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

NucPred

Fetching Q9FWX8 from www.uniprot.org...

The NucPred score for your sequence is 0.15 (see score help below)

   1  MNRDGAGEGDSVSHEHSTSKTDEKAKTVPLYKLFAFADSFDVFLMICGSL    50
  51  GAIGNGVCLPLMTLLFGDLIDSFGKNQNNKDIVDVVSKVCLKFVYLGLGR   100
 101  LGAAFLQVACWMITGERQAAKIRSNYLKTILRQDIGFFDVETNTGEVVGR   150
 151  MSGDTVHIQDAMGEKVGKFIQLVSTFVGGFALAFAKGWLLTLVMLTSIPF   200
 201  LAMAGAAMALLVTRASSRGQAAYAKAATVVEQTIGSIRTVASFTGEKQAI   250
 251  NSYKKYITSAYKSSIQQGFSTGLGLGVMIYVFFSSYALAIWFGGKMILEK   300
 301  GYTGGSVINVIIIVVAGSMSLGQTSPCVTAFAAGQAAAYKMFETIKRKPL   350
 351  IDAYDVNGKVLGDIRGDIELKDVHFSYPARPDEEIFDGFSLFIPSGATAA   400
 401  LVGESGSGKSTVINLIERFYDPKAGEVLIDGINLKEFQLKWIRSKIGLVC   450
 451  QEPVLFSSSIMENIAYGKENATLQEIKVATELANAAKFINNLPQGLDTKV   500
 501  GEHGTQLSGGQKQRIAIARAILKDPRVLLLDEATSALDTESERVVQEALD   550
 551  RVMVNRTTVVVAHRLSTVRNADMIAVIHSGKMVEKGSHSELLKDSVGAYS   600
 601  QLIRCQEINKGHDAKPSDMASGSSFRNSNLNISREGSVISGGTSSFGNSS   650
 651  RHHSLNVLGLFAGLDLGSGSQRVGQEETGTTSQEPLRKVSLTRIAALNKP   700
 701  EIPVLLLGTVVAAINGAIFPLFGILISRVIEAFFKPADQLKKDSRFWAII   750
 751  FVALGVTSLIVSPSQMYLFAVAGGKLIRRIQSMCFEKAVHMEVSWFDEPE   800
 801  NSSGTMGARLSTDAALIRALVGDALSLAVQNAASAASGLIIAFTASWELA   850
 851  LIILVMLPLIGINGFLQVKFMKGFSADAKSKYEEASQVANDAVGSIRTVA   900
 901  SFCAEEKVMQMYNKQCEGPIKDGVKQGFISGLGFGFSFFILFCVYATSFY   950
 951  AAARLVEDGKTTFIDVFQVFFALTMAAIGISQSSTFAPDSSKAKVAAASI  1000
1001  FAIIDRKSKIDSSDETGTVLENVKGDIELRHLSFTYPARPGIQIFRDLCL  1050
1051  TIRAGKTVALVGESGSGKSTVISLLQRFYDPDSGQITLDGVELKKLQLKW  1100
1101  LRQQMGLVGQEPVLFNDTIRANIAYGKGSEEAATESEIIAAAELANAHKF  1150
1151  ISSIQQGYDTVVGEKGIQLSGGQKQRVAIARAIVKEPKILLLDEATSALD  1200
1201  AESERLVQDALDRVIVNRTTVVVAHRLSTIKNADVIAIVKNGVIAENGTH  1250
1251  ETLIKIDGGVYASLVQLHMTASN                             1273

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.