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

NucPred

Fetching O48653 from www.uniprot.org...

The NucPred score for your sequence is 0.96 (see score help below)

   1  MDEGSADAGASGRRSRARGSEAVARSAALERLRAIRDGGARAAAAVQVRI    50
  51  EAPIYDTVAEEDYAALVARRRKDAGAFIVDDDGLGYADDGREEDWTHRTI   100
 101  HSSSDEGSDGEDGAPRKRKQPRPQSKRPPQQSAAAASLSAAAAMMGKQRL   150
 151  SSMFTSSVFRKPGSDRGRDSSLAADSIVDDVIAEFAPDDNDREERRRRVG   200
 201  RVCAPAPAPTTTAHIKAENVAVDTAMAFRSDNVFEAHEVSDHGNDMDMEL   250
 251  KPDVEMEPKLDTPLGASAELANNSNSLEEPKQEANGEVKIEKVHRLNAKI   300
 301  KTEDSRNGDMASATAGWMKICGDGDNAGGEGAVAANSNTGVDESSEFELK   350
 351  DGALPFYILDAYEEPFGANSGTVYLFGKVEVGKRFHSCCVVVKNMQRCIY   400
 401  AIPSSSIFPRDTISRLEKNSTTSDSSPSLRASLHELASGLKSEIADKLSD   450
 451  FNVSNFAMTPVKRNYAFERTDLPNGEQYVLKINYPYKDPALPTDLRGQHF   500
 501  HALLGTNNSALELLLIKRKIKGPSWLSISKFLACPATQRVSWCKFEVTVD   550
 551  SPKDISVLMTSTTLEVPPVVVAAVNLKTIINEKHNVHEIVSASVICCHRV   600
 601  KIDSPMRSEDWQKRGMLSHFTVMRKLEGSIFPIGLSKESSDRNQKAGSNV   650
 651  LALESSERALLNRLMIELSKLDCDVLVGHNISGFDLDVLLHRAQTCKVPS   700
 701  NMWSKIGRLRRSVMPRLTKGNTLYGSGASPGIMSCIAGRLLCDTYLCSRD   750
 751  LLKEVSYSLTQLAETQLKKERKEVSPHDIPPMFQSSGALLKLVEYGETDA   800
 801  CLALELMFHLSVLPLTRQLTNISGNLWGKTLQGSRAQRVEYLLLHAFHAR   850
 851  KFIVPDKFARSKEFNSTKRKMNPDTEAARPDEADPSIDDEGHHVDQGKTK   900
 901  KGPSYAGGLVLEPKKGLYDKYVLLLDFNSLYPSIIQEYNICFTTVDRSAD   950
 951  GNVPNLPASKTTGVLPELLKSLVERRRMVKSWLKTASGLKRQQFDIQQQA  1000
1001  LKLTANSMYGCLGFSNSRFYAKPLAELITLQGREILQNTVDLVQNNLNLE  1050
1051  VIYGDTDSIMIHTGLDDISRAKGIAGKVIQEVNKKYRCLEIDLDGIYKRM  1100
1101  LLLKKKKYAAIKVALDGSLRENIERKGLDMVRRDWSLLSKEIGDFCLNQI  1150
1151  LSGGSCDDVIESIHSSLVQVQEQMRGGQTELEKYIITKSLTKAPEDYPDA  1200
1201  KNQPHVQVALRLKQNGYSGCSAGDTVPYIICSQQDSESTHSGGIAQRARH  1250
1251  PEELKRNPDKWMIDIDYYLSQQIHPVVSRLCASIQGTSPARLAECLGLDS  1300
1301  SKFQSRLTESDNQDTSSMLLSVIDDEDERYRGCEPLRLSCPSCSTTFDCP  1350
1351  PVSSLIIGSSSGNVSNPNEGNDASINFWRRMRCPRCPDDTDESRVSPAVL  1400
1401  ANQMKRQADSFINLYYKGLLMCDDEGCKYSTHSVNLRVMGDSERGTICPN  1450
1451  YPRCNGHLVRQYTEADLYRQLSYFCYVVDATRCLEKLDQKARLPFEKEFA  1500
1501  ALSQTINLALMEVQKIRDRCAFGWVQLKDLAISI                  1534

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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