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

NucPred

Fetching Q6P9P0 from www.uniprot.org...

The NucPred score for your sequence is 0.98 (see score help below)

   1  MTRRCMPARPGFPSSPAPGSSPPRCHLRPGSTAPAAAGKRTESPGDRKQS    50
  51  IIDFFKPAAKQDKHMLDSPQKSNIKYRGNGLSITGTEQFERKLSSPKKLK   100
 101  PKRMSSEESPILEAFMKGGKEHHKDRGVHESRRPCMSLSKYLPKGAGIYA   150
 151  PSSYRLPKEIKAQKKKHQSPERRKSLFIHESNREKNDRDRGKNSEDSRKQ   200
 201  ATATEGDIFKHSSRSISSRSSLSRHHPGESTLGARFQLSLASYWREREQK   250
 251  KLRKEQMEQRINSENSFSEASNLSLKSSGVGKNCKPRHEHSKHTEAVPGK   300
 301  SNLSTLENGHLSRKRSSSDSWELSGSKQNKFSDKRTEELCGLRPEKHKRT   350
 351  YHTKSKRVLSREAPRHIPSERKVYQTHCTEDSWWCSALGRHSQGAGKTVS   400
 401  RGMSIASTLRLYLGRVISQLWKMDISQEKDHLQTRGNFQALNRINSPTKE   450
 451  QRNSVDSDLKSTKEPIIPKARESFLEKRPDTSHQREKFIRHIALKTPGGV   500
 501  LRLEDIAKEPEDETDRSSADSAPSNAGHHSSRNSDQVHSASTKETKIQKP   550
 551  HLPLPQEKSTIKRASNLQKNKPAGSVTSKETKLPLLSHVPSAVSSRVPLN   600
 601  AKNCTLPVPKKDKERSSSKERSGHSTESSKHKEHRAKTIKAVSNESSGKN   650
 651  SGGSLHSEYAPPTASPPAALEVVPSVPSPAAPSDKESSGNSNAGSNALKR   700
 701  KFRGDFDSDEESLGYTLESDEEEETLKSLEEIMALNFSRTPTTSGKPPAV   750
 751  SKGLRSQSSDMKEYAQSGTYTNTLERLVKEMEDTQRLDELQKKLQEDIRQ   800
 801  GRGIKSPLRTGDQDSTDDGDGLLEEHREFLKKFSVTVDAIPDHHPGEEIF   850
 851  NFLNSGKIFNQYTLDLRDSGFIGESAVEKLILKSGKTDQIFLTTQGFLTT   900
 901  AYHYVQCPVPVLKWLFRMMSVHTDCIVSVQILSTLMEITIRNDTFSDSPV   950
 951  WPWIPSLSDIAAVFFNMGVGFGSLFPLETLQPDFNEENLISETQKTLGGK  1000
1001  ESEDSPYSPVFSALPETNILNVVKFLGLCTSIHPEGYQDGELMLLILMLF  1050
1051  KMSLEKELKQIPLVDFQSLLINLMKNIRDWNTKVHELCLGINELSSHPHN  1100
1101  LLWLVQLVPNWTSRGRQLRQCLSLVMMSKLLDEKHEDIPNANNLQISVLH  1150
1151  RYLVQMKPSDLLKKMVLKKRAEQPNETIDDSLHLELEKQAYYLTYILLHL  1200
1201  VGEVSCSHSLSSGQRKHFVLLCGALEKHVKCDIREDARLFYRTKVKDLVA  1250
1251  RIHGKWQEIIQNCRPTQGQLHDFWVPDS                        1278

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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