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

NucPred

Fetching Q4HYQ4 from www.uniprot.org...

The NucPred score for your sequence is 0.82 (see score help below)

   1  MSNSMRDLISGEAELDDEEEDESFDERGGQRRHKNAVEDSSEEEEDDDDE    50
  51  EEARKVREGFIVDEDEDEDEGGESDADVRPLHKRKREHRDREEEAQLDED   100
 101  DLDLIGEQFGERPKPTTQSKFKRLKRGTRDEDRGNQRRGLDDIFSDEEDD   150
 151  AGEQRAYNNRSSYRQADEFDDFIEEDFPDDPEELEQQREDAEVARPRDRV   200
 201  IGNIADTANLDKDALDDMEAIFGNGEDYDWALQMEEEEEDREREEQAIEL   250
 251  KDVFEPSQLKEKLLTDEDNEIRFTDEPERFQIDRKTFKSLQLTAEQFKEE   300
 301  ARWITNQLWPKKGLASDLQSPFGKAVGKVLEFFIVDEVEVPYVFQHRKDY   350
 351  LLHTRKTRNPNRDDPDAPEYVISADKLLNQDDLWKILELDIKFRSFVDKR   400
 401  NALEKTVDNLKGMEIHDAMVDEMIPEATTMEELQDLQDYLHFQYGQQLKD   450
 451  LAALAGNLSLTKRPGSKSNLLERVRQGKAYGFVRAYGISADQLAKNALRH   500
 501  GKKVTPDDDAQYPMDLADSLIDDVFSTGDQVISAARQMYSEELFASPRMR   550
 551  KHFRNSYYQAAEISCRRTEKGLRRIDDSHPYYEIKYLQNQAIADLVHQPE   600
 601  LFLKMMKAEEEGLVTIKLDMPARYDFRQHLYQEFESENFSDRAEQWREER   650
 651  KKVLDLAYPKLEKIIAKNVKEVIRTFCQDEVLKMCREEYAKRLDQAPYKP   700
 701  KGMILGTTPRVLVLSNGMSDPARDPICWAWVEEDGRVIEQGKLGNLARDE   750
 751  RQREEFEELVKRRRPDVIGVSGWSAETTKLVRDLEGLVNEKGLMGPEFED   800
 801  PDTNDYRTEPLEVVVVNDEVARLYKDSPRALAEHPSLNPITRYCVALARY   850
 851  MQNPMKEYAALGKDVSSLSYHPCQNLLPADKLAKYLDSAMVDMVNLCGVD   900
 901  INEAMNDTYTANLLPYVSGLGPRKATSVIKAINANGGAVGTRDELVGDPD   950
 951  SGKLPVVGPRVWNNCASFLFIEYEATNPSSDPLDNTRVHPEDYELGRKMA  1000
1001  ADALELDEEDVKGETDENGPGAIVRKLFKMDEQDKVNELVLEEYAEQLER  1050
1051  NYSQRKRATLETIRAELQAPYEELRRNFALLSASEIFTMFTGETKHTLCE  1100
1101  GMIVPVNVRVVKDDFAIVKLDCGIEGRVEGHEVSHRSSIKEVLSSGQTSQ  1150
1151  AKILDINYKDFMAKLSMREDALRIPYKRPINLGRDGWDYVLEAADKEELR  1200
1201  EKDKTTGRTQRVVKHPNFKPFNGLQAEEYLGSQPNGEVVIRPSSKGNDHL  1250
1251  AVTWKVADGVFQHIDVLEMQKETEFAVGKLLRVGGKYTYTDLDELIVEHV  1300
1301  KAMARKVEELMRHDKYQNRSRGETEKWLTTYIDANPNRSTYAFCIDTKHP  1350
1351  GYFWLCFKASRAAKVIALPVRAIPQGFELKGYQYPDMRALCNGFKLRYQN  1400
1401  EFSKMGQR                                            1408

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.