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

NucPred

Fetching Q12873 from www.uniprot.org...

The NucPred score for your sequence is 0.91 (see score help below)

   1  MKAADTVILWARSKNDQLRISFPPGLCWGDRMPDKDDIRLLPSALGVKKR    50
  51  KRGPKKQKENKPGKPRKRKKRDSEEEFGSERDEYREKSESGGSEYGTGPG   100
 101  RKRRRKHREKKEKKTKRRKKGEGDGGQKQVEQKSSATLLLTWGLEDVEHV   150
 151  FSEEDYHTLTNYKAFSQFMRPLIAKKNPKIPMSKMMTILGAKWREFSANN   200
 201  PFKGSAAAVAAAAAAAAAAVAEQVSAAVSSATPIAPSGPPALPPPPAADI   250
 251  QPPPIRRAKTKEGKGPGHKRRSKSPRVPDGRKKLRGKKMAPLKIKLGLLG   300
 301  GKRKKGGSYVFQSDEGPEPEAEESDLDSGSVHSASGRPDGPVRTKKLKRG   350
 351  RPGRKKKKVLGCPAVAGEEEVDGYETDHQDYCEVCQQGGEIILCDTCPRA   400
 401  YHLVCLDPELDRAPEGKWSCPHCEKEGVQWEAKEEEEEYEEEGEEEGEKE   450
 451  EEDDHMEYCRVCKDGGELLCCDACISSYHIHCLNPPLPDIPNGEWLCPRC   500
 501  TCPVLKGRVQKILHWRWGEPPVAVPAPQQADGNPDVPPPRPLQGRSEREF   550
 551  FVKWVGLSYWHCSWAKELQLEIFHLVMYRNYQRKNDMDEPPPLDYGSGED   600
 601  DGKSDKRKVKDPHYAEMEEKYYRFGIKPEWMTVHRIINHSVDKKGNYHYL   650
 651  VKWRDLPYDQSTWEEDEMNIPEYEEHKQSYWRHRELIMGEDPAQPRKYKK   700
 701  KKKELQGDGPPSSPTNDPTVKYETQPRFITATGGTLHMYQLEGLNWLRFS   750
 751  WAQGTDTILADEMGLGKTIQTIVFLYSLYKEGHTKGPFLVSAPLSTIINW   800
 801  EREFQMWAPKFYVVTYTGDKDSRAIIRENEFSFEDNAIKGGKKAFKMKRE   850
 851  AQVKFHVLLTSYELITIDQAALGSIRWACLVVDEAHRLKNNQSKFFRVLN   900
 901  GYKIDHKLLLTGTPLQNNLEELFHLLNFLTPERFNNLEGFLEEFADISKE   950
 951  DQIKKLHDLLGPHMLRRLKADVFKNMPAKTELIVRVELSPMQKKYYKYIL  1000
1001  TRNFEALNSRGGGNQVSLLNIMMDLKKCCNHPYLFPVAAMESPKLPSGAY  1050
1051  EGGALIKSSGKLMLLQKMLRKLKEQGHRVLIFSQMTKMLDLLEDFLDYEG  1100
1101  YKYERIDGGITGALRQEAIDRFNAPGAQQFCFLLSTRAGGLGINLATADT  1150
1151  VIIFDSDWNPHNDIQAFSRAHRIGQANKVMIYRFVTRASVEERITQVAKR  1200
1201  KMMLTHLVVRPGLGSKAGSMSKQELDDILKFGTEELFKDENEGENKEEDS  1250
1251  SVIHYDNEAIARLLDRNQDATEDTDVQNMNEYLSSFKVAQYVVREEDKIE  1300
1301  EIEREIIKQEENVDPDYWEKLLRHHYEQQQEDLARNLGKGKRVRKQVNYN  1350
1351  DAAQEDQDNQSEYSVGSEEEDEDFDERPEGRRQSKRQLRNEKDKPLPPLL  1400
1401  ARVGGNIEVLGFNTRQRKAFLNAVMRWGMPPQDAFTTQWLVRDLRGKTEK  1450
1451  EFKAYVSLFMRHLCEPGADGSETFADGVPREGLSRQQVLTRIGVMSLVKK  1500
1501  KVQEFEHINGRWSMPELMPDPSADSKRSSRASSPTKTSPTTPEASATNSP  1550
1551  CTSKPATPAPSEKGEGIRTPLEKEEAENQEEKPEKNSRIGEKMETEADAP  1600
1601  SPAPSLGERLEPRKIPLEDEVPGVPGEMEPEPGYRGDREKSATESTPGER  1650
1651  GEEKPLDGQEHRERPEGETGDLGKREDVKGDRELRPGPRDEPRSNGRREE  1700
1701  KTEKPRFMFNIADGGFTELHTLWQNEERAAISSGKLNEIWHRRHDYWLLA  1750
1751  GIVLHGYARWQDIQNDAQFAIINEPFKTEANKGNFLEMKNKFLARRFKLL  1800
1801  EQALVIEEQLRRAAYLNLSQEPAHPAMALHARFAEAECLAESHQHLSKES  1850
1851  LAGNKPANAVLHKVLNQLEELLSDMKADVTRLPATLSRIPPIAARLQMSE  1900
1901  RSILSRLASKGTEPHPTPAYPPGPYATPPGYGAAFSAAPVGALAAAGANY  1950
1951  SQMPAGSFITAATNGPPVLVKKEKEMVGALVSDGLDRKEPRAGEVICIDD  2000

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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