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

NucPred

Fetching O70127 from www.uniprot.org...

The NucPred score for your sequence is 0.24 (see score help below)

   1  MSDSVILRSVKKFGEENHAFESDGSHNNDKKSRLQDKMKEGDIRVGFFEL    50
  51  FRFSSSKDIWLMLMGGVCALLHGMAQPGILIIFGIMTDIFIKYDIERQEL   100
 101  EIPGKACVNNTIVWINSSFHQNMTNGTVCGLVDIESEMIKFSGIYAGVGM   150
 151  TVLILGYFQIRLWVITGARQIRRMRKIYFRRIMRMEIGWFDCTSVGELNS   200
 201  RFADDIEKINDAIADQLAHFLQRMSTAMCGLLLGFYRGWKLTLVILAVSP   250
 251  LIGIGAAVIGLSIAKFTELELKAYAKAGSIADEVLSSIRTVAAFGGENKE   300
 301  VERYEKNLVFAQRWGIWKGMVMGFFTGYMWCLIFFCYALAFWYGSTLVLD   350
 351  EEEYTPGTLVQIFLCVILAAMNIGHASSCLEIFSTGCSAATNIFQTIDRQ   400
 401  PVIDCMSGDGYKLDRIKGEIEFHNVTFHYPSRPDVKILDNLSMVIKPGET   450
 451  TALVGSSGAGKSTALQLIQRFYDPCEGMVTLDGHDIRSLNIRWLRDQIGI   500
 501  VEQEPVLFSTTIAENIRFGREDATMEDIVQAAKDANAYNFIMALPQQFDT   550
 551  LVGEGGGQMSGGQKQRVAIARALIRNPKILLLDMATSALDNESEARVQEA   600
 601  LNKIQHGHTIISVAHRLSTVRAADVIIGFEHGVAVERGTHEELLERKGVY   650
 651  FMLVTLQSQGDNAHKETSIMGKDATEGGTLERTFSRGSYRDSLRASIRQR   700
 701  SKSQLSLLTHDPPLAVADHKSSYKDSKDNDVLVEEVEPAPVRRILKYNIP   750
 751  EWHYILVGSLSAAINGAVTPIYSLLFSQLLGTFSLLDKEQQRSEIHSMCL   800
 801  FFVILGCVSIFTQFLQGYTFAKSGELLTKRLRKFGFKAMLGQDIGWFDDL   850
 851  RNNPGVLTTRLATDASQVQGATGSQVGMMVNSFTNIIAALLIAFFFSWKL   900
 901  SLIITIFFPFLALSGAVQTKMLTGFASQDKQALEKAGQITSEALSNIRTV   950
 951  AGIGVEGRFIKAFEVELQTSYKTAVRKANIYGLCFAFSQGIAFLANSAAY  1000
1001  RYGGYLIAYEGLGFSHVFRVVSSVALSATAVGRTFSYTPSYAKAKISAAR  1050
1051  FFQLLDRKPPINVYSEAGEKWDNFQGKIDFIDCKFTYPSRPDIQVLNGLS  1100
1101  VSVNPGQTLAFVGSSGCGKSTSIQLLERFYDPDQGTVMIDGHDSKKVNIQ  1150
1151  FLRSNIGIVSQEPVLFDCSIMDNIKYGDNTKEISVERAIAAAKQAQLHDF  1200
1201  VMSLPEKYETNVGIQGSQLSRGEKQRIAIARAIVRDPKILLLDEATSALD  1250
1251  TESEKTVQTALDKAREGRTCIVIAHRLSTIQNSDIIAVVSQGVVIEKGTH  1300
1301  EKLMAQKGAYYKLVITGAPIS                               1321

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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