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

NucPred

Fetching Q9HGN1 from www.uniprot.org...

The NucPred score for your sequence is 0.94 (see score help below)

   1  MDAAKRLELCKEIQENEIEALKAIFMDDFEELKVRNAWNVTNGHVYCIHL    50
  51  CSRSANSKSIAKLDLCIELGRSYPYVKPVIKLQNGENVLNSQIRFLLDKL   100
 101  DTKAKDLLGEEMIFELASIVQDYLNDWQSDLSSQFASLEEERAVQLKHDR   150
 151  ERAEVDLQLRLKREKDALFEEEQTLQNKIQDELQRRSYETPQSSSKKKTN   200
 201  SKETTSLETLPTSIYFDCSISVRDCHDSLVTFNRVLPLYTISHSNLSTLT   250
 251  LVKPESKEISLQDCVFLLRTVRISTPYWSTEDGKREIQELEYELESLKVI   300
 301  RHDLLASIYEYQLERETRGYGWRLYVLQEYSPKFTLFSLLQTVLTLDVET   350
 351  VRAFSNNILEGLAELHRLGISHKSLHLDNVVLFHSGHRTFAKLMDFGFTR   400
 401  TLRDMNASHPFNINSQSITNILPEGLYPPEVSESSFAAASRKTDIWCFGL   450
 451  LVLQMLCGAHVLNKFSSLKLIMTHVIPLLPGSYQDLVRRCLMRDSRKRPS   500
 501  AIDLLSSHVIRLGTAVLPPVEQGTFSKSARPSYGGQQDGIIDLLYRKSVS   550
 551  RYETDFEELEFLGRGGFGEVVKVKNRIDGRFYAVKKLVLLSDDKENSRIL   600
 601  REVMTLSRLHHEHVVRYYTAWVETEANDTVTEIISSDSESLSQSLNMAVD   650
 651  FRQSSSLPADKLSSLDIHFEDDYNSSADEEDPEASDISFQYSNTSDKEGS   700
 701  SDKDSSIEEASSVKTQENGLNATLYIQMEYCEKLSLQDIIRDKIPVDEMW   750
 751  RLFRQILEALAYIHSRGMMHRDLKPGNIFLDENRNVKLGDFGLATENENY   800
 801  QDNNDKWKNRQSADEDLTTGVGTALYVAPELLSRRNGVRYDAKVDMYSLG   850
 851  IILFEMCMTFSTSMERIRIIDTIRSPSISFPSTFPFSRASHEFKVIHCLL   900
 901  QHDPTKRPSSQELLESEAIPPKVGEEFIQEGLRLLSNPNTPYYLKLLKVL   950
 951  FGQVPDRHKDFTYDFNLSEESGVLSKVSDRGWDSLLACLVRDHVVKVFRR  1000
1001  HGAKERESHILFPKSSQYDKDQASVSLLDKNGTLLQLPYDTVLPYARNVA  1050
1051  RNAVEEEKTYLISDVFREAKGGGRPKAIKEISFDITTNSDNLDWYDAETI  1100
1101  KALDEVLTEIPSLTESCILINHADILSSILDYLQVSKDKRRMATHILGQI  1150
1151  NQRLTLSQVRNQLRIESLVPSTTLDDLSLFDFRENYEEGASKLRKIFGKE  1200
1201  MPQKMRTALNYMERVVKLLRALKISHQLYFMPLCVYNFEFYDGGLMFQAI  1250
1251  NLAEKSELICAGGRYDKLVRFFDPPLMRTARKKHVVGICFALEKLVFSML  1300
1301  RYIRFHNSKQSSKHSPSPTLKSVGPWAPRRVDVLVTSIGKDSILEKCSLL  1350
1351  QELWALNIQADIVLRGASSLEEIVTHYRSEGINWVLVVRQKNTQMEHSVK  1400
1401  ARNILKNEDDEIRFDEVGMWLLGEINERKRNESMLQSKRILDSAQQDVAK  1450
1451  FVDTSQSNLDVQLISLKDVNDRKYKWKHKQNAMNKVYDLVQSAIRESSED  1500
1501  AIALAVDCDSEAMEKLRSTTTLDEESWKRLIESCPASQREYMQRLQKKLV  1550
1551  TLAEQDKKRVWICSFRTNEIYLYGLK                          1576

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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