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

NucPred

Fetching P40798 from www.uniprot.org...

The NucPred score for your sequence is 0.98 (see score help below)

   1  MAEYWQQLTNGAGEAGPGNESSAMADCNGGHESAAVGGSCNRHSNNNYVN    50
  51  FNQFIMQHNLGGGAPSNATSTMQHPVGSSYTNFSLGGGGGAFGLNPPVAS   100
 101  ASTSHFANVSHQSPNFYSQAMIPTYQNGDGIARVTVTSSYGSVNPSNSNF   150
 151  SSFYTPFGNNPFDFSASKLQASAPEFVPNFAKLSLEETPAAATTNGNSTA   200
 201  SLETAINETRPRTLRAQEPAERGANNQCSNHNYERERERERDRDRDRERD   250
 251  RDRDRDRDRDRDRDRDRDSRPGNTRQQRRSDYRDDREDRYERSDRRRPQK   300
 301  QQRYDNHRSNKRRDDWNRNRDRINGFPRAVDDLDTSNESAHPSPEKQSQL   350
 351  QQISPRRGPPLPPADNEKLSQREKLVRDIEQRRLECLVCVEAIKSHQPTW   400
 401  SCRNCYHMLHLKCTITWASSSKSEVGWRCPACQNVLQDLPRDYLCFCGKL   450
 451  KNPPVSRTELAHSCGEVCCRIEGCSHACTLLCHPGPCPPCQANVVRSCGC   500
 501  GRSTKTMQCAMKEEVLCGEICDKLLNCGEHRCQAECHSGKCAACSEQVVQ   550
 551  QCHCGKQERKVPCTRESQDKRTYSCKDSCGQPLPCGHHKCKDSCHAGSCR   600
 601  PCKLSPEQITSCPCGKMPVPAGQRSSCLDPIPTCEGICSRTLRCGKPAHP   650
 651  HQCGSKCHLGQCPPCPKQTGVKCRCGHMDQMIKCRQLCNRADDARCKRRC   700
 701  TKKRSCGKHKCNVECCIDIDHDCPLPCNRTLSCGKHKCDQPCHRGNCPPC   750
 751  YRSSFEELYCECGAEVIYPPVPCGTKKPICKLPCSRIHPCDHPPQHNCHS   800
 801  GPTCPPCMIFTTKLCHGNHELRKTIPCSQPNFSCGMACGKPLPCGGHKCI   850
 851  KPCHEGPCQSAGEICRQSCTKPRPTCGHKCAAACHEGACPETPCKELVEV   900
 901  QCECGNRKQNRSCQELAREHSRIATIQLASSMAEMSRGNYMELSEILAPA   950
 951  KKSNKTLDCNDECRLLERNRRLAAALSSGNSDTKQKCLTKYSEFVRGFAK  1000
1001  KNPALTKSVYETLTDLVKLAKESKQRSRSHSFPTMNREKRQLVHELCEVF  1050
1051  GIESVSYDKEPNRNVVATAHKDRCWFPATSIMEVLARESGQRRVPVPSNN  1100
1101  AWGLKK                                              1106

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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