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

NucPred

Fetching P21441 from www.uniprot.org...

The NucPred score for your sequence is 0.15 (see score help below)

   1  MVDNGHVTIAMADLGTVVEIAQVRCQQEAQRKFAEQLDELWGGEPAYTPT    50
  51  VEDQASWFQQLYYGWIGDYIYKAAAGNITEADLPPPTRSTRTYHIGRKLS   100
 101  RQAHADIDASRRWQGYIGCEVVYKSEAEAKGVLRWVGHLQQSDYPRSLVA   150
 151  GVEWRMPPRHRRLAVLGSAAALHNGVVHGERLFWPHEDNYLCSCEPVEQL   200
 201  YVKSKYNLIPPRPPPSPDLLRTLFKVHWYHVWAQILPKLLSDVTALMLPV   250
 251  LLEYFVKYLNADNATWGWGLGLALTIFLTNVIQSCSAHKYDHISIRTAAL   300
 301  FETSSMALLFEKCFTVSRRSLQRPDMSVGRIMNMVGNDVDNIGSLNWYVM   350
 351  YFWSAPLQLVLCLLLLIRLVGWLRVPGMAVLFVTLPLQAVISKHVQDVSE   400
 401  RMASVVDLRIKRTNELLSGVRIVKFMGWEPVFLARIQDARSRELRCLRDV   450
 451  HVANVFFMFVNDATPTLVIAVVFILYHVSGKVLKPEVVFPTIALLNTMRV   500
 501  SFFMIPIIISSILQCFVSAKRVTAFIECPDTHSQVQDIASIDVPDAAAIF   550
 551  KGASIHTYLPVKLPRCKSRLTAMQRSTLWFRRRGVPETEWYEVDSPDASA   600
 601  SSLAVHSTTVHMGSTQTVITDSDGAAGEDEKGEVEEGDREYYQLVSKELL   650
 651  RNVSLTIPKGKLTMVIGSTGSGKSTLLGALMGEYSVESGELWAERSIAYV   700
 701  PQQAWIMNATLRGNILFFDEERAEDLQDVIRCCQLEADLAQFCGGLDTEI   750
 751  GEMGVNLSGGQKARVSLARAVYANRDVYLLDDPLSALDAHVGQRIVQDVI   800
 801  LGRLRGKTRVLATHQIHLLPLADYIVVLQHGSIVFAGDFAAFSATALEET   850
 851  LRGELKGSKDVESCSSDVDTESATAETAPYVAKAKGLNAEQETSLAGGED   900
 901  PLRSDVEAGRLMTTEEKATGKVPWSTYVAYLKSCGGLEAWGCLLATFALT   950
 951  ECVTAASSVWLSIWSTGSLMWSADTYLYVYLFIVFLEIFGSPLRFFLCYY  1000
1001  LIRIGSRNMHRDLLESIGVARMSFFDTTPVGRVLNRFTKDMSILDNTLND  1050
1051  GYLYLLEYFFSMCSTVIIMVVVQPFVLVAIVPCVYSYYKLMQVYNASNRE  1100
1101  TRRIKSIAHSPVFTLLEESLQGQRTIATYGKLHLVLQEALGRLDVVYSAL  1150
1151  YMQNVSNRWLGVRLEFLSCVVTFMVAFIGVIGKMEGASSQNIGLISLSLT  1200
1201  MSMTLTETLNWLVRQVAMVEANMNSVERVLHYTQEVEHEHVPEMGELVAQ  1250
1251  LVRSESGRGANVTETVVIESAGAASSALHPVQAGSLVLEGVQMRYREGLP  1300
1301  LVLRGVSFQIAPREKVGIVGRTGSGKSTLLLTFMRMVEVCGGVIHVNGRE  1350
1351  MSAYGLRDVRRHFSMIPQDPVLFDGTVRQNVDPFLEASSAEVWAALELVG  1400
1401  LRERVASESEGIDSRVLEGGSNYSVGQRQLMCMARALLKRGSGFILMDEA  1450
1451  TANIDPALDRQIQATVMSAFSAYTVITIAHRLHTVAQYDKIIVMDHGVVA  1500
1501  EMGSPRELVMNHQSMFHSMVESLGSRGSKDFYELLMGRRIVQPAVLSD    1548

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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