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

NucPred

Fetching P22147 from www.uniprot.org...

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

   1  MGIPKFFRYISERWPMILQLIEGTQIPEFDNLYLDMNSILHNCTHGNDDD    50
  51  VTKRLTEEEVFAKICTYIDHLFQTIKPKKIFYMAIDGVAPRAKMNQQRAR   100
 101  RFRTAMDAEKALKKAIENGDEIPKGEPFDSNSITPGTEFMAKLTKNLQYF   150
 151  IHDKISNDSKWREVQIIFSGHEVPGEGEHKIMNFIRHLKSQKDFNQNTRH   200
 201  CIYGLDADLIMLGLSTHGPHFALLREEVTFGRRNSEKKSLEHQNFYLLHL   250
 251  SLLREYMELEFKEIADEMQFEYNFERILDDFILVMFVIGNDFLPNLPDLH   300
 301  LNKGAFPVLLQTFKEALLHTDGYINEHGKINLKRLGVWLNYLSQFELLNF   350
 351  EKDDIDVEWFNKQLENISLEGERKRQRVGKKLLVKQQKKLIGSIKPWLME   400
 401  QLQEKLSPDLPDEEIPTLELPKDLDMKDHLEFLKEFAFDLGLFITHSKSK   450
 451  GSYSLKMDLDSINPDETEEEFQNRVNSIRKTIKKYQNAIIVEDKEELETE   500
 501  KTIYNERFERWKHEYYHDKLKFTTDSEEKVRDLAKDYVEGLQWVLYYYYR   550
 551  GCPSWSWYYPHHYAPRISDLAKGLDQDIEFDLSKPFTPFQQLMAVLPERS   600
 601  KNLIPPAFRPLMYDEQSPIHDFYPAEVQLDKNGKTADWEAVVLISFVDEK   650
 651  RLIEAMQPYLRKLSPEEKTRNQFGKDLIYSFNPQVDNLYKSPLGGIFSDI   700
 701  EHNHCVEKEYITIPLDSSEIRYGLLPNAKLGAEMLAGFPTLLSLPFTSSL   750
 751  EYNETMVFQQPSKQQSMVLQITDIYKTNNVTLEDFSKRHLNKVIYTRWPY   800
 801  LRESKLVSLTDGKTIYEYQESNDKKKFGFITKPAETQDKKLFNSLKNSML   850
 851  RMYAKQKAVKIGPMEAIATVFPVTGLVRDSDGGYIKTFSPTPDYYPLQLV   900
 901  VESVVNEDERYKERGPIPIEEEFPLNSKVIFLGDYAYGGETTIDGYSSDR   950
 951  RLKITVEKKFLDSEPTIGKERLQMDHQAVKYYPSYIVSKNMHLHPLFLSK  1000
1001  ITSKFMITDATGKHINVGIPVKFEARHQKVLGYARRNPRGWEYSNLTLNL  1050
1051  LKEYRQTFPDFFFRLSKVGNDIPVLEDLFPDTSTKDAMNLLDGIKQWLKY  1100
1101  VSSKFIAVSLESDSLTKTSIAAVEDHIMKYAANIEGHERKQLAKVPREAV  1150
1151  LNPRSSFALLRSQKFDLGDRVVYIQDSGKVPIFSKGTVVGYTTLSSSLSI  1200
1201  QVLFDHEIVAGNNFGGRLRTNRGLGLDASFLLNITNRQFIYHSKASKKAL  1250
1251  EKKKQSNNRNNNTKTAHKTPSKQQSEEKLRKERAHDLLNFIKKDTNEKNS  1300
1301  ESVDNKSMGSQKDSKPAKKVLLKRPAQKSSENVQVDLANFEKAPLDNPTV  1350
1351  AGSIFNAVANQYSDGIGSNLNIPTPPHPMNVVGGPIPGANDVADVGLPYN  1400
1401  IPPGFMTHPNGLHPLHPHQMPYPNMNGMSIPPPAPHGFGQPISFPPPPPM  1450
1451  TNVSDQGSRIVVNEKESQDLKKFINGKQHSNGSTIGGETKNSRKGEIKPS  1500
1501  SGTNSTECQSPKSQSNAADRDNKKDEST                        1528

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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