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

NucPred

Fetching P40383 from www.uniprot.org...

The NucPred score for your sequence is 0.73 (see score help below)

   1  MGIPKFFRWMSERYPLCSQLIENDRIPEFDNLYLDMNGILHNCTHKNDDH    50
  51  SSPPLPEEEMYIAIFNYIEHLFEKIKPKKLLYMAVDGCAPRAKMNQQRSR   100
 101  RFRTAKDAHDARLKAERNGEDFPEEQFDSNCITPGTTFMERVSRQLYYFI   150
 151  HKKVTNDSQWQNIEVIFSGHDCPGEGEHKIMEYIRTQKAQPSYNPNTRHC   200
 201  LYGLDADLIMLGLLSHDPHFCLLREEVTFGPASRNRSKELAHQKFYLLHL   250
 251  SLLREYLEFEFQECRSTFTFKYDLEKILDDFILLAFFVGNDFLPHLPGLH   300
 301  INEGALALMFSIYKKVMPSAGGYINEKGVINMARLELILLELENFEKEIF   350
 351  KAEVSETKNNGNSDKPSFDFLKYITESTNDIKAMTGEQKNYFLQIKKFLS   400
 401  SREPFIDFSANISSVDQRFLRRLCNDLHLSFSKIIKVDGTHLLRITFRDL   450
 451  EFNDEDEDEIEQDEIERVLQKYDNIPLLNEEQALKEKNVEKDFIQWKDDY   500
 501  YRSKVGFSYYDEEALKAMAERYVEGLQWVLFYYYRGCQSWGWYYNYHFAP   550
 551  KISDVLKGLDVKIDFKMGTPFRPFEQLMAVLPARSQALVPPCFRDLMVNS   600
 601  ESPIIDFYPENFALDQNGKTASWEAVVIIPFIDETRLIDALASKDKFLTE   650
 651  EERKRNSFNAPTVFSLAEDYTSFYPSSLPSLFPDLVTRCIQKPYSLPSME   700
 701  GKEYLVGLCPGVFLGAFGMVGFPSFHTLKHKAELVYHGINVFGNESRNPS   750
 751  VIVNVEDVKSALTSEQIAMQYVGKRIFVDWPYLREAYVESAMDESYMYLA   800
 801  SNSTIEKRDLAEIEKSQWGRKCSHKIREYSKRFGVLFGDISLLLQVRPIK   850
 851  GLEYTREGALVKIFNESVLEDYPAQLVVEKIAIDDPRFTEREAPPVEVEY   900
 901  PPGTKAFHLGEYNYGRPAQITGCKDNKLIIWLSTAPGLDAQWGRVLVNDS   950
 951  KSKEKYYPSYIVAKLLNIHPLLLSKITSSFLISNGTKRENIGLNLKFDAR  1000
1001  NQKVLGFSRKSTKGWEFSNKTVALVKEYINTFPQLFNILTTHATKDNLTV  1050
1051  KDCFPKDDTQQLAAVKHWIKEKGINSLTRVSLDEDALDSDIIKLIEEKAS  1100
1101  TIDSTYQVPKKVFGVPRYALLKPSQTRGILHSQEFALGDRVVYVQDSGKV  1150
1151  PIAAYGTVVGIMLHHLDVVFDLPFMSGTTLDGRCSPYHGMQVEVSMVLNV  1200
1201  TNPQFVVNTRAGKNRKTNVSANNVSQGTDSRLVTKPTSTFPSPPSPPSSS  1250
1251  VWNKREHHPKPFSLHQVPPPESLIHKSKSKFSKGNHHSTNGTQSIRGRGG  1300
1301  KRGKPLRSKELNRKHDHIVQPMGKLQIN                        1328

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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