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

NucPred

Fetching P78992 from www.uniprot.org...

The NucPred score for your sequence is 0.27 (see score help below)

   1  MAEEDYLPVYQLRRDSSLLGTMNKILVANRGEIPIRIFRTAHELSMNTVA    50
  51  IYSHEDRLSMHRLKADEAYVIGERGQYSPVQAYLAIDEIIKIAVKHNVNM   100
 101  IHPGYGFCSENSEFARKVEENGILWVGPSDTVIDAVGDKVSARNLAYAAN   150
 151  VPTVPGTPGPIEDVAQATAFVEEYGYPVIIKAAFGGGGRGMRVVREGDDI   200
 201  EDAFLRASSEAKTAFGNGTVFIERFLDKPKHIEVQLLADNYGNVIHLFER   250
 251  DCSVQRRHQKVARNCSAKTLPVEVRNAILNDAVKLAKTANYRNAGTAEFL   300
 301  VDSQNRHYFIEINPRIQVEHTITEEITGVDIVAAQIQIAAGASLEQLGLL   350
 351  QEKITTRGFAIQCRITTEDPTKNFQPDTGKIEVYRSSGGNGVRLDGGNGF   400
 401  AGAVISPHYDSMLVKCSTSGSNYEIRRRKMIRALVEFRIRGVKTNIPFLL   450
 451  ALLTHPVFMTSECWTTFIDDTPELFKILTSQNRAQKLLAYLGDLAVNGSS   500
 501  IKGQIGLPKLHKEADIPSITDINGDVIDVSIPPPDGWRQFLLEKGPEQFA   550
 551  QQVRAFPGLMIMDTTWRDAHQSLLATRVRTHDLLNIAPATSYALHHAFAL   600
 601  ECWGGATFDVSMRFLHEDPWQRLRKLRKAVPNIPFSMLLRGGNGVAYYSL   650
 651  PDNAIDHFLKQAKDTGVDVFRVFDALNDIEQLKVGVDAVKKAGGVVEATM   700
 701  CYSGDMLKPGKKYNLEYYINLATEIVEMGTHILAVKDMAGTLKPTAAKQL   750
 751  ISALRRKFPSLPIHVHTHDSAGTGVASMVACARAGADVVTVRVNSMSGMT   800
 801  SQPSMSAFIASLDGEIETGIPEANAREIDAYWAEMRLLYSCFEADLKGPD   850
 851  PEVYQHEIPGGQLTNLLFQAQQVGLGEKWVETKKAYEAANRLLGDIVKVT   900
 901  PTSKVVGDLAQFMVSNKLSSEDVERLASELDFPDSVLDFFEGLMGTPYGG   950
 951  FPEPLRTNVISGKRRKLTSRPGLTLEPYNIPAIREDLEARFSKVTENDVA  1000
1001  SYNMYPKVYEAYKKQQELYGDLSVLPTRNFLSPPKIDEERHVTIVTIETR  1050
1051  KTLIIKCMAEGELSQSSGTREVYFELNGEMRKVTVEDKNGAVETITRPKA  1100
1101  DAHNPNEIGAPMAGVVVEVRVHENGEVKKGDPIAVLSAMKMEMVISSPVA  1150
1151  GRIGQIAVKENDSVDASDLIPKSSRLSKLLMFIILIILY             1189

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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