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

NucPred

Fetching Q06805 from www.uniprot.org...

The NucPred score for your sequence is 0.35 (see score help below)

   1  MVWLEPPLLLPIFFLASHVGAAVDLTLLADLRLTEPQRFFLTCVSGEAGA    50
  51  GRGSDAWGPPLLLEKDDRIVRTPRPWQPPHIARNGSSRVTVRGFSQPSDL   100
 101  VGVFSCVGGGGTRVLYVHNSPGAHLLPDKVTHTVNKGDTAVLSARVRKEK   150
 151  QTDVIWKSNGSYFYTLDRHEAQDGQFLLQLPNVQPSSSGIYSATYLEASP   200
 201  LGSAFFRLIVRGCEAGRWGQDCTKECPGCLHGGVCHDQDGECVCPPGFTG   250
 251  TRCEQACREGRFGQSCQEQCPGTSGCRGLTFCLPDPYGCSCGSGWRGSQC   300
 301  QEACAPGRFGADCHLQCQCQNGGTCDRFSGCVCPSGWHGMHCEKSDRIPQ   350
 351  ILDMVSELEFNLDTMPRINCAAAGNPFPVRGSMELRKPDGTVLLSTKAIV   400
 401  EPDRTTAEFEVPRLALGDSGLWECRVSTSGGQDSRRFRINVKVPPVPLTA   450
 451  PRLLAKQSRQLVVSPLVSFSGDGPIASVRLHYRPQDSTMAWSTIVVDPSE   500
 501  NVTLMNLRPKTGYSVRVQLSRPGEGGEGAWGPPTLMTTDCPEPLLKPWLE   550
 551  GWHVEGPDRLRVSWSLPPVPGPLVGDGFLLRLWDGARGQERRENVSSPQA   600
 601  RTALLTGLTPGTYYQLDVRLYHCTLLGPASPAARVLLPPSGPPAPRHLHA   650
 651  QALSDSEIQLMWQRPEAAAGPISKYIVEVQVAGGSGDPLWMDVDRPEETS   700
 701  TIVRGLNASTRYLFRVRASVQGPGDWSNVVEQSTLGNGLQIEGPVQEIHA   750
 751  AEEGLDQQLVLAVVGSVSATCLTILAALLTLACIRKSCLHRRRTFTYQSG   800
 801  SGEETILQFSSGTLTLTRRPKPQPEPLNYPVLEWEDITFEDLIGEGNFGQ   850
 851  VIRAMIKKDGLKMNAAIKMLKEYASENDHRDFAGELEVLCKLGHHPNIIN   900
 901  LLGACENRGYLYIAIEYAPYGNLLDFLRKSRVLETDPAFAREHGTASTLS   950
 951  SRQLLRFASDAANGMQYLSEKQFIHRDLAARNVLVGENLASKIADFGLSR  1000
1001  GEEVYVKKTMGRLPVRWMAIESLNYSVYTTKSDVWSFGVLLWEIVSLGGT  1050
1051  PYCGMTCAELYEKLPQAYRMEQPRNCDDEVYELMRQCWRDRPYERPPFAQ  1100
1101  IALQLGRMLEARKAYVNMSLFENFTYAGIDATAEEA                1136

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.)

Go back to the NucPred Home Page.