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

NucPred

Fetching P28481 from www.uniprot.org...

The NucPred score for your sequence is 0.32 (see score help below)

   1  MIRLGAPQSLVLLTLLIAAVLRCQGQDAQEAGSCLQNGQRYKDKDVWKPS    50
  51  SCRICVCDTGNVLCDDIICEDPDCLNPEIPFGECCPICPADLATASGKLG   100
 101  PKGQKGEPGDIRDIIGPRGPPGPQGPAGEQGPRGDRGDKGEKGAPGPRGR   150
 151  DGEPGTPGNPGPAGPPGPPGPPGLSAGNFAAQMAGGYDEKAGGAQMGVMQ   200
 201  GPMGPMGPRGPPGPAGAPGPQGFQGNPGEPGEPGVSGPMGPRGPPGPAGK   250
 251  PGDDGEAGKPGKSGERGLPGPQGARGFPGTPGLPGVKGHRGYPGLDGAKG   300
 301  EAGAPGVKGESGSPGENGSPGPMGPRGLPGERGRTGPAGAAGARGNDGQP   350
 351  GPAGPPGPVGPAGGPGFPGAPGAKGEAGPTGARGPEGAQGSRGEPGNPGS   400
 401  PGPAGASGNPGTDGIPGAKGSAGAPGIAGAPGFPGPRGPPGPQGATGPLG   450
 451  PKGQAGEPGIAGFKGDQGPKGETGPAGPQGAPGPAGEEGKRGARGEPGGA   500
 501  GPIGPPGERGAPGNRGFPGQDGLAGPKGAPGERGPSGLTGPKGANGDPGR   550
 551  PGEPGLPGARGLTGRPGDAGPQGKVGPSGAPGEDGRPGPPGPQGARGQPG   600
 601  VMGFPGPKGANGEPGKAGEKGLAGAPGLRGLPGKDGETGAAGPPGPSGPA   650
 651  GERGEQGAPGPSGFQGLPGPPGPPGEGGKQGDQGIPGEAGAPGLVGPRGE   700
 701  RGFPGERGSPGAQGLQGPRGLPGTPGTDGPKGAAGPDGPPGAQGPPGLQG   750
 751  MPGERGAAGIAGPKGDRGDVGEKGPEGAPGKDGGRGLTGPIGPPGPAGAN   800
 801  GEKGEVGPPGPSGSTGARGAPGERGETGPPGPAGFAGPPGADGQPGAKGD   850
 851  QGEAGQKGDAGAPGPQGPSGAPGPQGPTGVTGPKGARGAQGPPGATGFPG   900
 901  AAGRVGPPGANGNPGPAGPPGPAGKDGPKGVRGDSGPPGRAGDPGLQGPA   950
 951  GAPGEKGEPGDDGPSGLDGPPGPQGLAGQRGIVGLPGQRGERGFPGLPGP  1000
1001  SGEPGKQGAPGASGDRGPPGPVGPPGLTGPAGEPGREGSPGADGPPGRDG  1050
1051  AAGVKGDRGETGALGAPGAPGPPGSPGPAGPTGKQGDRGEAGAQGPMGPS  1100
1101  GPAGARGIAGPQGPRGDKGESGEQGERGLKGHRGFTGLQGLPGPPGPSGD  1150
1151  QGASGPAGPSGPRGPPGPVGPSGKDGSNGIPGPIGPPGPRGRSGETGPVG  1200
1201  PPGSPGPPGPPGPPGPGIDMSAFAGLGQREKGPDPMQYMRADEADSTLRQ  1250
1251  HDVEVDATLKSLNNQIESIRSPDGSRKNPARTCQDLKLCHPEWKSGDYWI  1300
1301  DPNQGCTLDAMKVFCNMETGETCVYPNPATVPRKNWWSSKSKEKKHIWFG  1350
1351  ETMNGGFHFSYGDGNLAPNTANVQMTFLRLLSTEGSQNITYHCKNSIAYL  1400
1401  DEAAGNLKKALLIQGSNDVEMRAEGNSRFTYTALKDGCTKHTGKWGKTVI  1450
1451  EYRSQKTSRLPIIDIAPMDIGGAEQEFGVDIGPVCFL               1487

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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