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

NucPred

Fetching Q8N0W3 from www.uniprot.org...

The NucPred score for your sequence is 0.15 (see score help below)

   1  MEQPKGVDWTVIILTCQYKDSVQVFQRELEVRQKREQIPAGTLLLAVEDP    50
  51  EKRVGSGGATLNALLVAAEHLSARAGFTVVTSDVLHSAWILILHMGRDFP   100
 101  FDDCGRAFTCLPVENPEAPVEALVCNLDCLLDIMTYRLGPGSPPGVWVCS   150
 151  TDMLLSVPANPGISWDSFRGARVIALPGSPAYAQNHGVYLTDPQGLVLDI   200
 201  YYQGTEAEIQRCVRPDGRVPLVSGVVFFSVETAERLLATHVSPPLDACTY   250
 251  LGLDSGARPVQLSLFFDILHCMAENVTREDFLVGRPPELGQGDADVAGYL   300
 301  QSARAQLWRELRDQPLTMAYVSSGSYSYMTSSASEFLLSLTLPGAPGAQI   350
 351  VHSQVEEQQLLAAGSSVVSCLLEGPVQLGPGSVLQHCHLQGPIHIGAGCL   400
 401  VTGLDTAHSKALHGRELRDLVLQGHHTRLHGSPGHAFTLVGRLDSWERQG   450
 451  AGTYLNVPWSEFFKRTGVRAWDLWDPETLPAEYCLPSARLFPVLHPSREL   500
 501  GPQDLLWMLDHQEDGGEALRAWRASWRLSWEQLQPCLDRAATLASRRDLF   550
 551  FRQALHKARHVLEARQDLSLRPLIWAAVREGCPGPLLATLDQVAAGAGDP   600
 601  GVAARALACVADVLGCMAEGRGGLRSGPAANPEWMRPFSYLECGDLAAGV   650
 651  EALAQERDKWLSRPALLVRAARHYEGAGQILIRQAVMSAQHFVSTEQVEL   700
 701  PGPGQWVVAECPARVDFSGGWSDTPPLAYELGGAVLGLAVRVDGRRPIGA   750
 751  RARRIPEPELWLAVGPRQDEMTVKIVCRCLADLRDYCQPHAPGALLKAAF   800
 801  ICAGIVHVHSELQLSEQLLRTFGGGFELHTWSELPHGSGLGTSSILAGTA   850
 851  LAALQRAAGRVVGTEALIHAVLHLEQVLTTGGGWQDQVGGLMPGIKVGRS   900
 901  RAQLPLKVEVEEVTVPEGFVQKLNDHLLLVYTGKTRLARNLLQDVLRSWY   950
 951  ARLPAVVQNAHSLVRQTEECAEGFRQGSLPLLGQCLTSYWEQKKLMAPGC  1000
1001  EPLTVRRMMDVLAPHVHGQSLAGAGGGGFLYLLTKEPQQKEALEAVLAKT  1050
1051  EGLGNYSIHLVEVDTQGLSLKLLGTEASTCCPFP                  1084

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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