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

NucPred

Fetching P97874 from www.uniprot.org...

The NucPred score for your sequence is 0.64 (see score help below)

   1  MSLLQSALDFLAGPGSLGGAAGRDQSDFVGQTVELGELRLRVRRVLAEGG    50
  51  FAFVYEAQDLGSGREYALKRLLSNEEEKNRAIIQEVCFLKKLSGHPNIVQ   100
 101  FCSAASIGKEESDTGQAEFLLLTELCKGQLVEFLRRVECKGPLSCDSILK   150
 151  IFYQTCRAVQHMHRQKPPIIHRDLKVENLLLSNQGTIKLCDFGSATTISH   200
 201  YPDYSWSAQKRAMVEEEITRNTTPMYRTPEIVDLYSNFPIGEKQDIWALG   250
 251  CILYLLCFRQHPFEDGAKLRIVNGKYSIPVNDTRYTVFHDLIRGMLKVNP   300
 301  EERLSIAEVVRQLQEIAAARNVNPKAPITELLEQNGGYGNSGPSRAQPPS   350
 351  GGPVNSSGVLALAEYDQPYGGFLDILRGGTERLFTNLKDTSSKVIQSVAN   400
 401  YAKGDLDISYITSRIAVMSFPAEGVESAIKNNIEDVRLFLDAKHPGHYAV   450
 451  YNLSPRIYRASKFHNRVTECGWAVRRAPHLHSLYTLCRSMHAWLREDHRN   500
 501  VCVVHCMDGRAASAVAVCAFLCFCRLFSTAEAAVYMFSMKRCPPGIWPSH   550
 551  KRYIEYVCDMVAEEPITPHSKPMLVKSVVMTPVPLFSKQRNGCRPFCEVY   600
 601  VGEERVTTTSQEYDRMKEFKIEDGKAVIPLGITVQGDVLTIIYHARSTLG   650
 651  GRLQAKMASMKMFQIQFHTGFVPRNATTVKFAKYDLDACDIQEKYPDLFQ   700
 701  VNLEVEVEPRDRPSRDVPPWENTSLRGLNPKILFSNREEQQDILSKFGKP   750
 751  ELPRQPGSTAQYDAEAGSPEAEITESDSPQSSSTDTNHFLHTLDWQEEKD   800
 801  PETGVDNTSPKESQSNLIADGDGSEVSDEEEASCPSEERKPGAGEDTPRL   850
 851  AAGTRQQDLIFDVGMLAAPQEPVQPEEGVDLLGLHSEGDLRPAAPLQASG   900
 901  VQSSNTDLLSSLLEPSDASQVGPPGDLLGGETPLLLASPVSLLGVQSNLQ   950
 951  GKVPDTVDPFDQFLLPSSSDTQPCSKPDLFGEFLNSDSVASSTAFPSTHS  1000
1001  APPPSCSTAFLHLGDLPAEPNKVIASSSHPDLLGGWDTWAETALPGPASM  1050
1051  PVPEGTLFSSAGHPAPPGPNPSQTKSQNPDPFADLSDLSSSLQGLPAGLP  1100
1101  AGSFVGTSATTHKSNSSWQTTRPTAPGTSWPPQAKPAPRASEQLRSHFSV  1150
1151  IGAREERGVRAPSFAQKPKVSENDFEDLLPNQGFSKSDKKGPKTMAEMRK  1200
1201  QELARDTDPFKLKLLDWIEGKERNIRALLSTLHTVLWDGESRWTPVSMAD  1250
1251  LVTPEQVKKQYRRAVLVVHPDKATGQPYEQSAKMIFMELNDAWSEFENQG  1300
1301  SRPLF                                               1305

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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