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

NucPred

Fetching Q12451 from www.uniprot.org...

The NucPred score for your sequence is 0.95 (see score help below)

   1  MSREDLSIAEDLNQVSKPLLKVKLLEVLGQGDFKHLKALVDNEFQPKDDP    50
  51  SVQQVLNLILHYAVQVAPILLIKEIVAHWVDQVGDEKSSSKSDDGIHLDL   100
 101  NYQDENGNTPLHLAAAQSRSDVISFLLSQKSINDCVKNKAHQQPLDMCKD   150
 151  LNVAQMIQLKRDDYFLETVHSLRAAMNKRDFSKLDSIWKNPRNLNLLDIN   200
 201  GIDPETGTTLLYEYSQKKDIEMCQWLLKHGAEATVKDGKGRSPLDLVKNI   250
 251  KLPAKPSNNVTPEIKLKNLLEKNLREQAIVHEDVASSKPPTYKGFLKKWT   300
 301  NFAHGYKLRWFILSGDGNLSYYKDQSHVDRPRGTLKVSTCRLHIDSSEKL   350
 351  NFELLGGITGTTRWRLKGNHPIETTRWVNAIQSAIRFAKDKEILNKKKAV   400
 401  PPSLALKNKSPALISHSKTQGSLPEASQYYQHTLHKEVIQPSSVSLYRRP   450
 451  SNNLSVVSSEIQLNDNLTESGKRFVSKMIENRLDGSKTPVGVHTGSALQR   500
 501  VRSSNTLKSNRSMQSGSGVASPIDKVPNGANLSQSNTTTGSTASLSDNNY   550
 551  IDNFEGDEANSDDEEEDLGINFDRDEEYIKAQYGPYKEKLDMYEQAISIE   600
 601  LSSLIELIEQEEPSPEVWLTIKKSLINTSTIFGKLKDLTYKRDKRLVDMV   650
 651  SKQGDVNNVWVQSVKELEMELSNKTERLASIDKERRGLKKILHKKLLESH   700
 701  ATAGNKESLENDKEQESDTTASTLGQIAKFISATKEEDEASDADEFYDAA   750
 751  ELVDEVTELTEAHPEISTAAAPKHAPPPVPNETDNDSQYVQDEKSKIESN   800
 801  VEKTSQKFEKQNNLVTEDEPKTDQSLKNFKAEDKESQVKEKTKEIASSVI   850
 851  GEKTIVAVTTVQKRKEEYLLKEGSYLGYEDGIRKRLSMDKDDRPKISLWA   900
 901  VLKSMVGKDMTRMTLPVTFNEPTSLLQRVAEDLEYSELLDQAATFEDSTL   950
 951  RTLYVAAFTASSYASTTKRVAKPFNPLLGETFEYSRPDKQYRFFTEQVSH  1000
1001  HPPISATWTESPRWDFWGESFVDTKFNGRSFNVKHLGLWHIKLRPNDNEK  1050
1051  EELYTWKKPNNTVIGILIGNPQVDNHGEVNVVNHTTGDHCKLYFKARGWR  1100
1101  SSGAYEITGEVYNKKKQKVWILGGHWNEAIFAKKVVKDGDLSLEKTRTAA  1150
1151  SAGNGPTDDGTKFLIWKANDRPEEPFNLTPFAITLNAPQPHLLPWLPPTD  1200
1201  TRLRPDQRAMEDGRYDEAGDEKFRVEEKQRAARRKREENNLEYHPQWFVR  1250
1251  DTHPITKAKYWRYTGKYWVKRRDHDLKDCGDIF                   1283

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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