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

NucPred

Fetching Q63505 from www.uniprot.org...

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

   1  MDALESLLDEVALEGLDGLCLPALWSRLESRSPAFPLPLEPYTQEFLWRA    50
  51  LVTHPGISFYEEPRERPDLQLQDRYEEIDLETGILESRRDPVTLEDVYPI   100
 101  HMILENKDGIQGSCRYFKERKDITSSIRSKCLQPRCTMVEAFSRWGKKLI   150
 151  IVASQDMRYRALIGLEGDPDLKLPDFSYCILERLGRSRWQGELQRDLHTT   200
 201  AFKVDAGKLHYHRKILNKNGLITMQSHVIRLPTGAQQHSILLLLNRFHVD   250
 251  RRSKYDILMEKLSMMLSTRSNQIETLGKLREELGLCERTFKRLYQYMLNA   300
 301  GLAKVVSLPLQEIHPECGPCKTKKGTDVMVRCLKLLKEFRRKMEDDHDDD   350
 351  DDEEAISKAVPPVDIVFERDMLTQTYELIERRGTKGISQAEIRVAMNVGK   400
 401  LEARMLCRLLQRFKVVKGFMEDEGRQRTTKYISCVFAEESDLSRQYAREK   450
 451  ARGELLTTVSLASVQDESLMPEGEEAFLSDSESEEESSCSGKRRGRGSRG   500
 501  HSRASGDAGPGSRPHHSTPAKGGWKVLNLHPLKKPKSAAVERSRRSSACR   550
 551  DGLDTSSSSELNIPFDPHSMDSHSGDIAVIEEVRLDNPKEGGGSQKGGRH   600
 601  GSGQDKPHKTYRLLKRRNLIIEAVTNLRLIESLFTIQKMIMDQEKQEGVS   650
 651  TKCCKKSIIRLVRNLSEEGLLRLYRTTVIQDGIKKKVDLVVHPSMDQNDP   700
 701  LVRSAIEQVRFRISNSSTANRVKVPPAPAPQEEAEEGNQEPEVPSRSADS   750
 751  EANTSSKPESTRVKKTDEKMGITPLKNYKPVIVPGLGRSIGFLPKMPRLR   800
 801  VMHLFLWYLVYGHPASHTGEQPTFHSERKTGKQEPSRPGVQPSSGDDWDS   850
 851  SEAKNSTESSSWEAEMELSTERVYVDEISWMRYVPPIPIHRDFGFGWALV   900
 901  SDILLCLPLSIFVQVVQVSYKVDNLEDFLNDPLKKHTLIRFLPRHIRQQL   950
 951  LYKRRYIFSVVENLQRLCYMGLLQFGPTEKFQDKDQVFVFLKKNAVIVDT  1000
1001  TICDPHYNLAHSSRPFERRLYVLDSMQDVESYWFDLQCICLNTPLGVVRC  1050
1051  PCAQKICPDPGSDPEGSLRKEQESAMDKHNLERKCAMLEYTTGSREVVDE  1100
1101  GLVPGDGLGAAGLDSSFYAHLKRNWVWTSYIINKARKNNTSENGLTGRLQ  1150
1151  TFLSKRPMPLGSGGSGRLPLWSEGKADAELCADKEEHFELDREPTPGRNR  1200
1201  KVRGGKSQKRKRLKKEPIRKTKRRRRGEHPEAKSKKLRYQDEADQNALRM  1250
1251  MTRLRVSWSMQEDGLLMLCRIASNVLNTKVKGPFVTWQVVRDILHATFEE  1300
1301  SLDKTSHSVGRRARYIVKNPQAFMNYKVCLAEVYQDKALVGDFMSRKDNY  1350
1351  EDPKVCAKEFKEFVEKLKEKFSSGLRNPNLEIPDTLQELFAKYRVLAIGD  1400
1401  EKDRVRKEDELNSVEDIHFLVLQNLIQSTLSLSNSQSNSCQSFQIFRLYR  1450
1451  EFREPVLVRAFMECQKRSLVNRRRVSHSQGPKKNRAVPFVPMSYQLSQSY  1500
1501  YKLFTWRFPTTVCTESFQFYDRLRANGILDQPDHFSFKDMDSNDPSSDLV  1550
1551  AFSLDSPGGHCVTALALFSLGLLSVDVRIPEQIVVVDSSMVESEVMKSLG  1600
1601  KDGGLDDDDEEEDLDEGSGTKRQSVEVKAHQASHTKYLLMRGYYTVPGMV  1650
1651  STRNLNPNDSIVVNSCQVKFRLRNTPAPTHLGPTGPTATPLEELQAGPSC  1700
1701  LPASFTSLVDPQLHTRCPEEFAHQMAQSGYSPEDVAASLEILQAVAAADC  1750
1751  FGVDREKLSRQFSALEKIADKRTRTFLDYIQDLLEQQQVMEVGGNTVRLV  1800
1801  AMASAQPWLLPSVRLKDVEIDTKASGDDSQSRLPAGSSIEDHTSEGAPIP  1850
1851  PVSSNGTKKRPYCSIQSPETDAEEATRLPAKKPTLQDVCVAASPRPGTEE  1900
1901  QTEAQAQFAAPEDAGAEGPRQESQESVGVSGLEQLGCEFQLPENSEDPRG  1950
1951  LTESNMAQVAWESGCERVCFVGRPWRGVDGRLNMPVCKGMMEAVLYHIMS  2000
2001  RPGVPESCLLQYYQGVLQPVAVLELLRGLESLGCIQKRMLKKPASVSLFS  2050
2051  RPVVEGLGQASEAEALSCQGSTVTFYEPTLDCTIRLGRVFPHDINWKQSG  2100
2101  SIYRCVPGQQRSLCPCLIVPPGLSQEPRPSHSCYQSSAQPSTGVATSR    2148

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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