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

NucPred

Fetching P62295 from www.uniprot.org...

The NucPred score for your sequence is 0.88 (see score help below)

   1  LRGNQVHQGSKMLKSSFLVIQVMFRRWKRRKMQLQVKAAVTLQRAFREWH    50
  51  LRKRAKEEKSAIVIQSWYRMHKQLQKYAYVRACVVIIQKRFRCFQAQKLY   100
 101  KRRKESILTIQKYYRAYLKGKIERTNYLQKRAAAIQLQAAFRRLKAHRLR   150
 151  RQIRAACVIQSYWRMRQDRVRFLNHRKIIIKLQAHVRKHQQLQKYKKMKK   200
 201  AAVVIQTRFQAYIFARKVLASYQKTRSAVILLQSAYRGMQARKMYIQIPT   250
 251  SVIKIQPYYRAYVSKKEFLSLKNATIKLQSIVKMKQTRKQYLHLRATAVF   300
 301  IQQHYRSKKLAAQKREEYMQMRESCIKLQAFVRGYLVRKQMRLQRKAVIS   350
 351  LQSYYRMRKARQCYLKMYKVVIIIQNYYHSYKAQVNQRKNFLQVKKAATC   400
 401  LQAAYRGYKVRQLIKQQSIAAVKIQSAFRGYSKRVRYQSVLQSIIKIQRW   450
 451  YRAYKTLSDIRTHFLKTKAAVISLQSAYRGWKVRKQIRREHQAAMKIQSA   500
 501  FRMAKAQKQFRLFKTAALVIQQHLRAWSTGRKQHMQYIELRHPVLMLQSM   550
 551  WKGKTLRRRLQRQHKCAVIIQSYYRMHVQQKKWKTMKKAALLIQKYYRAY   600
 601  SIGREQHHLYLETKAAVVTLQSAYRGMKVRKRIKDCKKAAVTIQSKYRAY   650
 651  KTKKKYAAYRSSAIIIQRWYRGIKITNHQYKEYHSLKKTVIKIQAVYRGI   700
 701  RIRRHIQHMHRAATFIKAMFKMHQSRIRYHTMRKAAIVIQVRYRAYYQGK   750
 751  MQRENYLKILRAVNVLQANFRGVRLRRTLRNLQIAATVIQSNYRRYREQT   800
 801  YFNKLKKITKTVQQRYRAVKERNILFQRYNKLRHSVIYIQAVFRGMKARR   850
 851  HLKTMHLAATLIQRRFRTLMMRRRFLSLKKTAIWIQRKYRAHLCTKHHLQ   900
 901  FLLLQNAAIKIQSSYRRWMIRKRMREMHRAATFIQATFRMHRVHRRYQAL   950
 951  KQASAMIQQQYQANRAAKLQRQHYLRQRHSAVILQAAFRGMKTRRHLKSM  1000
1001  HSSAVRIQSRFRSLLVRRRFISLKKAAIFIQRKYRATICAKHKLHQFLKL  1050
1051  RKAAITIQSSYRRLMVKKKLQEVHRAAVLIQATFRMHRTYLTFQTWKHAS  1100
1101  ILIQQHYRTYRASKLQRENYTKQWRSAVIIQAAYRGMKARQLLREKHKAA  1150
1151  VIIQSTYRMYRQYCLYQNLQWATKIIQEKYRANKKKHKALQHNELKKAET  1200
1201  CVQASFQDMNIKKLIQEQHQTSIIIQKHCKAFKIKKHYLHLREPVVSIQR  1250
1251  RYRKLTAVHTQAVICIQSYYRGFKVRRDIQNMHLAATRIQSFYRMHRAKV  1300
1301  DYQTKKTAIVVIQNYYRLYVRVKTERRNFLAVQKSVRTIQAAFRGMKVRQ  1350
1351  KLKNVSQEKIAAIVNRSALYCYGSKAQCEAVGSEGVIIQEWYKASCFACS  1400
1401  QEAEYRSQSRAAVTIQKAFRRMITRKLDTRKCAALRIQFFLQMAVYRRRR  1450
1451  ANFVQQKRAAVTLQHYFRMWQTRKQFLLYRKAAVVLQNHYRAFLSGKHQR  1500
1501  QVYLQIRSSVIIIQARIKGFIQKRKFQ                         1527

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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