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

NucPred

Fetching Q8CHE4 from www.uniprot.org...

The NucPred score for your sequence is 0.91 (see score help below)

   1  MEPAAAAPAQRLADPTGEDQALAAAAAEGGRCPDPALSAAAPSGGNGGAA    50
  51  REEAPCEAPPGPLPGRAGGTGRRRRRGAPQPAAGGAAPVPAAGGGANSLL   100
 101  LKRGRLKRNLSAAAAASSSSSPSSASSAAGGLPASCSASASLCTRSLDRK   150
 151  TLLLKHRQLLQLQPSDRDWVRHQLQRGCVHVFDRHMASSYLRPVLCTLDT   200
 201  TAAEVAARLLQLGHKGGGVVKVLGYGPPPAAAPAASDQTLDGEHGRDVEP   250
 251  PPSSGTVGAVRGPARAPPADLPLPGGAWTRCAPRISPAPSDSSPGELFAG   300
 301  GPGSPPRAPRPASDTESFSLSPSAESVSDRLDPYSSGGGGSSSSSEELEA   350
 351  DPAMPHRPGRPAQPRPPSPKTSALLQPKAPTGVDSTGVIAGEGPGDDKAM   400
 401  AAAAPDVPLSTSGRIRETVQKTSPPSLYVQLHGETTRRLEADEKPLQIQN   450
 451  DYLFQLGFGELWRVQEEGMDSEIGCLIRFYAGKPHSTGSSERIQLSGMYN   500
 501  VRKGKMQLPVNRWTRRQVILCGTCLIVSSVKDSVSGKMHVLPLIGGKVEE   550
 551  VKKHQHCLAFSSSGPQSQTYYICFDTFTEYLRWLRQVSKVASQRISSVDL   600
 601  SCCSLEHLPANLFYSQDLTHLNLKQNFLRQTPTLPAARGLGELQRFTKLK   650
 651  SLNLSNNHLGAFPSAVCSIPTLAELNVSCNALREVPAAVGDMQNLQTFLL   700
 701  DGNFLQSLPAELESMHQLSYLGLSFNEFTDIPEVLEKLTAVDKLCMAGNC   750
 751  VETLRLQALRRMPHIKHVDLRLNILRKLMADEVDFVQHVTQLDLRDNKLG   800
 801  DLDAMIFNNIEVLHCERNQLVTLNVCGYFLKALYASSNELAQLDVYPVPN   850
 851  YLSYMDVSRNCLESVPEWVCESRKLEVLDIGHNQICELPARLFCNSSLRK   900
 901  LLAGHNRLARLPERLERTSVEVLDVQHNQITELPPNLLMKADSLRFLNAS   950
 951  ANKLETLPPATLSEETSSILQELYLTNNCLTDKCVPLLTGHPRLKILHMA  1000
1001  YNRLQSFPASKMAKLEELEEIDISGNKLKAIPTTIMNCRRMHTVIAHSNC  1050
1051  IEVFPEVMQLPEVKCVDLSCNELSEITLPENLPPKLQELDLTGNPRLALD  1100
1101  HKSLELLNNIRCFKIDQPSAGDASGAPAVWSHGYTEASGVKNKLCVAALS  1150
1151  VNNFRDNREALYGVFDGDRNVEVPYLLQCTMSDILAEELQKTKNEEEYMV  1200
1201  NTFIVMQRKLGTAGQKLGGAAVLCHIKPDPVDLGGSFTLTSANVGKCQTV  1250
1251  LCRNGKPLSLSRSYIMSCEEERKRIKQHKAIITEDGKVNGVTESTRILGY  1300
1301  TFLHPSVVPRPHVQSVLLTPQDEFFILGSKGLWDSLSIDEAVEAVRNVPD  1350
1351  ALAAAKKLCTLAQSYGCHDSISAVVVQLSVTEDSFCCCELSAGGSMPPPS  1400
1401  PGIFPPSVNMVIKDRPSDGLGVPSSSSGMASEISSELSTSEMSSEVGSTA  1450
1451  SDEPPSGVLNESSPAYPNEQRCMLHPVCLSNSFQRQLSSATFSSAFSDNG  1500
1501  LDSDDEEPIEGVFSNGSRVEVEVDIHCSRAKEKERQQHLLQVPAEASDEG  1550
1551  IVISANEDESGLSKKADFSAVGTIGRRRANGSVAPQERSHNVIEVAADAP  1600
1601  LRKPGGYFAAPAQPDPDDQFIIPPELEEEVKEIMKHHQEQQQQQQQQQLP  1650
1651  PPPQPPQPQPQPQPQPQPQPQRHFQMDHLPDCYDTPL               1687

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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