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

NucPred

Fetching P60290 from www.uniprot.org...

The NucPred score for your sequence is 0.82 (see score help below)

   1  MLFYNKVMDRTAIKQLISRLITHFGITYTTYILDQLKTVGFKQATQAAIS    50
  51  LGIDDLLTAPSKSWLIQDAEQQGYISEKHYRYGNVHAVEKLRQLIETWYA   100
 101  TSEYLKQEMNPNFRMTDPLNPVHMMSFSGARGSTSQVHQLVGMRGLMSDP   150
 151  QGQIIDLPIQSNFREGLSLTEYIISCYGARKGVVDTAVRTSDAGYLTRRL   200
 201  VEVVQHIVVRKVDCGTSENIFVTPLQNNYKKNNKLIGRILADNIYINGRC   250
 251  IAIRNQDITTNLVISLINFQRKGIFIRSPLICKSMLWICQLCYGWSLTHG   300
 301  NLIELGEAVGIIAGQSIGEPGTQLTLRTFHTGGVFTGDIAEHIRTPFNGI   350
 351  IQFDTNSVYPTRTRHGHPAWICNNNLSVVIKSKKKLHNLVIPTQSLLLVQ   400
 401  SNQYVESKQVIAEVRAKTSPFKEKVQKYIYSNLSGEMHWSSKVQHSSEYI   450
 451  HSNVHLLRKTGHIWILAGNFDKDNKFSFIFYQNQDKLDNKLPIAKQTLNY   500
 501  FQLKEHFLNNFWNSIYSSIILYNYRFLEKKNNKYEKKLLFQFMLKLPKNG   550
 551  ILKQNDIFAIFNDPKYRIKNSGIIKYGNIKVDLINKKNDIFEDQKTKTVR   600
 601  PRYKILKEGNFFLLPEEVYILDQSSFSSILVKNNSFIKAGTKITFNISSK   650
 651  ITGFVKIKKKFNNFKIKILPGSIYYPKEKQKNFKQNGILIPPGEKIFEQF   700
 701  RAKNWIYLEWIVLSKDNSFFLIRPAIEYKIIFNDNPLTLPIPFYLDLLKE   750
 751  QKKIKIQTVKYILYEDSEEVEINPDTDIQLIQTCLILNWETKVFIKEAHI   800
 801  SFIKIRINKIIKNFFQINLIENINLMNKKKNNNIILNYLFKKKRYIINQK   850
 851  DCEKILLLSKTWGIIRTPSNKNQEKSFFLILSPFNLFQTILFDKTKQNLK   900
 901  IENNVEKLFTYEPKKIIKTFNIEKRKNFVEFLGLLGYLQNITKSFQLFSC   950
 951  KKFSDKSIPINFSIIDNLKKKIKISKWFFLNENKKVQKFFLTQNTILSLL  1000
1001  NWSFPIFDLAKKKTQLFNLGHFFCDGLSIAEYPTFSESGQIIAIYDDLSL  1050
1051  VIRLAKPYLATGGAIIHNNYGEIVKEGDILITLIYERLKSGDIIQGLPKV  1100
1101  EQLLEARLTNPVSINLEKGFGEWNKDMTNFFGSLWGYFLSAQISMEQSQV  1150
1151  NLVNQIQKVYRSQGVNISDKHIEIIVRQMTSKVFTLEDGMTNGFLPGELI  1200
1201  EFARAKRMNRALEEVIPYKPVLLGITKASLNTQSFISEASFQETTRVLAK  1250
1251  AALRGRIDWLKGLKENVILGGIIPTGTGCEEVLWQITLEKQKNILLKKNK  1300
1301  SKLFHNKVKDIFLYKKLSISFTSEKIHKNY                      1330

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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