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

NucPred

Fetching Q28107 from www.uniprot.org...

The NucPred score for your sequence is 0.91 (see score help below)

   1  MFLACPGFWVLVVLGSSWAGWGNLGAEAAKLRQFYVAAQSIRWNYRPEST    50
  51  HLSSKPFETSFKKIVYREYEAYFQKEKPQSRTSGLLGPTLYAEVGDIMKV   100
 101  HFKNKAHKPLSIHAQGIKYSKFSEGASYSDHTLPMEKMDDAVAPGQEYTY   150
 151  EWIISEHSGPTHDDPPCLTHIYYSYVNLVEDFNSGLIGPLLICKKGTLTE   200
 201  DGTQKMFEKQHVLMFAVFDESKSWNQTSSLMYTVNGYVNGTMPDITVCAH   250
 251  DHISWHLIGMSSGPELFSIHFNGQVLEQNHHKISAITLVSATSTTANMTV   300
 301  SPEGRWTIASLIPRHFQAGMQAYIDIKNCAKKTRNPKKLTRDQRRHIKRW   350
 351  EYFIAAEEVIWDYAPIIPANMDKKYRSLHLDNFSNRIGKHYKKVVYKQYQ   400
 401  DDSFTKRLEDPSSEGDGILGPIIRAQVRDTLKIVFKNMASRSYSIYPHGV   450
 451  TFSPYDNEVNSSSTSGSNTMIRAVRPGETYTYKWNILESDEPTENDAQCL   500
 501  TRPYYSNVDITRDLASGLIGLLLICKSRSLDRRGIQRAADIEQQAVFAVF   550
 551  DENKSWYIEDNIYKFCENPEKVKRDDPKFYESNIMSNFTLPAINGYVPES   600
 601  IPILGFCFDDTVQWHFCSVGTQNDILTIHFTGHSFIYGKRHEDTLTLFPM   650
 651  QGESVTVTMDNVGTWMLTTMNSNPRSKKLRLRFRDAKCIRNDDDDSYEII   700
 701  YEPSGSTAMTTKKIHDSSEIEDENDADSDYQDELALILGLRSFRNSSLNQ   750
 751  EKDELNLTALALEKDSEFIPPSANRSLDSNSSSRSHVSRLIAKNFAESLK   800
 801  TLLHLEAPAAGSPLEHAGLDKNSALNPPMAEHSSPYSEDPREDHPLSDVT   850
 851  GVSLLPFGTGFKNRKPAKHQRFQVGRGQAAKHKFSQTRFPAHKTRTRLSQ   900
 901  DNSSSSRMGPWEDIPSDLLLLQQKDPYKILNGEWHLVSEKGSYEIIQDAN   950
 951  ENKTVNKLPNSPQNDSRTWGENIPFKNSHGKQSGHPTFLVTRRKPLQDRQ  1000
1001  DRRNSRLKEGLPLIRTRRKKKEEKPAYHVPLSPRSFHPLRGEVNASFSDR  1050
1051  RHNHSLLLHASNETSLSIDLNQTFPSMNLSLAASLPDHDQTSPNDTTSQT  1100
1101  SSPPDLYPTVSPEEHYQIFPIQDSDPTHSTTAPSNRSPDPTHSTTAPSNR  1150
1151  SPPTQPSQIPNYDLRNRAIPTDVSQIFPSLELEVWQTATSLDLSQPSISP  1200
1201  DLGQMALSPDPGQESLSPDLGQTSLSPDLSQESLSPDLGQTALSPDPSQE  1250
1251  SLSPDLGQTALSPDPSQESLSPDLGQTALSPDPGQESLSPDLGQTSLSPD  1300
1301  LSQESLSPDLGQTALSPDPSQESLSPDLGQTALSPDPSQESLSPDLGQTS  1350
1351  LSPDLGQESLSPDLGQTALSPDPSQESLSPDLGQTSLSPDLGQESLSPDL  1400
1401  GQTALSPDLSQESLSPDLGQTPLSPDLSLESLSPDLSQLDLKQTSPPLDL  1450
1451  NQTSHTSESSQSLPLPEFGQTFPNADIGQMPSPPPDSTLNNTFIPEEFNP  1500
1501  LVVVGLSRDDGDYIEIIPRQKEESSEEDYGEFEFVAYNDPYQTDLRTDIN  1550
1551  SSRNPDNIAAWYLRSNTGNRKYYYIAAEEISWDYSKFVQSDDVDYVPEDT  1600
1601  VYKKVVFRKYLDSTFTKLDPQGEYEEHLGILGPVIRAEVDDVIQVRFKNL  1650
1651  ASRPYSLHAHGLSYEKSSEGKTYEDDSPEWFKEDNAIQPNKTYTYVWHAT  1700
1701  TRSGPENPGSACRAWAYYSAVNPEKDIHSGLIGPLLICRKGTLDKETNMP  1750
1751  VDMREFVLLFMVFDEKKSWYYDKKPTRSWRRASSEVKNSHEFHAINGMIY  1800
1801  NLPGLRMYEQEWVRLHLLNLGGSRDIHVVHFHGQTLLENGTQQHQLGVWP  1850
1851  LLPGSFKTLEMKASKPGWWLLDTEVGEIQRAGMQTPFLIVDRECKMPMGL  1900
1901  STGLIADSQIQASEFWGYWEPKLARLNNGGSYNAWIAEKLSTEFNPEPWI  1950
1951  QVDMQKEVLLTGIQTQGAKHYLKPYYTTEFCVAYSLDRKNWRIFKGNSTR  2000
2001  NVMYFGGNSDASTIKENQIDPPVVARYIRISPTGSYNKPALRLELQGCEV  2050
2051  NGCSTPLGMESGKIENKQITASSFKKSWWGNYWEPFLARLNAQGRVNAWQ  2100
2101  AKANNNNQWLQIDLLKIKKITAIVTQGCKSLSSEMYVKSYTIHYSDQGTD  2150
2151  WKPYREKSSMVDKIFEGNNNVRGHVKNFFNPPIISRFIRIIPKTWNQSIA  2200
2201  LRLELFGCDMY                                         2211

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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