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

NucPred

Fetching P20742 from www.uniprot.org...

The NucPred score for your sequence is 0.30 (see score help below)

   1  MRKDRLLHLCLVLLLILLSASDSNSTEPQYMVLVPSLLHTEAPKKGCVLL    50
  51  SHLNETVTVSASLESGRENRSLFTDLVAEKDLFHCVSFTLPRISASSEVA   100
 101  FLSIQIKGPTQDFRKRNTVLVLNTQSLVFVQTDKPMYKPGQTVRFRVVSV   150
 151  DENFRPRNELIPLIYLENPRRNRIAQWQSLKLEAGINQLSFPLSSEPIQG   200
 201  SYRVVVQTESGGRIQHPFTVEEFVLPKFEVKVQVPKIISIMDEKVNITVC   250
 251  GEYTYGKPVPGLATVSLCRKLSRVLNCDKQEVCEEFSQQLNSNGCITQQV   300
 301  HTKMLQITNTGFEMKLRVEARIREEGTDLEVTANRISEITNIVSKLKFVK   350
 351  VDSHFRQGIPFFAQVLLVDGKGVPIPNKLFFISVNDANYYSNATTNEQGL   400
 401  AQFSINTTSISVNKLFVRVFTVHPNLCFHYSWVAEDHQGAQHTANRVFSL   450
 451  SGSYIHLEPVAGTLPCGHTETITAHYTLNRQAMGELSELSFHYLIMAKGV   500
 501  IVRSGTHTLPVESGDMKGSFALSFPVESDVAPIARMFIFAILPDGEVVGD   550
 551  SEKFEIENCLANKVDLSFSPAQSPPASHAHLQVAAAPQSLCALRAVDQSV   600
 601  LLMKPEAELSVSSVYNLLTVKDLTNFPDNVDQQEEEQGHCPRPFFIHNGA   650
 651  IYVPLSSNEADIYSFLKGMGLKVFTNSKIRKPKSCSVIPSVSAGAVGQGY   700
 701  YGAGLGVVERPYVPQLGTYNVIPLNNEQSSGPVPETVRSYFPETWIWELV   750
 751  AVNSSGVAEVGVTVPDTITEWKAGAFCLSEDAGLGISSTASLRAFQPFFV   800
 801  ELTMPYSVIRGEVFTLKATVLNYLPKCIRVSVQLKASPAFLASQNTKGEE   850
 851  SYCICGNERQTLSWTVTPKTLGNVNFSVSAEAMQSLELCGNEVVEVPEIK   900
 901  RKDTVIKTLLVEAEGIEQEKTFSSMTCASGANVSEQLSLKLPSNVVKESA   950
 951  RASFSVLGDILGSAMQNIQNLLQMPYGCGEQNMVLFAPNIYVLNYLNETQ  1000
1001  QLTQEIKAKAVGYLITGYQRQLNYKHQDGSYSTFGERYGRNQGNTWLTAF  1050
1051  VLKTFAQARSYIFIDEAHITQSLTWLSQMQKDNGCFRSSGSLLNNAIKGG  1100
1101  VEDEATLSAYVTIALLEIPLPVTNPIVRNALFCLESAWNVAKEGTHGSHV  1150
1151  YTKALLAYAFSLLGKQNQNREILNSLDKEAVKEDNLVHWERPQRPKAPVG  1200
1201  HLYQTQAPSAEVEMTSYVLLAYLTAQPAPTSGDLTSATNIVKWIMKQQNA  1250
1251  QGGFSSTQDTVVALHALSRYGAATFTRTEKTAQVTVQDSQTFSTNFQVDN  1300
1301  NNLLLLQQISLPELPGEYVITVTGERCVYLQTSMKYNILPEKEDSPFALK  1350
1351  VQTVPQTCDGHKAHTSFQISLTISYTGNRPASNMVIVDVKMVSGFIPLKP  1400
1401  TVKMLERSSSVSRTEVSNNHVLIYVEQVTNQTLSFSFMVLQDIPVGDLKP  1450
1451  AIVKVYDYYETDESVVAEYIAPCSTDTEHGNV                    1482

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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