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

NucPred

Fetching Q6CVK3 from www.uniprot.org...

The NucPred score for your sequence is 0.96 (see score help below)

   1  MSDKEDEKQSQPVLKDDKQDQTEEPAIDDNVNGDEGPSDEEEGDDVFDSS    50
  51  EEDEDLDNDEEEAQKVREGFIVDDDEEGGEEDEVVKKKSRRKRRAREEEN   100
 101  EALDEDDLDLLMENAGFKRPSASEAAKQRSGKLKRLKRVGDDEEESASAE   150
 151  PESEVARTNKLDDFFSEEEEEEELEDDGTGRAPSRKGVEKTVTLADDMDD   200
 201  FIEEDEFSDEDEEARKFRIAEKKRIKEQRLAQPTQITGLSPDKVDEMFEV   250
 251  FGDGHDYDWALELENEEELDRLEESSENEQDENELGIDSKRKKKLTLQDI   300
 301  YDLQDLKKNLLTEEDMNIRKADIPERYQELRTGLKNYGKLSPEDLELEKN   350
 351  WISDKIAVDKNFDADYDTTEFKEAIGNAINFIQQENLEVSFIYAYRRNYI   400
 401  SSRSKDGFVLIEDDLWDIVFYDTEFHSIIYKRDYVKTFYEKLDIHDPIVD   450
 451  EYFSNQSMTELNSLQDIYDYVEFKYAQEINDVLLSTQQDATSKKHLKNSS   500
 501  YEKFKASALYQAINDTGITAEQVGENISAEHQLHPVVDHPSLKPTDSVAN   550
 551  ILEGPEAKDLQIFSQNPKLALETIEKYYALELSKNPKVRQKIRDDFYKYY   600
 601  IVDVALTSKGRKEIQRGSPYEDIKYALGRTPAHFRSEPDVFLRMLEAESL   650
 651  HLMNIQIHVSSQDQYTNHLFQTSLETSNTSEIASEWNSFRRDAFDSALNK   700
 701  VFSDVSQEIKDELKKTCLRLVTKSVRHQFMFKLDQAPFIPNPKDPKIPRV   750
 751  LTITCGQGKFGSDAIIAVYLNRKTEFVRDYKIVENPFDRKEPELFENALD   800
 801  DIIQHCQPNVIGINGPNPSTQRLYKKIQEIVQKKQIVDNRGSHVPVIYVE   850
 851  DEVAVRYQSSERAAQEFPSKPTLVKYCIALGRYIHSPLLEYANLTNEELL   900
 901  SLSIHSHQSLLTRELFLQALETSFVDIVNLVGIEVNKATDNHYYAKALRY   950
 951  IAGFGRRKSADFLESLQRLNEPLLARQQLITHDILTKTIFMNSAAFLYIS  1000
1001  WNEKNQRYEDLEHDQLDGTRIHPEDYHLATKVAADALEFDPDAIAEKEEQ  1050
1051  GTMSEFIELLREDPDRRTKLESLNLEAYAEELEKNTGQRKLNNLNTIVLE  1100
1101  LLEGFEELRNDFHPLHGDEVFKSLTGESEKTFFKGCIIPVRVERFRHNDI  1150
1151  YGVTNSGVECVINAQRHIGAQLKRPAEEVYEIGKTYPAKVIYIDYDNISC  1200
1201  EVSLLEHDIRRQYVPIHYSKDPSIWNVEQEMKDQEIEKKLALEEARAKRT  1250
1251  HRVINHPYYGNFTGPQAEDYLRSRERGDFVIRQSSRGDDHLAITWKLDKD  1300
1301  LFQHVDILEKDKENPLALGKTLIVEDQKYHDLDQIIVEYLQNKVRLLNEI  1350
1351  TSNEKFKKGTKKEVIKFIEDYSKVNPNRSVYYFSFNYEHPGWFYLMFKIN  1400
1401  AQSQLYVWNVKLTHTGFFLVNYNYPTVIQLCNGFKTLLKSSSRNKTQDNN  1450
1451  NNNSGGYYGY                                          1460

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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