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

NucPred

Fetching Q9DF49 from www.uniprot.org...

The NucPred score for your sequence is 0.85 (see score help below)

   1  MAGVLCPTEEDRSSRAALRMLPPQPCPDESGAYRRMSGPTLSQVQEEPAA    50
  51  EPPQPPASAAEDDVRKRGYLRKQKHGHKRYFVLRSQSHLGPARLEYYDNE   100
 101  KKFRSGQRSGCHPKRVIPLYLCFTVSRRADAKNKHLVALYTKDEYFAMAA   150
 151  ENEQEQDGWYQALSELINESKGACLDTEELEENYGTLRPGTVFKEVWQVN   200
 201  VKPRGLGQAKNLSGVYRLCLSSKAVHLVKLNSDVACVHLLLMNIRRCGHS   250
 251  ENYFFIEVGRSSSTGAGELWMQVDDCVVAQHMHETFLDTMKALKAYSEFR   300
 301  PRSKSQSSCTNPISFITTRRYLGNLPPSQTGLQRRARTESMVGTPPSAKN   350
 351  NSFRFRTSSEGEGTMTRPFRSVTGSLSHLNTARINLGKQEGAGRYVRAPF   400
 401  NSGYQSRSASLPVSHFPSATSPISVCSSSGHGSASETLTRPSSSSVCGSP   450
 451  SDGGFISSDEYGSSPGDLRYFRVRSNTPDSLGNTPPIQEENTLSDYMSMS   500
 501  THSQPDSRDDYMEADKCFRKRTYSLTKHTNSASKQKSQTAISLGEDSEEI   550
 551  NKQFAFAESPKLKDSSLVDDYSNGVIDSVCNQSRSKASDDGYMPMMPSNL   600
 601  YDSDYLPMAPKTVSAPKQINRCPSQADSKGYMMMFPINSSPVKNVFGGAA   650
 651  TKSNLEKLSNGGYMDMSYGNSTKQIHDSNLNNNSRGLSSYFSLPRSFKSL   700
 701  TKQTTDQNEYVPMSSPGKLLHLGAENGVDVCKDGAVHDIAKIELKSSSSI   750
 751  LDQQVKRPNKLTLGIRGSNTIPRMFDHSAPAEPTSPGEYINIDFSDKASS   800
 801  TPYSLSADGSPSSLGSSCDHRQSPLSDYMSVDIDVQSPKATAEQSNSLTD   850
 851  ISLYACTVVSRMQPNAEYAKLPCGTACVSKTDNIMDDYTTMTFNMAMTPP   900
 901  RSFASETENGTKVDSPSSIVNRLCIGELTSLNSGFSLPNPLPEPIAGPKV   950
 951  IRADSQGRRRHSSETFASSSTVTTSSSCFTESGKRHSSASFDNVWLKPDE  1000
1001  NSCEQENKMSRHCSTGFQNGLNYISLSMHNGVCEPTSPDCHQHQNGSRNL  1050
1051  ESGGYVSIDFTRCDCLKCPTSRKD                            1074

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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