITYLSIDLGVIEDSRAI   150
 151  CENFVAFKKVERLSIFQTNYGVERNTLNFAQSFDWICDNLEIKNIHIGAD   200
 201  VLEPKMVQKTNGEFDIKLCARRFEQVLTMDHIYLQHADWITSEDLLNLDV   250
 251  QTAMLIENNLTEQDLNAFIKQWLRSDSDKLWWLEVKGKMMFNREEVLKDL   300
 301  DVQDDAYRSLNTRWYVARRSRANPSGNGCARKKMGSLRPKLTELWPFKVY   350
 351  IIFGSILIVFGPAALNRMITLRRMDVETDRPSGSETGIFVSKSAVYPFGN   400
 401  KNEVVKVWWNIDKPENCLDWIGLFDNNDSSFYLDQKSLRQHISPVVFTLT   450
 451  SKNLLNASEVYFGLIDGMTGRLLAKSENVEICKSASLVVHEVKKPENINV   500
 501  YLNTNHGRIEIPKKRSFSRKNGSFRSSFEFDFDVEDLHISLVENSEKLNF   550
 551  DHFIASNQLQNNYIQSKSFSHSHVVEIVFSIEPKTSKKSAPDIMEIASSS   600
 601  QTPPESHWKTYLDAKKRKFYVNHVTKETRWTKPDTLNNNHIEPETPVHKR   650
 651  LSDRSASPRNSFITPRRTITVRSAGCPKSDLIQFFQRDEFKTALYENQDA   700
 701  MQIYNECSVVRHAIHRIQKDLDPPSKFENQPLFVRFVNLFADITQPLPSG   750
 751  WECITMNNRTVFLNHANKETSFYDPRIRRFETKTSRRGRSVPSRSSTAHK   800
 801  GKIDHALISKCEDLRKIAQDNFPQIAERISKKLMLIERFGGLAVASLAND   850
 851  LDITLALSMLDSNTEKLAGEGDNIKMFYEDMKKEKLGKGPSRLCWKVSRD   900
 901  RLLDDAFRIILNVDPFVLKKSRLHIRFEGELALDYGGLSREFFILLSREL   950
 951  FHPKNGYFEYEGNDYHLQLRPRGCETEKEKKWLILCGRVLALAVIHRCYI  1000
1001  DVFFTNVFYKSLQKRPVTLMDFKESDAEFYKSMNWLLENDVVDLEMSFVY  1050
1051  SSMVNGKLAEQELVPGGESQMVTEANKAEFIDLMCQKKAIRGVEKPLEIL  1100
1101  LTSFNQILNDNLLNSLESSDLKRILSGSLELDLNDWRTNTIYKGGYSDCH  1150
1151  IVVEWFWEVIETMTNQERFDLLLFVTGSSSVPFEGFSALRGNEEISKFCI  1200
1201  EKWGDATSFPRAHTCFNRLQLPSYNTKQQLKSKLQQAIVNGMSYSIE     1247

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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