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

NucPred

Fetching Q8TE82 from www.uniprot.org...

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

   1  MENLPAVTTEEPTPMGRGPVGPSGGGSTRDQVRTVVMRPSVSWEKAGPEE    50
  51  AKAPVRGDEAPPARVAGPAAGTPPCQMGVYPTDLTLQLLAVRRKSRLRDP   100
 101  GLQQTLRGQLRLLENDSREMARVLGELSARLLSIHSDQDRIVVTFKTFEE   150
 151  IWKFSTYHALGFTHHCLANLLMDQAFWLLLPSEEEETAIQVHVDENALRL   200
 201  THESLLIQEGPFFVLCPDHHVRVMTGPRDAGNGPQALRQASGAPQGEAAP   250
 251  ETDSSPPSPSVSSEEVAVAAAPEPLIPFHQWALRIPQDPIDDAMGGPVMP   300
 301  GNPLMAVGLASALADFQGSGPEEMTFRGGDLIEILGAQVPSLPWCVGRHA   350
 351  ASGRVGFVRSSLISMQGPVSELESAIFLNEEEKSFFSEGCFSEEDARQLL   400
 401  RRMSGTDVCSVYSLDSVEEAETEQPQEKEIPPPCLSLEPQETLQKVKNVL   450
 451  EQCKTCPGCPQEPASWGLCAASSDVSLQDPEEPSFCLEAEDDWEDPEALS   500
 501  SLLLFLNAPGYKASFRGLYDVALPWLSSVFRSFSDEEELTGRLAQARGAA   550
 551  KKAGLLMALARLCFLLGRLCSRRLKLSQARVYFEEALGALEGSFGDLFLV   600
 601  VAVYANLASIYRKQKNREKCAQVVPKAMALLLGTPDHICSTEAEGELLQL   650
 651  ALRRAVGGQSLQAEARACFLLARHHVHLKQPEEALPFLERLLLLHRDSGA   700
 701  PEAAWLSDCYLLLADIYSRKCLPHLVLSCVKVASLRTRGSLAGSLRSVNL   750
 751  VLQNAPQPHSLPAQTSHYLRQALASLTPGTGQALRGPLYTSLAQLYSHHG   800
 801  CHGPAITFMTQAVEASAIAGVRAIVDHLVALAWLHVLHGQSPVALDILQS   850
 851  VRDAVVASEDQEGVIANMVAVALKRTGRTRQAAESYYRALRVARDLGQQR   900
 901  NQAVGLANFGALCLHAGASRLAQHYLLEAVRLFSRLPLGECGRDFTHVLL   950
 951  QLGHLCTRQGPAQQGKGYYEWALLVAVEMGHVESQLRAVQRLCHFYSAVM  1000
1001  PSEAQCVIYHELQLSLACKVADKVLEGQLLETISQLYLSLGTERAYKSAL  1050
1051  DYTKRSLGIFIDLQKKEKEAHAWLQAGKIYYILRQSELVDLYIQVAQNVA  1100
1101  LYTGDPNLGLELFEAAGDIFFDGAWEREKAVSFYRDRALPLAVTTGNRKA  1150
1151  ELRLCNKLVALLATLEEPQEGLEFAHMALALSITLGDRLNERVAYHRLAA  1200
1201  LQHRLGHGELAEHFYLKALSLCNSPLEFDEETLYYVKVYLVLGDIIFYDL  1250
1251  KDPFDAAGYYQLALAAAVDLGNKKAQLKIYTRLATIYHNFLLDREKSLFF  1300
1301  YQKARTFATELNVRRVNLPPLPLCGWAPWLAPSHPR                1336

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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