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

NucPred

Fetching Q6ZQK0 from www.uniprot.org...

The NucPred score for your sequence is 0.98 (see score help below)

   1  MALQDLGENLQPWCPLGLSLEWVKTVWDLDFTEIEPLDPSIVGEILETGR    50
  51  DAFTKLYGSLFPFATDESGSLESIWTFFTENDISSNTLVALFCHFVQEAH   100
 101  KKSASAQYREYGLHAAGLYFLLLEIPGIVVNQVFHPVMFDKCIQILKRSW   150
 151  PQESNLTQKRKKDHSKSSKDNYRKSRKRGKPPRKEDYQVDELSREEEEEE   200
 201  EEIYFSGRDLCQIRDAIFNLLKNFLRLLPKFSLKEKPQSIQTCIEVFVAL   250
 251  TSFEPIPHKFLISQARNLNEVKHISELAYYGLYLLCSPVHGEENKVIGSI   300
 301  FHQMLNVILMLEVGEGSRCAPLAITSQVINCRNQAVQFVSSLVDELQASV   350
 351  YPVLGTLLQHICAKVVDKAEYRTYAAQSLVQLLTKLPSEEYATFIAWLYK   400
 401  YSRSSKIPHRVFTLDVALALLTLPERELDDTVSLEHQKFLKHKFFVQEII   450
 451  FDRCLDKAPTVRSKALSSFAHCLELSSSNTSESILEIFINSNLVPGIQNL   500
 501  SNTVLNPSPVLTSRNGYSAQSRTHNNDEQTLPGERCFMTMLRKRIKDEKI   550
 551  NVRKSALQVLMSILKHCDILSMEQDLLILQDHCRDPAISVRKQALQSLTE   600
 601  LVMAQPTCVPVQKAWLMGVIPVVMDCESTVQEKALECLDQLLLQNIKHHK   650
 651  KFHSADRSQVLAWSLLALLTIENQDLRRYLNKAFHIWSKKDKFSSTFINS   700
 701  VISHTDTERSAPAWMLLSKITCSSPKLDYTKIIESWERLSREQSPNSNTL   750
 751  GYMLCVIGHIAKHLPKGTRDKITGVIKAKLNGFQWSPELISSSVDALQKL   800
 801  CRASAKTVLEEQGLLKQVCGDVLATCEQHLSNILLKEDGTGNMDEGLVVK   850
 851  CIFTLGDIAQLCPAIVEKRVFLLIQSILASSAHSDHLPSSQGTTDALDSQ   900
 901  PPFQPRSSAMPSVIRAHAIITLGKLCLQHEDLAKKSIPALVRELEVSEDV   950
 951  AVRNNVIIVICDLCIRYTVMVDNYIPNISVCLKDSDPFIRKQTLVLLTNL  1000
1001  LQEEYVKWKGSLFFRFVSTLVDSHPDIASLGEFCLAHLLLKRNPTMFFQH  1050
1051  FIECIFHFNSYEKHGQYNKFSQSERGKQLFLLKGKTNKEKRMRIYKFLLE  1100
1101  HFTDEQRFNVTSKICLNILACFTDGILPMDMEASELLSDTFDILNSKEIK  1150
1151  LLAMRAQTSKDLLEEDDVALANVVMQEAQMKIISQVQKRNFIENIIPIII  1200
1201  SLKTVLEKNKIPALRELMNYLREVMQDYRDEINDFFAVDKQLASELEYDM  1250
1251  KKYNEQLAQEQALTEHANATKGPEDSDRVPSAQVAPDLEAVPALAAAPMA  1300
1301  AAAAAAPMAAAAAAAGQDNADVPPTQSRPSAPRSNFTPTLPPISENGPLK  1350
1351  IMSSTRPMSLSTIAILNSVKKAVASKNRTRSLGALPFNVETGSPENPSSH  1400
1401  ESSLSLEKESDRTVNHVTKRAISTPENSISDVTFAAGVSYIGTPATFFTK  1450
1451  EKHEAQEQGSDILCLSLLDKRPPQSPQWNVKSPARSHGSTRSSRRSLRKA  1500
1501  PLKTAN                                              1506

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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