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

NucPred

Fetching P22293 from www.uniprot.org...

The NucPred score for your sequence is 0.97 (see score help below)

   1  MSVALADEPLIDLEEDLEDGEIDDDEEDEQQSSKIQVQKKTFVGDDDVQF    50
  51  VGVEAKNQNDDEDVVYVGPSTDAVCLQNSNSTKSKKPRPLEDDHASSIEL   100
 101  AIANALKKKGIEPPMPRMRSSNQDTSDQSLEGSGEGLATANPLLQSTRSS   150
 151  RRRKRKKEREREQKKDKEQQNRSRRDENDVSVVPGGVEDMDEYEMMNVRG   200
 201  GSPPPGGAAPPLSSCGQRFSGADWDMDDGSAATGAAGLGAGGGGGYNSHS   250
 251  SYDSYSDEETNGPGLMNQRRRTRRDNEKEHQRGVNNRKRRDRDRLEGGLA   300
 301  GSGSKRNRRDSGEGGGGGQEKMGGSNRVEPRKLELCKFYLMDCCAKRDKC   350
 351  SYMHKEFPCKYYYLGMDCYAGDDCLFYHGEPLSEQLRNVLLKHMETAPKE   400
 401  ILGDFKRISRDIAIVQMTRRHEQLCDQLNRENTWNSIGCGLMGKRQDHQM   450
 451  QQQQQQLQHQQLQQQQEQQQTQQQAAADGGGCIPSLLDMVINPPLSENKR   500
 501  KSRWTEKMGAKAAAGAAGSSERDSTSPDAKPLPPHLDLANLSHVLSAENM   550
 551  AKLNKLGITNLEQMLQVPFGQLTEAGLTLVEIGEIQRKAEDAKPQTQAEL   600
 601  ESSTPPSKRETEANNSNSKSNGLIMVDYTQYLKDAHVSFSGNDPLDDDRD   650
 651  DDEQLIIDDGNDSTAEEDQQPKKAKAPPAATHESSTEEAPLPSVFDLPSF   700
 701  MNNMLGQGSSARQLLPASATSPNQENAHLPGGDQSTHKSAPIGGGTSTNV   750
 751  LGRILFGDKQSDPEARAAFYRDIIRNPFKAHSGDGDVDSSNENSNSNSHS   800
 801  LTPTPTPEPGSQSPKPEDHDQDMPELPVIAPALPPTTPSLYVRRSMYDFD   850
 851  PVKEQEHGRQELLTEEKEQYQRDTDMRLPFEPMKHYMPATEIDAAIFSHT   900
 901  PIRWQLHEVTIEESSYAQIRASALHKEQRELRDPRMRRILGLPETPDNSG   950
 951  PLGSVPIMGPSSFSVDNIARCATTIASPDLETAVRDSTPSSPPPSVVNLP  1000
1001  SMSVPPPSMRVPPPNIQVEKPTVRTDPRRDPRRAVLQAPTKGASTANTTA  1050
1051  PNASGGSKQISEIRSLLQVSNWYNNLGTNNKIMVNQQLALVFTELKKFHQ  1100
1101  LPNDAPKIFDVSFIVNNTTLQQIFAKLFIFVDDNGEVVQIPEEPNGNGAA  1150
1151  LGGGGDSGGGVGGGGGGGGVVLPNLSQPPPNLSQMLRLPPPNIRMLRMSG  1200
1201  MMMQMGNVGPPFNQPPPRGGLMGMPPNGNGLNQGVGNLGGLGQLGINQGG  1250
1251  GPVPNGNPFNPFGGNNGGGAGVMNNMNSMGNMGMGFNNFNNNGGRGGHFP  1300
1301  GGGSGGNGNGNNRNQRGGNHRNRNI                           1325

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.