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

NucPred

Fetching Q12816 from www.uniprot.org...

The NucPred score for your sequence is 0.48 (see score help below)

   1  MDRRNDYGYRVPLFQGPLPPPGSLGLPFPPDIQTETTEEDSVLLMHTLLA    50
  51  ATKDSLAMDPPVVNRPKKSKTKKAPIKTITKAAPAAPPVPAANEIATNKP   100
 101  KITWQALNLPVITQISQALPTTEVTNTQASSVTAQPKKANKMKRVTAKAA   150
 151  QGSQSPTGHEGGTIQLKSPLQVLKLPVISQNIHAPIANESASSQALITSI   200
 201  KPKKASKAKKAANKAIASATEVSLAATATHTATTQGQITNETASIHTTAA   250
 251  SIRTKKASKARKTIAKVINTDTEHIEALNVTDAATRQIEASVVAIRPKKS   300
 301  KGKKAASRGPNSVSEISEAPLATQIVTNQALAATLRVKRGSRARKAATKA   350
 351  RATESQTPNADQGAQAKIASAQTNVSALETQVAAAVQALADDYLAQLSLE   400
 401  PTTRTRGKRNRKSKHLNGDERSGSNYRRIPWGRRPAPPRDVAILQERANK   450
 451  LVKYLLVKDQTKIPIKRSDMLRDVIQEYDEYFPEIIERASYTLEKMFRVN   500
 501  LKEIDKQSSLYILISTQESSAGILGTTKDTPKLGLLMVILSVIFMNGNKA   550
 551  SEAVIWEVLRKLGLRPGVRHSLFGEVRKLITDEFVKQKYLEYKRVPNSRP   600
 601  PEYEFFWGLRSYHETSKMKVLKFACRVQKKDPKDWAVQYREAVEMEVQAA   650
 651  AVAVAEAEARAEARAQMGIGEEAVAGPWNWDDMDIDCLTREELGDDAQAW   700
 701  SRFSFEIEARAQENADASTNVNFSRGASTRAGFSDGASISFNGAPSSSGG   750
 751  FSGGPGITFGVAPSTSASFSNTASISFGGTLSTSSSFSSAASISFGCAHS   800
 801  TSTSFSSEASISFGGMPCTSASFSGGVSSSFSGPLSTSATFSGGASSGFG   850
 851  GTLSTTAGFSGVLSTSTSFGSAPTTSTVFSSALSTSTGFGGILSTSVCFG   900
 901  GSPSSSGSFGGTLSTSICFGGSPCTSTGFGGTLSTSVSFGGSSSTSANFG   950
 951  GTLSTSICFDGSPSTGAGFGGALNTSASFGSVLNTSTGFGGAMSTSADFG  1000
1001  GTLSTSVCFGGSPGTSVSFGSALNTNAGYGGAVSTNTDFGGTLSTSVCFG  1050
1051  GSPSTSAGFGGALNTNASFGCAVSTSASFSGAVSTSACFSGAPITNPGFG  1100
1101  GAFSTSAGFGGALSTAADFGGTPSNSIGFGAAPSTSVSFGGAHGTSLCFG  1150
1151  GAPSTSLCFGSASNTNLCFGGPPSTSACFSGATSPSFCDGPSTSTGFSFG  1200
1201  NGLSTNAGFGGGLNTSAGFGGGLGTSAGFSGGLSTSSGFDGGLGTSAGFG  1250
1251  GGPGTSTGFGGGLGTSAGFSGGLGTSAGFGGGLVTSDGFGGGLGTNASFG  1300
1301  STLGTSAGFSGGLSTSDGFGSRPNASFDRGLSTIIGFGSGSNTSTGFTGE  1350
1351  PSTSTGFSSGPSSIVGFSGGPSTGVGFCSGPSTSGFSGGPSTGAGFGGGP  1400
1401  NTGAGFGGGPSTSAGFGSGAASLGACGFSYG                     1431

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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