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

NucPred

Fetching Q8BQZ4 from www.uniprot.org...

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

   1  MYSEWRSLHLVIQSDQGHTSVLHSYPESVGREVANAVVRPLGQALGTSSV    50
  51  AGSESLLKTDKEVKWTMEVICYGLTLPLDGETVKYCVDVYTDWIMALVLP   100
 101  KDSIPLPIIKEPNLYVQSILKHLQNLFVPRQEQGSSQIRLCLQVLRAIQK   150
 151  LARESSIMARETWEVLLLFLLQINDILLAPPTVQGGIAENLAEKLIGVLF   200
 201  EVWLLACTRCFPTPPYWKTAKEMVANWRHHPAVVEQWSKVICALTSRLLR   250
 251  FTYGPSFPPFKVPDEDANLIPPEMDNECIAQTWFRFLHMLSNPVDLSNPA   300
 301  VISSTPKFQEQFLNVSGMPQELSQYPCLKHLPQIFFRAMRGISCLVDAFL   350
 351  GISRPRSDSAPPTPVNRLSMPQSAAVNTTPPHNRRHRAVTVNKATMKTST   400
 401  VTTAHTSKVQHQASSTSPLSSPNQTSSEPRPLPAPRRPKVNSILNLFGSW   450
 451  LFDAAFVHCKLHNGINRDNSMTASFIQILLSYKSSIATQASMEFRRKGSQ   500
 501  MSTDTMVSNPVFDASEFPDNYEAGRAEACGTLCRIFCSKKTGEEILPAYL   550
 551  SSVILNSPPLFCCDLKGIDVVVPYFISALETILPDRELSKFKSYVNPTEL   600
 601  RRSSINILLSLLPLPHHFGTVRSEVVLEGKFSNDDSSSYDKPITFLSLKL   650
 651  RLVNILIGALQTETDPNNTQMILGAMLNIVQDSALLEAIGCQMEMGGGEN   700
 701  NLKSHSRTNSGISSASGGSTEPTTPDSERPAQALLRDYGSTDSAAGLLIR   750
 751  SIHLVTQRLNSQWRQDMSISLAALELLSGLAKVKVMVDSGDRKRAISSVC   800
 801  SYIVYQCSRPAPLHSRDLHSMIVAAFQCLCVWLTEHPDMLDEKDCLKEVL   850
 851  EIVELGISGSKSKNSEQEVKYKGDKEPNPASMRVKDAAEATLTCIMQLLG   900
 901  AFPSPSGPASPCSLVNETTLIKYSRLPTINKHSFRYFVLDNSVILAMLEQ   950
 951  PLGNEQNDFFPSVTVLVRGMSGRLAWAQQLCLLPRGAKANQKLFVPEPRP  1000
1001  VPKNDVGFKYSVKHRPFPEEVDKIPFVKADLSIPDLHEIVTEELEERHEK  1050
1051  LRSGMAQQIAYEMHLEQQSEGELQKRSFPDPVTDCKPPPPAQEFQTARLF  1100
1101  LSHFGFLSLEALKEPANSRLPPHLIALDSTIPGFFDDIGYLDLLPCRPFD  1150
1151  TVFIFYMKPGQKTNQEILKNVESSRNVQPHFLEFLLSLGWSVDVGKHPGW  1200
1201  TGHVSTSWSINSCDDGEGSEPDEITSSEDVGASIFNGQKKVLYYADALTE  1250
1251  IAFVVPSPVESLTDSLESNISDQDSDSNMDLMPGILKQPPLTLELVPNHT  1300
1301  DSLNSSQRLSPSSRMKKLPQGRPVPPLGPETRVSVVWVERYDDIENFPLS  1350
1351  DLMTEISTGVETTANSSTSLRSTTLEKEVPVIFIHPLNTGLFRIKIQGAT  1400
1401  GKFNMVIPLVDGMIVSRRALGFLVRQTVINICRRKRLESDSYSPPHVRRK  1450
1451  QKITDIVNKYRNKQLEPEFYTALFQEVGLKNCSS                  1484

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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