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

NucPred

Fetching Q923P0 from www.uniprot.org...

The NucPred score for your sequence is 0.27 (see score help below)

   1  MSLQGSYQHFCLWMFLGTTLALGQGQVSSRLRLAVLPEDQLQMKWREAEG    50
  51  SGLGFLVQVTPMAGDLEQELILTTKTPKATVGGLNPSKSYTLQIFELTDS   100
 101  GPILLARREFVIEDLKSQSLGRGSRRLAGATLEPTSLPLRGPDSEKTSEP   150
 151  SIAFTLSRDLPILDHPQFQCTPPTPADIIFLVDGSWSIGHNHFQQVKDFL   200
 201  ASIITQFAIGPDKVQVGLTQYSGDPQTEWDLNSFQTKEQVLAAVHHLRYK   250
 251  GGNTFTGLALTHVLEQNLKPAAGVRPEAAKVLILVTDGKSQDDVRTAARI   300
 301  LKDQDIDVFVVGVKNVDEAELKLLASQPLDITVHNVLDFPQLDTLAPLLS   350
 351  RLICQKIQGRGPVKPAAGTRVLDPLPTPTRLILTHATSSSIHLSWTPALY   400
 401  PPLKYLIVWQPSRGGAPKEVVVEGPVSSMELGNLTSSTEYLVSVLPVYES   450
 451  GVGKSLQGRATTAPLPPPGPLTLAAVTPRTLHVTWPPSAGVTQYLVQYLL   500
 501  ATSTGEEQKREVHVGQPEVLLDGLEPGQDYDVSVQSLRGPEASEVQSIRA   550
 551  RTSALGPPRHLTFSDVRYNSTCVSWEAQRPVRLVKVSYISSDGSHSGQTQ   600
 601  VPGNLTSATLGPLSSSTMYTVRVTCFYLGGGSSVLTGHVTTQKAPSPGQL   650
 651  SVMELPGDAVKLSWLATALSGVLVYQIKWMPLGEGKAREISVPGTLGTAT   700
 701  LPGLMKHVEYEITILAYYRDGTRSDPVSLRYTPSAASRSPPSSLALSSET   750
 751  PNSLQVNWTPPSGHVLHYRLNYTLASGSGPEKSISVPGTRSHAVLRDLMS   800
 801  ATKYRVLVSAVYRAGESMAVSATYRTAACPALHPDSSLSGFDLMVAFGLV   850
 851  AKEYASIRGVAMEPSALGVVPTFTLFKDAQLMRRVSDIYPATLPPEHTIV   900
 901  FLVRLLPETPREAFALWQMMAEDFQPILGVLLDAGRKSLTYFNHDSRAAL   950
 951  QEVTFDLQDAKKIFFGSFHKVHIAVGHSKVRLYVDCRKVAERPIGDAGSP  1000
1001  PTGGFITLGRLAKARGPRSSSATFQLQMLQIVCSDTWADKDRCCEIPALR  1050
1051  DGETCPAFPSACAYSSETPGPPGPQGPPGLPGRNGPPGQQGHPGPKGEPG  1100
1101  PPGQTGPEGPGGQQGSPGTQGRAVQGPMGPPGAKGEKGDQGLSGLQGLSG  1150
1151  QQGIPGKTGLQGPKGMRGLEGPAGLPGPPGPRGFQGLAGARGTNGERGAP  1200
1201  GAVGPTGLPGSKGERGEKGEPQSLATIFQLVSQACESAIRTHVLKLNSFL  1250
1251  HENARPPMPFMAETAKLGRPRSIDPGLHNEALLPGDWGHILRPEDQGEPV  1300
1301  TISHTSNPRLQEVQTPESLE                                1320

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.