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

NucPred

Fetching Q7TPV4 from www.uniprot.org...

The NucPred score for your sequence is 0.99 (see score help below)

   1  MAEMKSPTKAEPATPAEAAQSDRHSLLEHSREFLDFFWDIAKPDQETRLR    50
  51  ATEKLLEYLRTRPNDSEMKYALKRLITGLGVGREAARPCYSLALAQLLQS   100
 101  FEDIPLCDILDQIQEKYSLQAMNKAMMRPSLFANLFGVLALFQSGRLVKD   150
 151  KEALMKSVQLLKILSQHPNHLQGQPIKALVDILSEVPESMFQEILPKVLK   200
 201  GNMKVILRSPKYLELFLLAKQRVPTKLESLMGSVDLFSEDNIPSLVNILK   250
 251  VAANSVKKEHKLPNVALDLLRLALKESRFELFWKKVLEEGLLKNPSWTSS   300
 301  YMCFRLLGASLPLLSEEQLQLVMRGDLIRHFGENMVISKPQNLFKIIPEI   350
 351  STYVGTFLEGCQDDPKRQLTMMVAFTTITNQGLPVMPTFWRVTRFLNAEA   400
 401  LQSYVAWLRDMFLQPDLNSLVDFSTANQKRAQDASLNVPERAVFRLRKWI   450
 451  IHRLVSLVDHLHLEKDEAVVEQIARFCLFHAFFKTKKATPQIPETKQHFS   500
 501  FPLDDRNRGVFVSAFFSLLQTLSVKFRQTPDLAENGKPWTYRLVQLADML   550
 551  LNHNRNVTSVTSLTTQQRQAWDQMMSTLKELEARSSETRAIAFQHLLLLV   600
 601  GLHIFKSPAESCDVLGDIQTCIKKSMEQNPRRSRSRAKASQEPVWVEVMV   650
 651  EILLSLLAQPSNLMRQVVRSVFGHICPHLTPRCLQLILAVLSPVTNEDED   700
 701  DNVVVTDDADEKQLQHGEDEDSDNEDNKNSESDMDSEDGEESEEEDRDKD   750
 751  VDPGFRQQLMEVLKAGNALGGVDNEEEEELGDEAMMALDQNLASLFKEQK   800
 801  MRIQARNEEKNKLQKEKKLRRDFQIRALDLIEVLVTKQPEHPLILELLEP   850
 851  LLNVIQHSMRSKGSTKQEQDLLHKTARIFMHHLCRARRYCHEVGPCAEAL   900
 901  HAQVERLVQQAGSQADASVALYYFNASLYLLRVLKGNTNKRHQDGHKLHG   950
 951  ADTEDSEDQAANCLDLDFVTRVYSASLESLLTKRNSSLTVPMFLSLFSRY  1000
1001  PVICKNLLPVLAQHVAGPSRPRHQAQACLMLQKTLSARELRVCFEDPEWE  1050
1051  QLITQLLGKATQTLQTLGEAQSKGEHQKELSILELLNTLLRTVNHEKLSV  1100
1101  DLTAPLGVLQSKQQKLQQSLQQGNHSSGSNRLYDLYWQAMRMLGVQRPKS  1150
1151  EKKNAKDIPSDTQSPVSTKRKKKGFLPETKKRKKLKSEGTTPEKNAASQQ  1200
1201  DAVTEGAMPAATGKDQPPSTGKKKRKRVKASTPSQVNGITGAKSPAPSNP  1250
1251  TLSPSTPAKTPKLQKKKEKLSQVNGATPVSPIEPESKKHHQEALSTKEVI  1300
1301  RKSPHPQSALPKKRARLSLVSRSPSLLQSGVKKRRVASRRVQTP        1344

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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