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

NucPred

Fetching Q40762 from www.uniprot.org...

The NucPred score for your sequence is 0.48 (see score help below)

   1  MSTTRPRAATHSASSGSVSRSSKHSARVITQTPVDAKLQAEFEGSVHSFD    50
  51  YTKSIDISGDSSSVPSETVKAYLQRLQKEMLIQPFGCVLAVEEGSCAVVG   100
 101  YSENAPEMLDVVGGAHAVPSIGGQQQEGGGGGGGLLRIGMDARTLFKPAS   150
 151  AAALQKAATFADMHLVNPIFVRCNRSGKPFYAILNRIDAGLVIDFEPVMP   200
 201  SDVPVSAAGALQSYKLAAKAISRLQSLPGGDIRLLCDTVVQEVRELTGYD   250
 251  RVMAYRFHEDEHGEVVAEMRRPDLEPYLGLHYPATDIPQASRFLFMKNRV   300
 301  RMICDCCAPPVNVIQDKRLRQPLSLCGSTLRAPHGCHAQYMANMGSIASL   350
 351  VMSVTTNENGDDSEGGGQQQPQNRRKLWGLVVCHHTSPRVIPFPLRYACE   400
 401  FLMQVFGIQLNKEVELAAQLREKHILRVQPVLCDMLLRDAPVGIVSQTPN   450
 451  IMDLVKCDGAALLYGKRLWLLGTTPTEAQILDIADWLLEHHRDSTGLSTD   500
 501  SLAEAGYPGAASLGDAVCGIAAARITSKDFLFWFRSHTAKEIIWGGAKHD   550
 551  PNDKDDGRRMHPRSSFKAFLEVVKRRSLPWEDVEMDAIHSLQLILRDSFH   600
 601  DIDDSDSKTMIHARLNDLRLQGIDELSAVTNEMVRLIETATVPILAIDSN   650
 651  GLVNGWNTKAAELTGLLADEVIGRPLIDLVQHDSVEIVKKMLYLALQGEE   700
 701  EQNVEIKLKTFGIQEEKGPVVLIVNACSSRDLEENVVGVCFVAQDVTWQR   750
 751  IAMDKFTHLQGDYRAIVQNPNPLIPPIFGADEYGYCSEWNPAMEKLTGWK   800
 801  REEVIGKMLVGEVFGIHRMSCQLKGQDGLTKLRIVLNNAMAGKETEKFPF   850
 851  SFFDRHGKNTEALLSANKRTDAEGIITGVFCFLHVTSTELQQALQVQRMA   900
 901  EQAAMDRLKELAYIRQEIRNPLYGIIFTRKLMESTDLSEEQKQIVQTSAL   950
 951  CQRQLVKVLDDADLESIEDGYLELDTIEFTLGTVLDAVVSQGMILSREKG  1000
1001  LQLIRDSPEEIKTMCLYGDQLRLQQILSNFLINALRFSTSEGWVGNKVVP  1050
1051  TKRHLGSGVNVMHMEFRITHSGQGIPEELIKEMFVHNQDMFQEGLGLYMC  1100
1101  QQLVKIMNGDVQYLREAGRSSFIINVEFPLAQTDKQ                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.)

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