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

NucPred

Fetching Q9Z277 from www.uniprot.org...

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

   1  MAPLLGRKPFPLVKPLPGEEPLFTIPHTQEAFRTREEYEARLERYSERIW    50
  51  TCKSTGSSQLTHKEAWEEEQEVAELLKEEFPNWYEKLVLEMVHHNTASLE   100
 101  KLVDSAWLEIMTKYAVGEECDFEVGKEKMLKVKIVKIHPLEKVDEEAVEK   150
 151  KSDGACDSPSSDKENSSQMAQDLQKKETVVKEDEGRRESINDRARRSPRK   200
 201  LPTSLKKGERKWAPPKFLPHKYDVKLQNEDKIISNVPADSLIRTERPPNK   250
 251  EILRYFIRHNALRAGTGENAPWVVEDELVKKYSLPSKFSDFLLDPYKYMT   300
 301  LNPSTKRRNTGSPDRKPSKKPKRDSSSLSSPLNPKLWCHVHLEKSLNGPP   350
 351  LKVKNSKNSKSPEEHLEGVMKIMSPNNNKLHSFHIPKKGPAAKKPGKHSD   400
 401  KPLKAKGRGKGILNGQKSTGNSKSPSKCVKTPKTKMKQMTLLDMAKGTQK   450
 451  MTRTPRSSGGVPRSSGKPHKHLPPAALHLIAYYKENKDKEDKKSALSCVI   500
 501  SKTARLLSNEDRARLPEELRALVQKRYELLEHKKRWASMSEEQRKEYLKK   550
 551  KRQELKERLREKAKERREREMLERLEKQKRFEDQELGGRNLPAFRLVDTP   600
 601  EGLPNTLFGDVALVVEFLSCYSGLLLPDAQYPITAVSLMEALSADKGGFL   650
 651  YLNRVLVILLQTLLQDEIAEDYGELGMKLSEIPLTLHSVSELVRLCLRRC   700
 701  DVQEDSEGSETDDNKDSTPFEDNEVQDEFLEKLETSEFFELTSEEKLRIL   750
 751  TALCHRILMTYSVQDHMETRQQVSAELWKERLAVLKEENDKKRAEKQKRK   800
 801  EMEARNKENGKEENVLGKVDRKKEIVKIEQQVEVEADDMISAVKSRRLLS   850
 851  MQAKRKREIQERETKVRLEREAEEERMRKHKAAAEKAFQEGIAKAKLVLR   900
 901  RTPIGTDRNHNRYWLFSNEVPGLFIEKGWVHNSIDYRFKHHRKDHSNLPD   950
 951  DDYCPRSKKANLGKNASVNAHHGPALEAVETTVPKQGQNLWFLCDSQKEL  1000
1001  DELLSCLHPQGIRESQLKERLEKRYQEITHSIYLARKPNLGLKSCDGNQE  1050
1051  LLNFLRSDLIEVATRLQKGGLGYMEGTSEFEARVISLEKLKDFGECVIAL  1100
1101  QASVIKKFLQGFMAPKQKKRKLQSEDSTKSEEVDEEKKMVEEAKVASALE  1150
1151  KWKTAIREAQTFSRMHVLLGMLDACIKWDMSAENARCKVCRKKGEDDKLI  1200
1201  LCDECNKAFHLFCLRPALYEVPDGEWQCPACQPPTARRNSRGRNYTEEST  1250
1251  SEGSEGDESGEEEEEEEEEEEEEEDYEVAGLRLRPRKTIRGKQSVIPAAR  1300
1301  PGRPPGKKSHPARRSRPKDDPEVDDLVLQTKRISRRQSLELQKCEDILHK  1350
1351  LVKYRFSWPFREPVTRDEAEDYYDVIEHPMDFQTIQNKCSCGNYRSVQEF  1400
1401  LTDMKQVFANAELYNCRGSHVLSCMEKTEQCLLALLQKHLPGHPYVRRKR  1450
1451  RKFPDRLADDEGDSDSESVGQSRGRRQKK                       1479

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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