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

NucPred

Fetching P40976 from www.uniprot.org...

The NucPred score for your sequence is 0.15 (see score help below)

   1  MSQTAPSDTEYNQRLERWSERLKSQTISHLPTDYSRPVPSRLVEAVFERT    50
  51  LPEDAKTALIKVYVAAQAKGILVTPFNILLTIFIILVSRMTGDEDISIGT   100
 101  SSENAIPFVLRTFIQPSDSFLDLLAKVCDLEKEGSSDAVDFSDLINFLNA   150
 151  KLSKKDDPRKTLVHLRFYNAPDAPSENFLSTTGLDVDLTVLVSVKKPSDQ   200
 201  LTSLRSQFTFPDLQLKLIYNQLLFSESRVNIVADQLLKLVVSASKDVTGP   250
 251  IGALDLMTPTQMNVLPDPTVDLDWSGYRGAIQDIFASNAAKFPDRECIVV   300
 301  TPSVTIDAPVTSYTYRQIDESSNILAHHLVKNGIERGDVVMVYAYRGVDL   350
 351  VVAVMGVLKAGATFSVIDPAYPPARQIIYLSVAKPRALVVLEDAGVLSPT   400
 401  VVEYVEKSLELKTYVPALKLAKDGSLTGGSVSKGADDILQHVLHLKSEQT   450
 451  GVVVGPDSTPTLSFTSGSEGIPKGVKGRHFSLAYYFDWMAQEFNLSESDR   500
 501  FTMLSGIAHDPIQRDIFTPLFLGASLIVPTAEDIGTPGQLAQWANKYKVT   550
 551  VTHLTPAMGQLLAAQADEPIPSLHHAFFVGDILTKRDCLRLQVLANNVNV   600
 601  VNMYGTTETQRSVSYFVVPARSQDQTFLESQKDVIPAGRGMKNVQLLVIN   650
 651  RFDTNKICGIGEVGEIYLRAGGLAEGYLGNDELTSKKFLKSWFADPSKFV   700
 701  DRTPENAPWKPYWFGIRDRMYRSGDLGRYLPTGNVECSGRADDQIKIRGF   750
 751  RIELGEINTHLSRHPNVRENITLVRRDKDEEPTLVAYIVPQGLNKDDFDS   800
 801  ATESEDIVVNGLKKYRKLIHDIREYLKTKLPSYAIPSVIVPLHKMPLNPN   850
 851  GKIDKPALPFPDTSQLAAASRSHSKHGVDETLTATERDIRDIWLRIIPHA   900
 901  TDVNKKASFFDIGGHSILATRLIFELRKKFAVNVPLGLVFSEPTIEGLAK   950
 951  EIERMKSGEMISVMDIGKEETREPEIEYGKDALDLVDLIPKEFPTSKDLG  1000
1001  IDEPKTVFLTGANGYLGVFILRDLMTRSSNLKVIALVRASSEEHGLKRLK  1050
1051  DSCTAYGVWDESWAQKISVVNGDLALENWGIEERKWNKLTEVVDYVIHNG  1100
1101  ALVHWVYPYSKLRGPNVMGTITALKLCSLGKGKSLSFVSSTSTVDTEYYV  1150
1151  NLSNEITSKGGNGIPESDPLQGSSKDLHTGYGQSKWVSEYLVRQAGLRGL  1200
1201  RGVVVRPGYILGDSKSGAINTDDFLVRMVKGCIELGLYPNINNTVNMVPA  1250
1251  DHVARVVTASAFHPEQGVIVAHVTSHPRLRFNQFLGTLSTFGFNTKLSEY  1300
1301  VNWRIALERFVINESHDSALYPLLHFVLDNLPANTKAPELDDTNTREILK  1350
1351  RDASWTNVDVSNGAAILEHEMGLYLSYLVAIGFLPKPTLEGKKLPEVKIN  1400
1401  EATLEKLASAGGRGGAPTH                                 1419

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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