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

NucPred

Fetching Q5S2C4 from www.uniprot.org...

The NucPred score for your sequence is 0.64 (see score help below)

   1  MANSRQYYPSQDESMSPTSVRSREWEGPSRWTEYLGPEMAASVSSTRSSK    50
  51  QIDGHVGGSTKALNIQWVVQMIEVADGLMAKMYRLNQILEYPDPVGHVFS   100
 101  EAFWKAGVFPNHPRICTLLSKKFPEHFSKLQLERIDKFSLDSLHDGAELH   150
 151  LQSLEPWIQLLLDLMAFREQALRLILDLSSTVITLLPHQNSLILHAFMDL   200
 201  FCAFVRVNLFAEKIPRKMLLQVYNLLHALSRNDRDCDFYHRLVQFIDSYD   250
 251  PPLKGLQEDLNFVSPRIGEVLEAVGPSIFLSADTRKLRNEGFLSPYHPRF   300
 301  PDILTNSAHPMRAQDLANVTSYREWVLLGYLVCPDELLRVTSIDIALVVL   350
 351  KENLVVTLFRDEVSLYQMVCEKEFGIGISFASADSINLTMQYILLHEDYQ   400
 401  LYVLPRVLESKKMAKSGRTKQKEADLEYSVAKQVEKMISEVHEQALQLCD   450
 451  TIHRERRILLKQEIGRMVLFFTDQPSLLAPNIQMVFSALALAQSEVLWYF   500
 501  QHAGIASSRSKAARVIPVDIDPNDPTIGFLLDGMDRLCCLVRKYISAARG   550
 551  YALSYLSSSAGRIRYLMGTPGIVALDLDPTLKGLFQRIVQHLESIPKAQG   600
 601  ENVSAITCDLSDFRKDWLSILMIVTSSRSSINIRHLEKATVSTGKEGLLS   650
 651  EGNAAYNWSRCVDELESQLSKHGSLKKLYFYHQHLTTVFRNTMFGPEGRP   700
 701  QHCCAWLSVASSFPECASLIIPEEVTKFGRDAVLYVESLIESIMGGLEGL   750
 751  INILDSEGGFGALESQLLPEQAAAYLNNASRISAPSVKSPRVVGGFTLPG   800
 801  HESYPENNKSIKMLEAAIQRLTNLCSILNDMEPICVINHVFVLREYMREC   850
 851  ILGNFKRRFLTALQTDNDLQRPSVLESLIRRHMGIVHLAEQHVSMDLTQG   900
 901  IREILLTEAFSGPVSSLHTFEKPAEQQQTTGSAVEVVCNWYMDNIIKDVS   950
 951  GAGILFAPRHKYFKSTRPVGGYFAESVTDLKELQAFVRIFGGYGVDRLDR  1000
1001  MMKVHTAALVNCIETSLRSNRELIEAAAASMHSGDRVERDASVRQIVDLD  1050
1051  TVIGFCIEAGQALAFDDLLAEASGAVLEDNASLIHSMISGIVEHIPEEIP  1100
1101  EKKEIRRIKGVANGVGVAGDHDSEWVRLILEEVGGANDNSWSLLPYFFAS  1150
1151  FMTSNAWNTTGFNIETGGFSNNIHCLARCISAVIAGSEYVRLQREYQQQH  1200
1201  QSLSNGHHSSENLDSEFPPRVTAEASIKSSMLLFVKFAASIVLDSWSEAN  1250
1251  RSHLVAKLIFLDQLCEISPYLPRSSLESHVPYTILRSIYTQYYSNTPSTP  1300
1301  LSTASPYHSPSVSLIHASPSMKNSTTPQRGSGSGSSSTAAPDSGYFKGSS  1350
1351  SSLYGQEHYTESETGNSRNNENNNNNKQRGSSRRSGPLDYSSSHKGGSGS  1400
1401  NSTGPSPLPRFAVSRSGPISYKQHN                           1425

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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