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

NucPred

Fetching Q9UIG0 from www.uniprot.org...

The NucPred score for your sequence is 0.99 (see score help below)

   1  MAPLLGRKPFPLVKPLPGEEPLFTIPHTQEAFRTREEYEARLERYSERIW    50
  51  TCKSTGSSQLTHKEAWEEEQEVAELLKEEFPAWYEKLVLEMVHHNTASLE   100
 101  KLVDTAWLEIMTKYAVGEECDFEVGKEKMLKVKIVKIHPLEKVDEEATEK   150
 151  KSDGACDSPSSDKENSSQIAQDHQKKETVVKEDEGRRESINDRARRSPRK   200
 201  LPTSLKKGERKWAPPKFLPHKYDVKLQNEDKIISNVPADSLIRTERPPNK   250
 251  EIVRYFIRHNALRAGTGENAPWVVEDELVKKYSLPSKFSDFLLDPYKYMT   300
 301  LNPSTKRKNTGSPDRKPSKKSKTDNSSLSSPLNPKLWCHVHLKKSLSGSP   350
 351  LKVKNSKNSKSPEEHLEEMMKMMSPNKLHTNFHIPKKGPPAKKPGKHSDK   400
 401  PLKAKGRSKGILNGQKSTGNSKSPKKGLKTPKTKMKQMTLLDMAKGTQKM   450
 451  TRAPRNSGGTPRTSSKPHKHLPPAALHLIAYYKENKDREDKRSALSCVIS   500
 501  KTARLLSSEDRARLPEELRSLVQKRYELLEHKKRWASMSEEQRKEYLKKK   550
 551  REELKKKLKEKAKERREKEMLERLEKQKRYEDQELTGKNLPAFRLVDTPE   600
 601  GLPNTLFGDVAMVVEFLSCYSGLLLPDAQYPITAVSLMEALSADKGGFLY   650
 651  LNRVLVILLQTLLQDEIAEDYGELGMKLSEIPLTLHSVSELVRLCLRRSD   700
 701  VQEESEGSDTDDNKDSAAFEDNEVQDEFLEKLETSEFFELTSEEKLQILT   750
 751  ALCHRILMTYSVQDHMETRQQMSAELWKERLAVLKEENDKKRAEKQKRKE   800
 801  MEAKNKENGKVENGLGKTDRKKEIVKFEPQVDTEAEDMISAVKSRRLLAI   850
 851  QAKKEREIQEREMKVKLERQAEEERIRKHKAAAEKAFQEGIAKAKLVMRR   900
 901  TPIGTDRNHNRYWLFSDEVPGLFIEKGWVHDSIDYRFNHHCKDHTVSGDE   950
 951  DYCPRSKKANLGKNASMNTQHGTATEVAVETTTPKQGQNLWFLCDSQKEL  1000
1001  DELLNCLHPQGIRESQLKERLEKRYQDIIHSIHLARKPNLGLKSCDGNQE  1050
1051  LLNFLRSDLIEVATRLQKGGLGYVEETSEFEARVISLEKLKDFGECVIAL  1100
1101  QASVIKKFLQGFMAPKQKRRKLQSEDSAKTEEVDEEKKMVEEAKVASALE  1150
1151  KWKTAIREAQTFSRMHVLLGMLDACIKWDMSAENARCKVCRKKGEDDKLI  1200
1201  LCDECNKAFHLFCLRPALYEVPDGEWQCPACQPATARRNSRGRNYTEESA  1250
1251  SEDSEDDESDEEEEEEEEEEEEEDYEVAGLRLRPRKTIRGKHSVIPPAAR  1300
1301  SGRRPGKKPHSTRRSQPKAPPVDDAEVDELVLQTKRSSRRQSLELQKCEE  1350
1351  ILHKIVKYRFSWPFREPVTRDEAEDYYDVITHPMDFQTVQNKCSCGSYRS  1400
1401  VQEFLTDMKQVFTNAEVYNCRGSHVLSCMVKTEQCLVALLHKHLPGHPYV  1450
1451  RRKRKKFPDRLAEDEGDSEPEAVGQSRGRRQKK                   1483

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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