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

NucPred

Fetching Q9JL70 from www.uniprot.org...

The NucPred score for your sequence is 0.76 (see score help below)

   1  MPGSPARGAAMGGGPRGLRKTWTELLAGRVKKQKYDPEREQKLKDSALKL    50
  51  LRYHQNMHDLLLEVEEPQCKRLRLSELIDRDSADASSDRSASFIRSAFRD   100
 101  QASRLGVPVGVLSAKVFARSVQQVCVEPSHPVLLSPEQSKKLSSLLMIAR   150
 151  HLLAQNMFSRLTFCQELWKAQNSLLLEAMWRLHTHSVVSLQELLQSHPDS   200
 201  EAMAMWLFRNLRSLCEQIGASCPSPDTTEAMLSGLVQLLISRGFQGSSDP   250
 251  RRLVEPERLPQVATDVLQRMLAFSLDTLEADPQTTLDCQAVSGWIPIYSG   300
 301  HTCCGVVTENSLKSFFSHTLTQILTHKPVLKVSDAIQMQKEWSFAKTHHL   350
 351  LTDLHCRVLATLGPEESVGRLQEVLEMQEVNWQHVLSCVSTLVVCFPEAQ   400
 401  QLVKGWVASLMARAFESYHLDSMVTAFLIVRQATLEGPYVFPSYADWFKE   450
 451  SFGSSHGYHSCSKKTLVFLFKFLSDLVPWEAPRYMQVHIFHPPLVPSKYH   500
 501  SLLTDYISLAKTRLADLKVSLENVGLYEDLSSPGDIAERESQAVQDVKKA   550
 551  IMVFEQTGKIPMPVLEASIFRRPYYVSHFLPTLLAPRVLPEVPDPRVALI   600
 601  ETLKRADKIPSSIYDAYRKACASAEKQQPENATSAQRTEADCAKEPLGLL   650
 651  TAALEELRALMTDPTQYSVISAQVAVVSEKLNAVLGHRNDGGSLQRAKIQ   700
 701  LSVLPSTLQKQDQAVVDLLLTAFCQNLMAASSFVPPERQSPWAVLFVRTL   750
 751  CGHVLLPAVLTRLRQLLRHQGQSLSTSHVLGLAALAVHLGECRSMLPEVD   800
 801  PDVLAPSAGSLCVPDFLNSLLTCRTRDSLLFCMNFCTAAVSYCLCKFSAL   850
 851  RNCLSPGLIKKFQFVVLRLFPEARAPCAPEHAACVPWRPLYLPSADWQRA   900
 901  ALSLWRRDSFQELLKDKEFYLTYRDWVQLELEIQPEADVLSDMERHDFHQ   950
 951  WAIYERYLPAPTALGGCGGDLEEACTVLVSEIMDFHQSSRSYNHSEDSDL  1000
1001  VLGGRTGNKDILSRLQEIALDLELDQGSAVPHGCSTPQSHFLFRVFRRRL  1050
1051  QALARPDSMATSLRRQQELLTCKRLLLCLPPSVLVGGPQAGQPISPNCGE  1100
1101  FFSLVNSELRNFCCHGSVLTSDITIHFFRGLLRVCLRSQDPALVANQTLT  1150
1151  ECQTKCPVILTSALLWWSSLEPVLCGRWMRCYQSPLPRELRRLQEAREFA  1200
1201  SNFASASASPAPSPAWIAAAALHFAWRGVRKEDVTAHLQRLDCQREELLI  1250
1251  ALFFFSLMGLLSSYLTQRDTAEHLKAVDICAEVLTCLERRKVSWLVLFQL  1300
1301  TEKDAKLGHLLHLAPDQHTRLLPLAFYSLLSCFSEGAAVREAAFLHVAVD  1350
1351  MYLKLLQLFVDGETRLQGHSESQGSPVQLITKARVFLLQLIPQCPKQCFS  1400
1401  NMTELLAGRGDCDPEVSNALRQRQQADPSFDLYQEPQLF             1439

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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