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

NucPred

Fetching P91711 from www.uniprot.org...

The NucPred score for your sequence is 0.23 (see score help below)

   1  MSGQQQATSVLVFFVNGKKVTDTNPDPECTLLTYLRDKLRLCGTKLGCAE    50
  51  GGCGACTVMISRMDRGQHKIRHLAVNACLTPVCAMHGCAVTTVEGIGSTR   100
 101  TRLHPVQERLAKAHGSQCGFCTPGIVMSMYALLRNAEQPSMRDLEVAFQG   150
 151  NLCRCTGYRPILEGYKTFTKEFLCGMGEKCCRVNGKGCGGGDDPESVTDD   200
 201  TLFERSKFQPLDASQEPIFPPELQLSNAYDSESLVFSSERVTWYRPTTLQ   250
 251  ELLQLKAAHPAAKLVVGNTEVGVEVKFKHFLYPHLINPTLVAELQEVRES   300
 301  EESIYFGAAVSLMEIDALLRQRIEELPEAQTRLFQCTVDMLHYFAGKQIR   350
 351  NVACLGGNIMTGSPISDMNPVLTAAGARLEVASIVEGKISQRTVHMGTGF   400
 401  FTGYRRNVIEPQEVLLGIHFQKTTPDQHVVAFKQARRRDDDIAIVNAAVN   450
 451  VRFEPKSNVVAEISMAFGGMAPTTVLAPRTSQLMVKQPLDHQLLERVAES   500
 501  LCGELPLAASAPGGMIAYRRALVVSLIFKAYLAISSKLSEAGIIAGDAIP   550
 551  PKERSGAELFHTPTLRSAQLFERVCSDQPVCDPIGRPEVHAAALKQATGE   600
 601  AIYTDDIPRMDGELYLGFVLSTKPRAKITKLDASAALALEGVHAFFSHKD   650
 651  LTVHENEVGPVFHDEHVFAAGEVHCYGQIVGAVAADNKALAQRASRLVRV   700
 701  EYEDLSPVIVTIEQAIEHGSYFPDYPRYVTKGNMAEAFAQAEHTYEGSCR   750
 751  MGGQEHFYLETHAAVAVPRDSDELELFCSTQHPSEVQKLVAHVTSLPAHR   800
 801  VVCRAKRLGGGFGGKESRGISVALPVALAAYRLRRPVRCMLDRDEDMLIT   850
 851  GTRHPFLFKYKVAFSSDGLITACDIECYNNAGWSMDLSFSVLERAMYHFE   900
 901  NCYHIPNVRVGGWVCKTNLPSNTAFRGFGGPQGMFAGEHIIRDVARIVGR   950
 951  DVLDVMRLNFYRTGDTTHYNQQLEHFPIERCLDDCLTQSRYHERRAEIAK  1000
1001  FNRENRWRKRGVAVIPTKYGIAFGVMHLNQAGALLNVYGDGSVLLSHGGV  1050
1051  EIGQGLNTKMIQCAARALGIPSELIHISETATDKVPNTSPTAASVGSDIN  1100
1101  GMAVLDACEKLNKRLAPIKEALPQATWQEWINKAYFDRVSLSATGFYAMP  1150
1151  GIGYHPETNPNARTYSYYTNGVGISVVEIDCLTGDHQVLSTDIVMDIGSS  1200
1201  INPAIDIGQIEGAFMQGYGLFTLEELMYSPQGMLYSRGPGMYKLPGFADI  1250
1251  PGEFNVSLLTGAPNPRAVYSSKAVGEPPLFIGASAFFAIKEAIAAARQEH  1300
1301  GLTGDFPLEAPSTSARIRMACQDKFTNLLEVPEAGSFTPWNIVP        1344

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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