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

NucPred

Fetching Q9JL04 from www.uniprot.org...

The NucPred score for your sequence is 0.88 (see score help below)

   1  MGNQDGKLKRSAGDASHEGGGAEDAAGPRDAEITKKASGSKKALGKHGKG    50
  51  GGGSGETSKKKSKSDSRASVFSNLRIRKNLTKGKGACDSREDVLDSQALP   100
 101  IGELDSAHSIVTKTPDLSLSAEETGLSDTECADPFEVIHPGASRPAEAGV   150
 151  GIQATAEDLETAAGAQDGQRTSSGSDTDIYSFHSATEQEDLLSDIQQAIR   200
 201  LQQQQQQKLLLQDSEEPAAPPTAISPQPGAFLGLDQFLLGPRSEAEKDTV   250
 251  QALPVRPDLPETTKSLVPEHPPSSGSHLTSETPGYATAPSAVTDSLSSPA   300
 301  FTFPEAGPGEGAAGVPVAGTGDTDEECEEDAFEDAPRGSPGEEWVPEVEE   350
 351  ASQRLEKEPEEGMRESITSAVVSLPGSPAPSPRCFKPYPLITPCYIKTTT   400
 401  RQLSSPNHSPSQSPNQSPRIKKRPDPSVSRSSRTALASAAAPAKKHRLEG   450
 451  GLTGGLSRSADWTEELGVRTPGAGGSVHLLGRGATADDSGGGSPVLAAKA   500
 501  PGAPATADGFQNVFTGRTLLEKLFSQQENGPPEEAEKFCSRIIAMGLLLP   550
 551  FSDCFREPCNQNAGSSSAPFDQDQLYTWAAVSQPTHSMDYSEGQFPRREP   600
 601  SMWPSSKLPEEEPSPKDVDTEPKSSILESPKKCSNGVQQEVFDVKSEGQA   650
 651  TVIQQLEQTIEDLRTKIAELEKQYPALDLEGPRGLSGLENGLTASADVSL   700
 701  DALVLHGKVAQPPRTLEAKSIQTSPTEEGRILTLPPPKAPPEGLLGSPAA   750
 751  ASGESALLTSPSGPQTKFCSEISLIVSPRRISVQLDAQQIQSASQLPPPP   800
 801  PLLGSDSQGQPSQPSLHTESETSHEHSVSSSFGNNCNVPPAPPLPCTESS   850
 851  SFMPGLGMAIPPPPCLSDITVPALPSPTAPALQFSNLQGPEMLPAPPQPP   900
 901  PLPGLGVPPPPPAPPLPGMGIPPPPPLPGMGIPPPPPLPGMGISPLPPLP   950
 951  GMGIPPPPPLPGVGIPPPPPLPGVGIPPPPPLPGVGIPPPPPLPGVGIPP  1000
1001  PPPLPGVGIPPPPPLPGVGIPPPPPLPGVGIPPPPPLPGVGIPPPPPLPG  1050
1051  SGIPPPPALPGVAIPPPPPLPGMGVPPPAPPPPGAGIPPPPLLPGSGPPH  1100
1101  SSQVGSSTLPAAPQGCGFLFPPLPTGLFGLGMNQDRVARKQLIEPCRPMK  1150
1151  PLYWTRIQLHSKRDSSPSLIWEKIEEPSIDCHEFEELFSKTAVKERKKPI  1200
1201  SDTISKTKAKQVVKLLSNKRSQAVGILMSSLHLDMKDIQHAVVNLDNSVV  1250
1251  DLETLQALYENRAQSDELEKIEKHSRSSKDKENAKSLDKPEQFLYELSLI  1300
1301  PNFSERVFCILFQSTFSESICSIRRKLELLQKLCETLKNGPGVMQVLGLV  1350
1351  LAFGNYMNAGNKTRGQADGFGLDILPKLKDVKSSDNSRSLLSYIVSYYLR  1400
1401  NFDEDAGKEQCVFPLAEPQELFQASQMKFEDFQKDLRKLKKDLKACEAEA  1450
1451  GKVYQVSSAEHMQPFKENMEQFISQAKIDQESQEAALTETHKCFLETTAY  1500
1501  YFMKPKLGEKEVSPNVFFSVWHEFSSDFKDAWKKENKLILQERVKEAEEV  1550
1551  CRQKKGKSLYKVKPRHDSGIKAKISMKT                        1578

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.