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

NucPred

Fetching Q8VXP3 from www.uniprot.org...

The NucPred score for your sequence is 0.45 (see score help below)

   1  MLPLEHKASGRVQATGRGVRASVELSSVLPQQRAAQLQHQKCNTGARLGR    50
  51  DPRRGVDAERTLVCTAATTASVPSTSGASPSGSQLSSKALRPRRFSAPVI   100
 101  ARLLRSTTTVQELADLVQQQSLYMDSSHVGIAMLHLALLVSRAEQQAAAQ   150
 151  LQLQLAAKQAATRRAGSGASTSGRARGWGSGPGRNGSGSSSVSVNGSGSS   200
 201  SNGSSSSSSSLAMGMQLSMASIGDDVVSGVNAGPVPSGGADALLDLEMSS   250
 251  ILDDDDGAGARQLQQMSDDLAAGLEAAATTTAAPEAGVAAAGGTGAGAAA   300
 301  DAAASSSAPSLVAAAAAAAAAAASPASSPDVARTLRTLLSRAFSLGLDSL   350
 351  SGPQLAAVFTGLAVLRRPRQQQQQQQQAGAAGAGANAGAGGVGGVGVSAG   400
 401  DRLVAEQLLAAMGPKLYECRPQDLANTLASVALLGLPPDADLRTSFYAAV   450
 451  RQQQRRFGPRELATTLWAYGAMGTYVQEDAVQLVLELSRARLTSFSPLQL   500
 501  AKAVQGLAALRYRPSPEWVEAYCSVLRPALRRMSSRELCAVLLALASLQV   550
 551  GLDGGTRAALLVHTFSGPLPGMAPGEVALSLWALGRLSAVDMDLPALIDL   600
 601  DMSGRVLDLTSRLLAAGGFSGGELQQLLEGLTRLALQPPLEWMQAFVAAL   650
 651  QPQLDKLDAQQLAGVLNSLAAQQYRPQPQMQEVVLAATQANMKQLLADTT   700
 701  CSAALLTALRRLNIEPPPGWVGALLEESRSALKNRCTDLHLANLAGSLAA   750
 751  WGVRPDGRWAARLMWRSQVLMNEDRMSPRALVALLQAMVSLGLSPNPVWT   800
 801  QLCLQAAVRRASQPAFEPHHYGTLMASLHALGIQPPQEWLTRMLLSTYRC   850
 851  WDRFSVTHWSSLLPALVLLKARPPREWLRRFEATSAARLADCSALQLLTL   900
 901  AVSLAQLHQLHAAGAVADTPLLLPGAAAAAAAAAPAGASSAAAAGDSPAA   950
 951  LSAVPAAAGDGALVPSFMSIDDDGTAAVAAAATALAAAEPAAHAATSTTT  1000
1001  ATAVAHPQPQLLPQAQALPQPGPEWQAAWWAASTRLLLRVRYAPSELVLT  1050
1051  AGWLGSLGLRPPPEWLQACAEVAARYSKVMDAAERQQLAAAVAPLALEAV  1100
1101  APPSAPPAGAASTAH                                     1115

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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