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

NucPred

Fetching Q9BX66 from www.uniprot.org...

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

   1  MSSECDGGSKAVMNGLAPGSNGQDKATADPLRARSISAVKIIPVKTVKNA    50
  51  SGLVLPTDMDLTKICTGKGAVTLRASSSYRETPSSSPASPQETRQHESKP   100
 101  GLEPEPSSADEWRLSSSADANGNAQPSSLAAKGYRSVHPNLPSDKSQDAT   150
 151  SSSAAQPEVIVVPLYLVNTDRGQEGTARPPTPLGPLGCVPTIPATASAAS   200
 201  PLTFPTLDDFIPPHLQRWPHHSQPARASGSFAPISQTPPSFSPPPPLVPP   250
 251  APEDLRRVSEPDLTGAVSSTDSSPLLNEVSSSLIGTDSQAFPSVSKPSSA   300
 301  YPSTTIVNPTIVLLQHNREQQKRLSSLSDPVSERRVGEQDSAPTQEKPTS   350
 351  PGKAIEKRAKDDSRRVVKSTQDLSDVSMDEVGIPLRNTERSKDWYKTMFK   400
 401  QIHKLNRDTPEENPYFPTYKFPELPEIQQTSEEDNPYTPTYQFPASTPSP   450
 451  KSEDDDSDLYSPRYSFSEDTKSPLSVPRSKSEMSYIDGEKVVKRSATLPL   500
 501  PARSSSLKSSSERNDWEPPDKKVDTRKYRAEPKSIYEYQPGKSSVLTNEK   550
 551  MSRDISPEEIDLKNEPWYKFFSELEFGKPPPKKIWDYTPGDCSILPREDR   600
 601  KTNLDKDLSLCQTELEADLEKMETLNKAPSANVPQSSAISPTPEISSETP   650
 651  GYIYSSNFHAVKRESDGAPGDLTSLENERQIYKSVLEGGDIPLQGLSGLK   700
 701  RPSSSASTKDSESPRHFIPADYLESTEEFIRRRHDDKEKLLADQRRLKRE   750
 751  QEEADIAARRHTGVIPTHHQFITNERFGDLLNIDDTAKRKSGSEMRPARA   800
 801  KFDFKAQTLKELPLQKGDIVYIYKQIDQNWYEGEHHGRVGIFPRTYIELL   850
 851  PPAEKAQPKKLTPVQVLEYGEAIAKFNFNGDTQVEMSFRKGERITLLRQV   900
 901  DENWYEGRIPGTSRQGIFPITYVDVIKRPLVKNPVDYMDLPFSSSPSRSA   950
 951  TASPQFSSHSKLITPAPSSLPHSRRALSPEMHAVTSEWISLTVGVPGRRS  1000
1001  LALTPPLPPLPEASIYNTDHLALSPRASPSLSLSLPHLSWSDRPTPRSVA  1050
1051  SPLALPSPHKTYSLAPTSQASLHMNGDGGVHTPSSGIHQDSFLQLPLGSS  1100
1101  DSVISQLSDAFSSQSKRQPWREESGQYERKAERGAGERGPGGPKISKKSC  1150
1151  LKPSDVVRCLSTEQRLSDLNTPEESRPGKPLGSAFPGSEAEQTERHRGGE  1200
1201  QAGRKAARRGGSQQPQAQQRRVTPDRSQTSQDLFSYQALYSYIPQNDDEL  1250
1251  ELRDGDIVDVMEKCDDGWFVGTSRRTKQFGTFPGNYVKPLYL          1292

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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