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

NucPred

Fetching Q9W705 from www.uniprot.org...

The NucPred score for your sequence is 0.96 (see score help below)

   1  MGENLSDPSRAEPRKRKESLDQLGPSPKRSTEKRNREQENKYIEELAELI    50
  51  FANFNDIDNLNFKPDKCAILKETVKQIRQIKEHEKTAAANEDEVQKADVS   100
 101  STGQSVIDKDALGPMMLEALDGFFFVVNREGNVVFVSENVTQYLRYNQEE   150
 151  LMNTSVYSILHVGDHSEFIKNLLPKSLVNGVPRRNSHTFNCRMLVKPMME   200
 201  CEEERHDGQETHQKYESMQCFAVSQPKSIKEEGEDFQSCLICVARRVPVK   250
 251  ERPVPPPSESFTTRQDFQGKITSLDTTSMRALMRPGWEDMVRRCIQRFHS   300
 301  QHDGEISYSRRHHQEVLRQGHATSPFYRFSLSDGTTVVAQTKSRLMRSQT   350
 351  NNEPPLVLSLHVLQREQNVCGLNQDLAGQAMGKTLNPVQSSSPAHQAMYG   400
 401  GNPGQDTTISSNMNYAISGPKEQMGLATGRFVGSGGMNHISSLQATTPQG   450
 451  NNYALKMNSPSHGSPGMGQGQPNSMLSPRHRVSPGVAGSPRIAPSPFSPA   500
 501  GSLHSPVSVCSSTGNSHSYTNSSLNALQALSEGQGPLAPPLSSPDLKGGN   550
 551  LQHSPGNMNPPQLRKMGSIDSKESFGLYEEQPESATGQGESGCHSNEQKD   600
 601  CGENLSSVVDKTEGQSRLLDGKGQQKLLKLLTTKSDQMEPSTLPSNTLGD   650
 651  MNKDSLSNFASNSMSASAHGTSLKEKHKILHRLLQDSSSPVDLAKLTAEA   700
 701  TGKELSQESNSTGPGSEVTIKQEPVSPKKKEHALLRYLLDKDDTTDNVAD   750
 751  ITPKLERADNKVDPSSCPKLSAVKAEKEEPNFGHTDQPGSDFDNLDEILD   800
 801  DLQNSQLSQLFSDTRHDGNSADKQAIMNDLMQLAGENSTGLPAWAQKQRM   850
 851  LRMQQNNGFNSQLAAQLGRLPNQNLPLDIHFQSQASAGSFAQMRSSGPYT   900
 901  TVPQSGVINNQAMMGSQGNVRNSSPGIVGVNGPRPPLKPGDWGSQASAVR   950
 951  PACPTTSTAMNRHDMSRSPTASIPMRPGSQVCPRQVLQSAVMNMGSSELD  1000
1001  MNISGPQYTQQQAPPNQTAPWPNRILTIEQPSFNNQNRQPFGSPADDLIC  1050
1051  QPIVSESPADDGNLLDQLYMALRNFDGLEEIDRALGIPEMVSQGQAVEQE  1100
1101  SFGSPESNLMMEQKPPVYNHAYANQGQMAQNSYQPMQDPGFNPMGQRPSY  1150
1151  GILRMQNRPGLRPTGMVQNQPNQLRLQLQHRLQAQNRQQLMNPINNVSNM  1200
1201  NLAMRPGVPGQLREQGPINAQMLAQRQREILSQHLRQKQLQQQQQQQQQQ  1250
1251  QQQQQQQQQQQQQQQQQQQQQQQHRAMMMRSQGLAMPPNMVGSGGIPASI  1300
1301  NSPRIPQGSTQQFPFPPNYGTGIPSPPPFTSPFSPVPPSPGSQSLSHSSL  1350
1351  HGSQMNLANQGIMGSMGGQYGPVMNPQMQHNAFQFANSGMSQQSDPGFTG  1400
1401  ATTPQSPIMSPRMGHIQSSMMQQSQANPAYQSELNGWAQGNPAGNSMFSQ  1450
1451  QSPPHFGQQSGTSMYNSNNMNISVSMAANGNGMNNMNQMTGQINMTSVTS  1500
1501  VPTSGLSSMGPEQKYC                                    1516

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.)

Go back to the NucPred Home Page.