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

NucPred

Fetching Q60997 from www.uniprot.org...

The NucPred score for your sequence is 0.40 (see score help below)

   1  MGISTVIFEICLLWGQILSTASQTAVPTDGTDSGLAVRLVNGGDRCQGRV    50
  51  EILYQGSWGTVCDDSWDLNDANVVCRQLGCGLAVSAPGNARFGQGSGPIV   100
 101  MDDVACGGYEDYLWRCSHRGWLSHNCGHQEDAGVICSDSQTSSPTPGWWN   150
 151  PGGTNNDVFYPTEQTTAEQTTIPDYTPIGTDSGLAVRLVNGGDRCQGRVE   200
 201  ILYQGSWGTVCDDSWDVSDANVVCRQLGCGWAVSAPGNAYFGQGQGPIVL   250
 251  DDVACGGYENYLWSCSHQGWLSHNCGHQEDAGVICSASQSSSPTPGWWNP   300
 301  GGTNNDVFYPTEQTTAGTDSGLAVRLVNGGDRCQGRVEILYQGSWGTVCD   350
 351  DSWDTNDANVVCRQLGCGWAVSAPGNAYFGPGSGSIVLDDVACTGHEDYL   400
 401  WRCSHRGWLSHNCGHHEDAGVICSASQSSSPTPDVFYPTDQTTAEQTTVP   450
 451  DYTPIGTDSGLAVRLVNGGDRCQGRVEILYQGSWGTVCDDSWDLNDANVV   500
 501  CRQLGCGLAVSAPGSARFGQGTGPIVMDDVACGGYEDYLWRCSHRGWLSH   550
 551  NCGHHEDAGVICSASQSSSPTPDVFYPTDQTTAEQTTVPDYTPIGTDSGL   600
 601  AVRLVNGGDRCQGRVEILYQGSWGTVCDDSWDLNDANVVCRQLGCGLAVS   650
 651  APGSARFGQGTGPIVMDDVACGGYEDYLWRCSHRGWLSHNCGHHEDAGVI   700
 701  CSASQSSSPTPDVFYPTDQTTAEQTTVPDYTTIGTENSLAVRLENGGDRC   750
 751  QGRVEILYQGSWGTVCDDSWDLNDANVVCRQLGCGLAVSAPGSARFGQGT   800
 801  GPIVMDDVACGGYEDYLWRCSHRGWLSHNCGHHEDAGVICSASQSSSPTP   850
 851  DVFYPTDQTTVEQTTVPDYTPIGTENSLAVRLENGGDRCQGRVEILYQGS   900
 901  WGTVCDDSWDTKDANVVCRQLGCGWAVSAPGNAYFGPGSGSIVLDDVACT   950
 951  GHEDYLWSCSHRGWLSHNCGHHEDAGVICSDAQIQSTTRPDLWPTTTTPE  1000
1001  TTTELLTTTPYFDWWTTTSDYSCGGLLTQPSGQFSSPYYPSNYPNNARCS  1050
1051  WKIVLPNMNRVTVVFTDVQLEGGCNYDYILVYDGPEYNSSLIARVCDGSN  1100
1101  GSFTSTGNFMSVVFITDGSVTRRGFQAHYYSTVSTNYSCGGLLTQPSGQF  1150
1151  SSPYYPSNYPNNARCSWEILVPNMNRVTVVFTDVQLEGGCNYDYILVYDG  1200
1201  PQYNSSLIARVCDGSNGSFTSTGNFMSVVFITDGSVTRRGFQAHYYSTVS  1250
1251  TTPPVPIPTTDDYSCGGLLTLPSGQFSSPHYPSNYPNNARCSWEILVPNM  1300
1301  NRVTVAFTDVQLEGGCNYDYILVYDGPEYNSSLIARVCDGSNGSFTSTGN  1350
1351  FMSVVFITDGSVTRRGFQAHYYSTVSTNYSCGGLLTQPSGQFSSPHYPSN  1400
1401  YPNNVRCSWEILVPSMNRVTVAFTDVQLEGGCSFDYILVYDGPEYNSSLI  1450
1451  APVCDGFNGSFTSTGNFMSVVFITDGSVTRRGFQAYYYSTVSTPPSFHPN  1500
1501  ITGNDSSLALRLVNGSNRCEGRVEILYRGSWGTVCDDSWGISDANVVCRQ  1550
1551  LGCGSALSAPGNAWFGQGSGLIVLDDVSCSGYESHLWNCHHPGWLVHNCR  1600
1601  HSEDAGVICALPEVTSPSPGWWTTSPSYVNYTCGGFLTQPSGQFSSPFYP  1650
1651  GNYPNNARCLWNIEVPNNYRVTVVFRDLQLERGCSYDYIEIFDGPHHSSP  1700
1701  LIARVCDGSLGSFTSTSNFMSIRFITDHSITARGFQAHYYSDFDNNTTNL  1750
1751  LCQSNHMQASVSRSYLQSMGYSARDLVIPGWNSSYHCQPQITQREVIFTI  1800
1801  PYTGCGTIKQADNETINYSNFLRAVVSNGIIKRRKDLNIHVSCKMLQNTW  1850
1851  VNTMYITNNTVEIQEVQYGNFDVNISFYTSSSFLFPVTSSPYYVDLDQNL  1900
1901  YLQAEILHSDASLALFVDTCVASPHPNDFSSLTYDLIRSGCVRDDTYQSY  1950
1951  SSPSPRVSRFKFSSFHFLNRFPSVYLQCKLVVCRAYDTSSRCYRGCVVRS  2000
2001  KRDVGSYQEKVDVVLGPIQLQSPSKEKRSLDLAVEDVKKPASSQAVYPTA  2050
2051  AIFGGVFLAMVLAVAAFTLGRRTHIDRGQPPSTKL                 2085

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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