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

NucPred

Fetching Q96L93 from www.uniprot.org...

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

   1  MASVKVAVRVRPMNRREKDLEAKFIIQMEKSKTTITNLKIPEGGTGDSGR    50
  51  ERTKTFTYDFSFYSADTKSPDYVSQEMVFKTLGTDVVKSAFEGYNACVFA   100
 101  YGQTGSGKSYTMMGNSGDSGLIPRICEGLFSRINETTRWDEASFRTEVSY   150
 151  LEIYNERVRDLLRRKSSKTFNLRVREHPKEGPYVEDLSKHLVQNYGDVEE   200
 201  LMDAGNINRTTAATGMNDVSSRSHAIFTIKFTQAKFDSEMPCETVSKIHL   250
 251  VDLAGSERADATGATGVRLKEGGNINKSLVTLGNVISALADLSQDAANTL   300
 301  AKKKQVFVPYRDSVLTWLLKDSLGGNSKTIMIATISPADVNYGETLSTLR   350
 351  YANRAKNIINKPTINEDANVKLIRELRAEIARLKTLLAQGNQIALLDSPT   400
 401  ALSMEEKLQQNEARVQELTKEWTNKWNETQNILKEQTLALRKEGIGVVLD   450
 451  SELPHLIGIDDDLLSTGIILYHLKEGQTYVGRDDASTEQDIVLHGLDLES   500
 501  EHCIFENIGGTVTLIPLSGSQCSVNGVQIVEATHLNQGAVILLGRTNMFR   550
 551  FNHPKEAAKLREKRKSGLLSSFSLSMTDLSKSRENLSAVMLYNPGLEFER   600
 601  QQREELEKLESKRKLIEEMEEKQKSDKAELERMQQEVETQRKETEIVQLQ   650
 651  IRKQEESLKRRSFHIENKLKDLLAEKEKFEEERLREQQEIELQKKRQEEE   700
 701  TFLRVQEELQRLKELNNNEKAEKFQIFQELDQLQKEKDEQYAKLELEKKR   750
 751  LEEQEKEQVMLVAHLEEQLREKQEMIQLLRRGEVQWVEEEKRDLEGIRES   800
 801  LLRVKEARAGGDEDGEELEKAQLRFFEFKRRQLVKLVNLEKDLVQQKDIL   850
 851  KKEVQEEQEILECLKCEHDKESRLLEKHDESVTDVTEVPQDFEKIKPVEY   900
 901  RLQYKERQLQYLLQNHLPTLLEEKQRAFEILDRGPLSLDNTLYQVEKEME   950
 951  EKEEQLAQYQANANQLQKLQATFEFTANIARQEEKVRKKEKEILESREKQ  1000
1001  QREALERALARLERRHSALQRHSTLGMEIEEQRQKLASLNSGSREQSGLQ  1050
1051  ASLEAEQEALEKDQERLEYEIQQLKQKIYEVDGVQKDHHGTLEGKVASSS  1100
1101  LPVSAEKSHLVPLMDARINAYIEEEVQRRLQDLHRVISEGCSTSADTMKD  1150
1151  NEKLHNGTIQRKLKYERMVSRSLGANPDDLKDPIKISIPRYVLCGQGKDA  1200
1201  HFEFEVKITVLDETWTVFRRYSRFREMHKTLKLKYAELAALEFPPKKLFG  1250
1251  NKDERVIAERRSHLEKYLRDFFSVMLQSATSPLHINKVGLTLSKHTICEF  1300
1301  SPFFKKGVFDYSSHGTG                                   1317

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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