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

NucPred

Fetching Q8GU92 from www.uniprot.org...

The NucPred score for your sequence is 0.29 (see score help below)

   1  MDAAAEMQKVVSLRRGGGGSSSRGAASMWWSADNGVFSRSRASSSGEDGE    50
  51  DDEEALRWAALEKLPTYDRVRRAVLPVVEEGGGGGEAGKKVVDVLSLGPQ   100
 101  ERRALLERLVRVAEDDNERFLLKLKERIDRVGIDIPTIEVRFEHLEAEAE   150
 151  VRVGNSGLPTVLNSMTNKLEGAANALGILPNKKQTMPILHDVSGIVKPRR   200
 201  MTLLLGPPGSGKTTLLLALAGRLGKDIKFSGQVTYNGHQMEDFVPQRTAA   250
 251  YISQHDLHIGEMTVRETLSFSARCQGVGSRFDMLTELSRREKAANIKPDA   300
 301  DIDAFMKASAMEGQETNLITDYILKILGLDICADTMVGDDMVRGISGGQR   350
 351  KRVTTGEMLVGPANALFMDEISTGLDSSTTFQIVKSLRQAIHILGGTAVI   400
 401  SLLQPAPETYDLFDDIILLSDGQIVYQGPREGVLEFFELMGFKCPERKGV   450
 451  ADFLQEVTSRKDQKQYWMQHDKPYRYVPVKDFASAFQSFHTGKSIANELA   500
 501  TPFDKSKNHPAALTTSRYGVSAMELLKANIDREFLLMKRNSFVYIFRACQ   550
 551  LMVVSAIAMTVFFRTKMHRDSVTDGVIFMGALFFSVMMIMFNGLSELPLT   600
 601  IFKLPVFFKQRDLLFFPAWTYTIPSWILKIPMSFIEVGGFVFMSYYVIGF   650
 651  DPSAGRFFKQYLLMLAINQMAAALFRFVGGAARNMIVANVFGSFMLLIFM   700
 701  VLGGFILVREKVKKWWIWGYWISPMMYAQNAISVNEFLGHSWDKVLNNSL   750
 751  SNETLGVQALRSRGVFPEAKWYWIGFGALLGFIMLFNGLFTLALTYLKPY   800
 801  GKSQPSVSEEELKEKQANINGNVLDVDTMASSTNLAIVDNTETSSEIADN   850
 851  SQPTQRGMVLPFAPLSLTFDNIKYSVDMPQEMKAHGIVEDRLELLKGVSG   900
 901  SFRPGVLTALMGVSGAGKTTLMDVLAGRKTGGYIEGNITISGYPKKQETF   950
 951  ARVSGYCEQNDIHSPQVTVSESLLFSAWLRLPKDVDSNTRKMFIEEVMEL  1000
1001  VELKPLRDALVGLPGVNGLSTEQRKRLTIAVELVANPSIIFMDEPTSGLD  1050
1051  ARAAAIVMRTVRNTVDTGRTVVCTIHQPSIDIFEAFDELFLMKRGGEEIY  1100
1101  VGPLGHQSSELIKYFEGIKGVSRIKDGYNPATWMLEVSTISQEQALGVDF  1150
1151  CDIYRKSELFQRNKALIQELSTPPPGSSELYFPTKYSLSFLNQCLACLWK  1200
1201  MHLSYWRNPPYNAIRLFFTTVIALLFGTIFWDLGGKTGKSQDLFNAMGSM  1250
1251  YSAVLFIGVLNSQSVQPVVSVERTVFYRERAAGMYSAFPYAFGQVAIEFP  1300
1301  YTLVQSIIYGIIVYSMIGFKWTAAKFFWYLFFMFFTFLYFTFYGMMAVGL  1350
1351  TPSYHVASIVSSAFYGIWNLFSGFIIPRPKVPIWWRWYCWICPVAWTLYG  1400
1401  LVASQFGDIMTPMDDGTPVKIFVENYFDFKHSWLGVVAVVIVAFTMLFAF  1450
1451  LFGFAIMKLNFQKR                                      1464

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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