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

NucPred

Fetching Q12769 from www.uniprot.org...

The NucPred score for your sequence is 0.41 (see score help below)

   1  MLHLSAAPPAPPPEVTATARPCLCSVGRRGDGGKMAAAGALERSFVELSG    50
  51  AERERPRHFREFTVCSIGTANAVAGAVKYSESAGGFYYVESGKLFSVTRN   100
 101  RFIHWKTSGDTLELMEESLDINLLNNAIRLKFQNCSVLPGGVYVSETQNR   150
 151  VIILMLTNQTVHRLLLPHPSRMYRSELVVDSQMQSIFTDIGKVDFTDPCN   200
 201  YQLIPAVPGISPNSTASTAWLSSDGEALFALPCASGGIFVLKLPPYDIPG   250
 251  MVSVVELKQSSVMQRLLTGWMPTAIRGDQSPSDRPLSLAVHCVEHDAFIF   300
 301  ALCQDHKLRMWSYKEQMCLMVADMLEYVPVKKDLRLTAGTGHKLRLAYSP   350
 351  TMGLYLGIYMHAPKRGQFCIFQLVSTESNRYSLDHISSLFTSQETLIDFA   400
 401  LTSTDIWALWHDAENQTVVKYINFEHNVAGQWNPVFMQPLPEEEIVIRDD   450
 451  QDPREMYLQSLFTPGQFTNEALCKALQIFCRGTERNLDLSWSELKKEVTL   500
 501  AVENELQGSVTEYEFSQEEFRNLQQEFWCKFYACCLQYQEALSHPLALHL   550
 551  NPHTNMVCLLKKGYLSFLIPSSLVDHLYLLPYENLLTEDETTISDDVDIA   600
 601  RDVICLIKCLRLIEESVTVDMSVIMEMSCYNLQSPEKAAEQILEDMITID   650
 651  VENVMEDICSKLQEIRNPIHAIGLLIREMDYETEVEMEKGFNPAQPLNIR   700
 701  MNLTQLYGSNTAGYIVCRGVHKIASTRFLICRDLLILQQLLMRLGDAVIW   750
 751  GTGQLFQAQQDLLHRTAPLLLSYYLIKWGSECLATDVPLDTLESNLQHLS   800
 801  VLELTDSGALMANRFVSSPQTIVELFFQEVARKHIISHLFSQPKAPLSQT   850
 851  GLNWPEMITAITSYLLQLLWPSNPGCLFLECLMGNCQYVQLQDYIQLLHP   900
 901  WCQVNVGSCRFMLGRCYLVTGEGQKALECFCQAASEVGKEEFLDRLIRSE   950
 951  DGEIVSTPRLQYYDKVLRLLDVIGLPELVIQLATSAITEAGDDWKSQATL  1000
1001  RTCIFKHHLDLGHNSQAYEALTQIPDSSRQLDCLRQLVVVLCERSQLQDL  1050
1051  VEFPYVNLHNEVVGIIESRARAVDLMTHNYYELLYAFHIYRHNYRKAGTV  1100
1101  MFEYGMRLGREVRTLRGLEKQGNCYLAALNCLRLIRPEYAWIVQPVSGAV  1150
1151  YDRPGASPKRNHDGECTAAPTNRQIEILELEDLEKECSLARIRLTLAQHD  1200
1201  PSAVAVAGSSSAEEMVTLLVQAGLFDTAISLCQTFKLPLTPVFEGLAFKC  1250
1251  IKLQFGGEAAQAEAWAWLAANQLSSVITTKESSATDEAWRLLSTYLERYK  1300
1301  VQNNLYHHCVINKLLSHGVPLPNWLINSYKKVDAAELLRLYLNYDLLEEA  1350
1351  VDLVSEYVDAVLGKGHQYFGIEFPLSATAPMVWLPYSSIDQLLQALGENS  1400
1401  ANSHNIALSQKILDKLEDYQQKVDKATRDLLYRRTL                1436

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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