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

NucPred

Fetching P53125 from www.uniprot.org...

The NucPred score for your sequence is 1.00 (see score help below)

   1  MVLYKRKPILLPDPKPLPLDLNVQVWHIEETGEWFSSYEEFLERFDFYTR    50
  51  HHFTCEITGTSCLTFFQALDSEETQFKYVEDRFPLKLREPVARFLHFNGI   100
 101  RRLDALVEKVYARFKNDFFPGEVVYLRKQKDSSTTSSNSQQSTPQPDDMV   150
 151  EINSVGNPGLPQYQYQRRYVIKEKVQFNATINPESREIVMPAHTKYMLIE   200
 201  EAASSNKSFIVDQGQIYRDRSTFTKHLIKCFFKITLQRASSKMGAPWCVK   250
 251  PEYLAMYGLTMEWPKDMLKYKEDEPVVARRSNSANVSSPESEKNKRQSKS   300
 301  SGKSNTSNDASNKKETKKKRKPTEVNDSENNSSEEDKKKGQNVTSETHSK   350
 351  KRKKEANEEPNTENVESVPTPANAEPQAVTITSIMDDLALPYQHPPNIFP   400
 401  NLTYYNEKLECISLGSTKLSRPFDSFGKLLQAYQFLNTFGSKICLSHFSL   450
 451  DQFITSLKCTDPYELKGEVVLVNIRTQTSKEQEIENNGLPMKNKAETTTE   500
 501  EDSENPSDWQRNSFIRDMIMKRNSDKVEYKIVHDDPASDDILDNINHNGS   550
 551  ALLIEVFTALLRLFINEEGDWSCIVVENWIIDDKGVLMERKDERGEGEAK   600
 601  QKRNAHGYFLQDKEKIDNLKDTLKENATEVQKESDAKNETNSESDSKSDS   650
 651  DSEERDPKLEKCLNYRNVNWIERLTKRQFNNSYWLIILLGVLEDCRHLPM   700
 701  YTEFIDSFIEKIIPKDISATQLPKQLWRNFCRKLSFSDKVNALWILVDLV   750
 751  SHFSPDIKAAVDDSMELCGQIRSERFKVARELKTEAAVLSNLQGDLQAIQ   800
 801  EKLNKTDENTPSADGADKKDDSESNSEPIDLIIIEKKQKLIEEQDKKVQA   850
 851  LQSDKNFLDNCLFENDLQRLKPLGLDRYGNRYFWLDHNGVPFPQYPAGMN   900
 901  ETPKSNNSLSYHSGRLLIQGPKASSAKFFLNVSDEQLSNWQKIRNSEGIS   950
 951  EATREVFGISKTSSGSYNYVENGIEVELLDSNDRVNPLIELTPIQKKIMD  1000
1001  ETPSRLLLSPDQWYCIDKLEDLSRIMDWLDNWGRKEHDLLRQIRPIMERI  1050
1051  KSSLSLRDHALSLTAFTKNEEKLLKELENNEFTENELNVDSMDVDDKNSG  1100
1101  VKSEVDVQVDAEEKREAVIDEKLEVIADELMKLDDSSKTRNVLNRIQELE  1150
1151  DQRDELLEQKKSIINSQRPGARILARSERKRTKISRGNKVNKQIEILTDL  1200
1201  VNYRHFKAMEDVIAWKNVLANSIWGSSLRKNASGNKRSGVIETVDDKLKD  1250
1251  IVGQTSRTVTPAPN                                      1264

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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