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

NucPred

Fetching P62284 from www.uniprot.org...

The NucPred score for your sequence is 0.89 (see score help below)

   1  TRKRFLKLKYYSIILQSRIRMIIAVTSYKRYLWATVTIQRHWRAYLRRKQ    50
  51  DQQRYEMLKSSSLIIQAMFRRWKQRKMQLQVKATITLQRAFREWHLRKRA   100
 101  KEEKSAIVIQSWYRMHKQLRKYVYVRSCVVIIQKRFRCFQAQRLYKRKRE   150
 151  SILTIQKYYRAYLKGKIERIHYLQKRAAAIQLQAAFKILKAHNLHRPIRA   200
 201  ACVIQSYWRMRQDRVRFLNLKKNIIKLQAHVRKHQQLQKYKKIKKAAVII   250
 251  QTHFQAYIFARKVLASYQKTRSAVIVLQSAYRGMQARKMYIHILTSVIKI   300
 301  QSYYRAYVSKKEFLSLKNATIKLQSIVKMKQTRKQYVHLRATALFIQQCY   350
 351  HSKKLAAQKREEYMQMRESCIKLQAFVRGYLVRKQIRLQRKAVISLQSYF   400
 401  RMRKARQYYLKMYKAVIIIQNYYHSYKAQVNQRKNFLRVKKAATCLQAAY   450
 451  RGYKVRQLIKQQSVAAVKIQSAFRGYSKRVKYLSVLQSIIKIQRWYRAYK   500
 501  TLYDIRTRFLKAKAAVISLQSAYRGWKVRKQIRREHQAAMKIQSAFRMAK   550
 551  AQKQFRLFKTAALVIQQHLRAWIAGRKQRMEYIELRHSVLMLQSMWKGKT   600
 601  LRRDLQRQHTCAVIIQSYYRMHVQQKKWKIMKEAALLIQKYYRACRIGRE   650
 651  QHCLYLETKAAVLTLQSAYRGMKVRKRIKACNTAAITIQSKYRAYKTKKK   700
 701  YAAYRASAIIIQRWYRGIKITNHQYKEYLNLKKTAIKIQAVYRGIRVRRH   750
 751  IQHMHRAATFIKAMFKMHQPRIRYHTMRKATIVIQVRYRAYHQGKMQREN   800
 801  YLKILKAVNILQANFRGVRVRRTLRKLRIAATLIQSNYRRYRQQTYFNKL   850
 851  KKITRTVQQRYRAVKERNIQFQRYNKLRHSVIYIQALFRGMKARRHLKTM   900
 901  HIAATLIQRRFRALMLRRRFLSLKKTAIWIQRKYRAHLRTKRHLQFLRLQ   950
 951  NAAIKIQSSYRRWMIRKKMREMHRAAAFIQATFRMHRVHMRYHALKQASV  1000
1001  VIQQRYQANRAAKLQRQHYLRQRYSAVILQAAFRGMKTRRHLKSMYFSAI  1050
1051  LIQSRFRSLLVRRRFISLKKAAIFIQRKYRATICAKHKLRQFLQLRKAAI  1100
1101  TIQSSYRRLMVKKKLQEMHRAAVLIQATFRMHRTHITFQTWKHASILIQQ  1150
1151  HYRTYRASKLQRENYTKQWHSAVIIQAAYRGMKARQLLREKHKAAIIIQS  1200
1201  TYRMYRQYCLYQKLQWATKIIQEKYRADKKKHKALQHTELRKAETCVQAS  1250
1251  FQDVNIEKLIQEQHQTSIIIQKHCKAFKIKKHYLHLRAPVVSIQRRYGKL  1300
1301  TAVHTQAVICIQSYYRGFKVRRDIQNMHLAATRIQSFYRMHRAKVHYQTK  1350
1351  KTAIVIIQNYYRLYVRVKTERKSFLAVQKSVRTIQAAFRGMKVRQKLKNI  1400
1401  PKEKMAAIVDQSALYCYRSKGQDEAVRSEGVIIQEWCKASCLACSQEEYH  1450
1451  SQSRAAVTIQKAFRRMITRKLETQKCATLRIQSFLRMAVYRRRRANSVQQ  1500
1501  KRAAVTLQHYFRMWQTRKQFLLYRKAAVVLQNHYRAFLSGKHQRQVYLQI  1550
1551  RSSVIIIQARIKGF                                      1564

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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