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

NucPred

Fetching P48034 from www.uniprot.org...

The NucPred score for your sequence is 0.26 (see score help below)

   1  MEGGSELLFYVNGRKVTEKNVDPETMLLPYLRKKLRLTGTKYGCGGGGCG    50
  51  ACTVMISRYNPITKKIRHYPANACLTPICSLYGAAVTTVEGIGSTKTRIH   100
 101  PVQERIAKCHGTQCGFCTPGMVMSLYTLLRNHPEPTLTQLNDALGGNLCR   150
 151  CTGYRPIINACKTFCKTSGCCQSKENGVCCLDQGMNGLPEFEEGNETSLK   200
 201  LFSEEEFLPLDPTQELIFPPELMTMAEKKTQKTRIFGSDRMTWISPVTLK   250
 251  ELLEAKVKYPQAPVVMGNTSVGPDMKFKGIFHPVIISPDRIEELSVVNYT   300
 301  DNGLTLGAAVSLAEVKDILANVTRKLPEEKTQMYHALLKHLETLAGPQIR   350
 351  NMASLGGHIVSRHPDSDLNPLLAVGNCTLNLLSKEGRRQIPLNEQFLRKC   400
 401  PSADLKPEEILISVNIPYSRKWEFVSAFRQAQRQQNALAIVNSGMRVCFG   450
 451  KGDGIIRELSIAYGGVGPTTILANNSCQKLIGRPWNEEMLDAACRLILDE   500
 501  VSLPGSAPGGRVEFKRTLIVSFLFKFYLEVSQILKGMDLVHYPSLASKYE   550
 551  SALEDLHSRHYWSTLKYQNADLKQLSQDPIGHPIMHLSGIKHATGEAIYC   600
 601  DDMPVVDRELFLTFVTSSRAHAKIVSIDVSAALSLPGVVDILTGEHLPGI   650
 651  NTTFGFLTDADQLLSTDEVSCVGQLVCAVIADSEVQARRAAQQVKIVYQD   700
 701  LEPVILTIEEAIQNKSFFEPERKLEYGNVDEAFKMVDQILEGEIHMGGQE   750
 751  HFYMETQSMLVVPKGEDREIDVYVSAQFPKYIQDITASVLKVSANKVMCH   800
 801  VKRVGGAFGGKVTKTGVLAAITAFAANKHGRPVRCILERGEDILITGGRH   850
 851  PYLGKYKAGFMNDGRILALDMEHYNNAGAFLDESLFVIEMGLLKLENAYK   900
 901  FPNLRCRGWACRTNLPSNTALRGFGFPQAGLITEACITEVAAKCGLPPEK   950
 951  VRMINMYKEIDQTPYKQEINTKNLTQCWKECMATSSYTLRKAAVEKFNSE  1000
1001  NYWKKKGLAMVPLKYPIGLGSVAAGQAAALVHIYLDGSVLVTHGGIEMGQ  1050
1051  GVHTKMIQVVSRELRMPLSSIHLRGTSTETIPNTNPSGGSVVADLNGLAV  1100
1101  KDACQTLLKRLKPIISKNPKGTWKDWAQAAFNESISLSATGYFRGYESNI  1150
1151  NWETGEGHPFEYFVYGAACSEVEIDCLTGAHKNIRTDIVMDVGYSINPAL  1200
1201  DVGQIEGAFIQGMGLYTIEELNYSPQGVLYTRGPNQYKIPAICDIPMELH  1250
1251  ISFLPPSENSNTLYSSKGLGESGIFLGCSVFFAIHDAIRAARQERGLPGP  1300
1301  LRLNSPLTPEKIRMACEDKFTKMIPRDEPGSYVPWSVPI             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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