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

NucPred

Fetching Q6YUU5 from www.uniprot.org...

The NucPred score for your sequence is 0.14 (see score help below)

   1  MGGGDGGAGKAKARPVFSSFMTVFMHADAADVALMVLGLLGAMGDGISTP    50
  51  VMLLITSRIFNDLGSGADIVKEFSSKVNVNARNLVFLAAASWVMAFLEGY   100
 101  CWARTAERQASRMRARYLRAVLRQDVEYFDLKKGSTAEVITSVSNDSLVV   150
 151  QDVLSEKVPNFVMNAAMFAGSYAVGFALLWRLTLVALPSVVLLIIPGFMY   200
 201  GRILVGLARRIREQYTRPGAIAEQAVSSARTVYSFVAERTTMAQFSAALE   250
 251  ESARLGLKQGLAKGIAVGSNGITFAIWAFNVWYGSRLVMYHGYQGGTVFA   300
 301  VSAAIVVGGLALGSGLSNVKYFSEASSAAERILEVIRRVPKIDSESDTGE   350
 351  ELANVTGEVEFRNVEFCYPSRPESPIFVSFNLRVPAGRTVALVGGSGSGK   400
 401  STVIALLERFYDPSAGEVMVDGVDIRRLRLKWLRAQMGLVSQEPALFATS   450
 451  IRENILFGKEEATAEEVVAAAKAANAHNFISQLPQGYDTQVGERGVQMSG   500
 501  GQKQRIAIARAILKSPKILLLDEATSALDTESERVVQEALDLASMGRTTI   550
 551  VIAHRLSTIRNADIIAVMQSGEVKELGPHDELIANDNGLYSSLVRLQQTR   600
 601  DSNEIDEIGVTGSTSAVGQSSSHSMSRRFSAASRSSSARSLGDARDDDNT   650
 651  EKPKLPVPSFRRLLMLNAPEWKQALMGSFSAVVFGGIQPAYAYAMGSMIS   700
 701  VYFLTDHAEIKDKTRTYALIFVGLAVLSFLINIGQHYNFGAMGEYLTKRI   750
 751  REQMLAKILTFEIGWFDRDENSSGAICSQLAKDANVVRSLVGDRMALVIQ   800
 801  TISAVLIACTMGLVIAWRLALVMIAVQPLIIVCFYARRVLLKSMSKKSIH   850
 851  AQAESSKLAAEAVSNLRTITAFSSQERILRLFEQSQDGPRKESIRQSWFA   900
 901  GLGLGTSMSLMTCTWALDFWYGGRLMAEHHISAKELFQTFMILVSTGRVI   950
 951  ADAGSMTTDLAKGADAVASVFAVLDRETEIDPDNPQGYKPEKLKGEVDIR  1000
1001  GVDFAYPSRPDVIIFKGFTLSIQPGKSTALVGQSGSGKSTIIGLIERFYD  1050
1051  PIRGSVKIDGRDIKAYNLRALRRHIGLVSQEPTLFAGTIRENIVYGTETA  1100
1101  SEAEIEDAARSANAHDFISNLKDGYDTWCGERGVQLSGGQKQRIAIARAI  1150
1151  LKNPAILLLDEATSALDSQSEKVVQEALDRVMIGRTSVVVAHRLSTIQNC  1200
1201  DLITVLEKGTVVEKGTHASLMAKGLSGTYFSLVNLQQGGNQQVQH       1245

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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