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

NucPred

Fetching Q9C8G9 from www.uniprot.org...

The NucPred score for your sequence is 0.24 (see score help below)

   1  MGFEPLDWYCKPVPNGVWTKTVDYAFGAYTPCAIDSFVLGISHLVLLILC    50
  51  LYRLWLITKDHKVDKFCLRSKWFSYFLALLAAYATAEPLFRLVMRISVLD   100
 101  LDGAGFPPYEAFMLVLEAFAWGSALVMTVVETKTYIHELRWYVRFAVIYA   150
 151  LVGDMVLLNLVLSVKEYYGSFKLYLYISEVAVQVAFGTLLFVYFPNLDPY   200
 201  PGYTPVGTENSEDYEYEELPGGENICPERHANLFDSIFFSWLNPLMTLGS   250
 251  KRPLTEKDVWHLDTWDKTETLMRSFQKSWDKELEKPKPWLLRALNNSLGG   300
 301  RFWWGGFWKIGNDCSQFVGPLLLNELLKSMQLNEPAWIGYIYAISIFVGV   350
 351  VLGVLCEAQYFQNVMRVGYRLRSALIAAVFRKSLRLTNEGRKKFQTGKIT   400
 401  NLMTTDAESLQQICQSLHTMWSAPFRIIVALVLLYQQLGVASIIGALFLV   450
 451  LMFPIQTVIISKTQKLTKEGLQRTDKRIGLMNEVLAAMDTVKCYAWENSF   500
 501  QSKVQTVRDDELSWFRKAQLLSAFNMFILNSIPVLVTVVSFGVFSLLGGD   550
 551  LTPARAFTSLSLFSVLRFPLFMLPNIITQMVNANVSLNRLEEVLSTEERV   600
 601  LLPNPPIEPGQPAISIRNGYFSWDSKADRPTLSNINLDIPLGSLVAVVGS   650
 651  TGEGKTSLISAMLGELPARSDATVTLRGSVAYVPQVSWIFNATVRDNILF   700
 701  GAPFDQEKYERVIDVTALQHDLELLPGGDLTEIGERGVNISGGQKQRVSM   750
 751  ARAVYSNSDVCILDDPLSALDAHVGQQVFEKCIKRELGQTTRVLVTNQLH   800
 801  FLSQVDKILLVHEGTVKEEGTYEELCHSGPLFQRLMENAGKVEDYSEENG   850
 851  EAEVDQTSVKPVENGNANNLQKDGIETKNSKEGNSVLVKREERETGVVSW   900
 901  KVLERYQNALGGAWVVMMLVICYVLTQVFRVSSSTWLSEWTDSGTPKTHG   950
 951  PLFYNIVYALLSFGQVSVTLINSYWLIMSSLYAAKKMHDAMLGSILRAPM  1000
1001  VFFQTNPLGRIINRFAKDMGDIDRTVAVFVNMFMGSIAQLLSTVILIGIV  1050
1051  STLSLWAIMPLLVVFYGAYLYYQNTSREIKRMDSTTRSPVYAQFGEALNG  1100
1101  LSSIRAYKAYDRMAEINGRSMDNNIRFTLVNMAANRWLGIRLEVLGGLMV  1150
1151  WLTASLAVMQNGKAANQQAYASTMGLLLSYALSITSSLTAVLRLASLAEN  1200
1201  SLNSVERVGNYIEIPSEAPLVIENNRPPPGWPSSGSIKFEDVVLRYRPEL  1250
1251  PPVLHGVSFLISPMDKVGIVGRTGAGKSSLLNALFRIVELEKGRILIDEC  1300
1301  DIGRFGLMDLRKVLGIIPQAPVLFSGTVRFNLDPFSEHNDADLWESLERA  1350
1351  HLKDTIRRNPLGLDAEVTEAGENFSVGQRQLLSLARALLRRSKILVLDEA  1400
1401  TAAVDVRTDVLIQKTIREEFKSCTMLIIAHRLNTIIDCDKVLVLDSGKVQ  1450
1451  EFSSPENLLSNGESSFSKMVQSTGTANAEYLRSITLENKRTREANGDDSQ  1500
1501  PLEGQRKWQASSRWAAAAQFALAVSLTSSHNDLQSLEIEDDNSILKKTKD  1550
1551  AVVTLRSVLEGKHDKEIEDSLNQSDISRERWWPSLYKMVEGLAVMSRLAR  1600
1601  NRMQHPDYNLEGKSFDWDNVEM                              1622

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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