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

NucPred

Fetching Q80XI3 from www.uniprot.org...

The NucPred score for your sequence is 0.90 (see score help below)

   1  MNSQPQARSPFFQRPQIQPPRAAIPNSSPSIRPGVQTPTAVYQANQHIMM    50
  51  VNHLPMPYPVTQGHQYCIPQYRHSGPPYVGPPQQYPVQPPGPGPFYPGPG   100
 101  PGDFANAYGTPFYPSQPVYQSAPIIVPTQQQPPPAKREKKTIRIRDPNQG   150
 151  GKDITEEIMSGGGSRNPTPPIGRPASTPTPPQQLPSQVPEHSPVVYGTVE   200
 201  SAHLAASTPVTAASDQKQEEKPKPDPVFQSPSTVLRLVLSGEKKEQAGQM   250
 251  PETAAGEPTPEPPRTSSPTSLPPLARSSLPSPMSAALSSQPLFTAEDKCE   300
 301  LPSSKEEDAPPVPSPTSCTAASGPSLTDNSDICKKPCSVAPHDSQLISST   350
 351  ILINEMNGVGEKLSAKENTVGMLRQEVLPLTLELEILEHPQEELKVECTP   400
 401  TPIAPSMLPAFSPAPPTPPTSPPCPPVVLSAAIARSPAVATEVQRVADEG   450
 451  ESLRTCLSKDAKEMQDKAESESDGQAEETADPQSLHSGRSPAPVQTATTA   500
 501  PKSWKKTKEQTRTPDEVLEAEAEPKAEEELAVDSVLEPEQEKMSQGFPSE   550
 551  RDPSALKRGKAEEGNGEEAEPVRNGAESASEGEGGDGNSGSADSSADGLT   600
 601  FPFKAESWKPADTEGKKQYDREFLLDIQFMPACIQKPEGLPPISDVVLDK   650
 651  INQPRLSMRTLDPRILPRGPDFTPAFADFPRQTPGGRGVPLLNVGPRRSQ   700
 701  PGQRREPRKIITVSVKEDVHLRKAENAWKPSQKRDSHADDPESIKTQELF   750
 751  RKVRSILNKLTPQMFNQLMKQVSALTVDTEERLKGVIDLVFEKAIDEPSF   800
 801  SVAYANMCRCLVTLKVPMADKPGNTVNFRKLLLNRCQKEFEKDKADDDVF   850
 851  EKKQKELEAASAPEERTRLHDELEEAKDKARRRSIGNIKFIGELFKLKML   900
 901  TEAIMHDCVVKLLKNHDEESLECLCRLLTTIGKDLDFEKAKPRMDQYFNQ   950
 951  MEKIVKERKTSSRIRFMLQDVIDLRLCNWVSRRADQGPKTIEQIHKEAKI  1000
1001  EEQEEQRKVQQLMTKEKRRPGVQRVDEGGWNTVQGAKNSRVLDPSKFLKI  1050
1051  TKPTIDEKIQLVPKAQLGSWGKGSSGGAKASESDALRSSASSLNRFSPLQ  1100
1101  PPAPSGSPSATPLEFDSRRALTSRGSMGREKSDKPIPAGTARPNTFLRGS  1150
1151  SKDLLDNQSQEEQRREMLETVKQLTGGLDAERASTEADRSKTRELAKSEM  1200
1201  CAVPAPDKPALSEEEVERKSKSIIDEFLHINDFKEATQCIEELSAQGPLH  1250
1251  VFVKVGVEFTLERSQITRDHMGHLLYQLVQSEKLSKQDFFKGFSETLELA  1300
1301  DDMAIDIPHIWLYLAELVTPMLKEGGISMRELIVEFSKPLLPVGRAGVLL  1350
1351  SEILHLLCRQMSHKKVGALWREADLSWKDFLPEGEDVHHFLLEQKLDFTE  1400
1401  SEGPCSSEALSKKELSAEELSQRLEKLIMEEKADDERIFDWVEANLDESQ  1450
1451  MSSPTFLRALMTAVCKAAIIADCSTFRVDTAVIKQRVPILLKYLDSDTEK  1500
1501  ELQALYALQASIVKLDQPANLLRMFFDCLYDEEVISEDAFYKWESSKDPA  1550
1551  EQAGKGVALKSVTAFFTWLREAEEESEDN                       1579

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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