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

NucPred

Fetching P22811 from www.uniprot.org...

The NucPred score for your sequence is 0.27 (see score help below)

   1  MSGQQKTSELVFFVNGKKVTDTNPDPECTLLTYLRDKLRLCGTKLGCAEG    50
  51  GCGACTVVISRMDRGQNKIRHLAVNACLTPVCAMHGCAVTTVEGIGSTRT   100
 101  RLHPVQERLAKAHGSQCGFCTPGIVMSMYALLRSAEQPSMRDLEVAFQGN   150
 151  LCRCTGYRPILEGYKTFTKEFACGMGDKCCKVNGKGCGGGDDTQSVTDDT   200
 201  LFERSQFQPLDPSQEPIFPPELQLTPTYDSESLIFSSERVTWYRPTTLQE   250
 251  LLQLKSDHPSAKLVVGNTEVGVEVKFKHFLYPHLINPTQVPELLEVRESE   300
 301  ESIYFGAAVSLMEIDALLRQRIEELPEAQTRLFQCAVDMLHYFAGKQIRN   350
 351  VACLGGNIMTGSPISDMNPVLTAAGARLEVASLVGGKTSHRTVHMGTGFF   400
 401  TGYRRNVIEPHEVLLGIHFQKTTPDQHVVAFKQARRRDDDIAIVNAAVNV   450
 451  RFEPRTNVVAGISMAFGGMAPTTVLAPRTSQLMVKQPLDHHLVERVAESL   500
 501  CGELPLAASAPGGMIAYRRALVVSLIFKAYLSISRKLSEAGIISTDAIPA   550
 551  EERSGAELFHTPVLRSAQLFERVCSEQPVCDPIGRPEVHAAALKQATGEA   600
 601  IYTDDIPRMDGELYLGLVLSTKPRAKITKLDASEALALEGVHAFFSHKDL   650
 651  TEHENEVGPVFHDEHVFAAAEVHCYGQIVGAVAADNKALAQRAARLVRVE   700
 701  YEELAPVIVTIEQAIEHGSYFPDYPRYVNKGNVEEAFAAAEHTYEGSCRM   750
 751  GGQEHFYLETHAAVAVPRDSDELELFCSTQHPSEVQKLVAHVTTLPAHRV   800
 801  VCRAKRLGGGFGGKESRGISVALPVALAAYRLRRPVRCMLDRDEDMLITG   850
 851  TRHPFLFKYKVAFASDGLITACDIECYNNAGWSMDLSFSVLERAMYHFEN   900
 901  CYRIPNVRVGGWVCKTNLPSNTAFRGFGGPQGMFAGEHIIRDVARIVGRD   950
 951  VLDVMRLNFYKTGDITHYNQKLEHFPIERCLDDCLAQSRYHEKRTEIAKF  1000
1001  NRENRWRKRGMAVIPTKYGIAFGVMHLNQAGALINVYGDGSVLLSHGGVE  1050
1051  IGQGLNTKMIQCAARALGIPIELIHISETATDKVPNTSPTAASVGSDLNG  1100
1101  MAVLDACEKLNKRLAPIKEALPQGTWQEWINKAYFDRVSLSATGFYAMPG  1150
1151  IGYHPETNPNARTYSYYTNGVGISVVEIDCLTGDHQVLSTDIVMDIGSSI  1200
1201  NPAIDIGQIEGAFMQGYGLFTLEELMYSPQGMLYSRGPGMYKLPGFADIP  1250
1251  GEFNVSLLTGAPNPRAVYSSKAVGEPPLFIGSSAFFAIKEAIAAARQEQG  1300
1301  LTGDFPLEAPSTSARIRMACQDKFTNLLEIPEEGSFTPWNIVP         1343

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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